Secretome analysis of Trichoderma reesei and Aspergillus niger cultivated by submerged and sequential fermentation processes: Enzyme production for sugarcane bagasse hydrolysis

A Multiomics Perspective on Plant Cell Wall-Degrading Enzyme Production: Insights from the Unexploited Fungus Trichoderma erinaceum

Trichoderma erinaceum is a filamentous fungus that was isolated from decaying sugarcane straw at a Brazilian ethanol biorefinery. This fungus shows potential as a source of plant cell wall-degrading enzymes (PCWDEs). In this study, we conducted a comprehensive multiomics investigation of T. erinaceum to gain insights into its enzymatic capabilities and genetic makeup. Firstly, we performed genome sequencing and assembly, which resulted in the identification of 10,942 genes in the T. erinaceum genome. We then conducted transcriptomics and secretome analyses to map the gene expression patterns and identify the enzymes produced by T. erinaceum in the presence of different substrates such as glucose, microcrystalline cellulose, pretreated sugarcane straw, and pretreated energy cane bagasse. Our analyses revealed that T. erinaceum highly expresses genes directly related to lignocellulose degradation when grown on pretreated energy cane and sugarcane substrates. Furthermore, our secretome analysis identified 35 carbohydrate-active enzymes, primarily PCWDEs. To further explore the enzymatic capabilities of T. erinaceum, we selected a β-glucosidase from the secretome data for recombinant production in a fungal strain. The recombinant enzyme demonstrated superior performance in degrading cellobiose and laminaribiose compared to a well-known enzyme derived from Trichoderma reesei. Overall, this comprehensive study provides valuable insights into both the genetic patterns of T. erinaceum and its potential for lignocellulose degradation and enzyme production. The obtained genomic data can serve as an important resource for future genetic engineering efforts aimed at optimizing enzyme production from this fungus.

Rice straw hydrolysis using in-situ produced enzymes: Feedstock influences fungal enzyme composition and hydrolytic efficiency

Trichoderma reesei RUT-C30 was cultivated on differentially pretreated rice straw and pure cellulose as a carbon source/inducer for cellulase production, and the enzymes were evaluated for hydrolysis of sequential acid and alkali pretreated rice straw. Growth on pretreated rice straw enhanced protein secretion and cellulase activities compared to pure cellulose as a carbon source. The yield of cellulolytic enzymes was higher for alkali pretreated rice straw (ALP-RS), while H2O2-treated (HP-RS) could not induce cellulases to a larger level compared to pure cellulose. Protein concentration was 3.5-fold higher on ALP-RS as compared to pure cellulose, with a maximum filter-paper cellulase (FPase) activity of 1.76 IU/ml and carboxy-methyl cellulase (CMCase) activity of 40.16 IU/ml (2.18 fold higher). Beta-glucosidase (BGL) activity was more or less the same with the different substrates and supplementation of heterologous BGL could result in a quantum jump in hydrolytic efficiencies, which in the case of ALP-RS induced enzymes was 34% (increased from 69.26% to 92.51%). The use of lignocellulosic biomass (LCB) itself as a substrate for the production of cellulase is advantageous not only in terms of raw material costs but also for obtaining a more suitable enzyme profile for biomass hydrolysis.

Ruminal degradation characteristics of bagasse with different fermentation treatments in the rumen of beef cattle

This experiment aimed to study the degradation characteristics of bagasse after three fermentation treatments in beef cattle. Bagasse 1 was treated with 0.3% lactic acid bacteria (w/w). Bagasse 2 was treated with 0.3% mixed strains (Saccharomyces cerevisiae, Aspergillus niger, Aspergillus oryzae, and lactic acid bacteria at 2:1:1:1). Bagasse 3 was treated with 0.1% cellulase and 0.1% xylanase in addition to 0.3% mixed strains of bagasse 2. The dry matter (DM), crude ash (ASH), crude protein (CP), neutral detergent fiber (NDF), and acid detergent fiber (ADF) in the bagasses were determined. Compared to the control bagasse (without the strain and enzyme treatments), three fermented bagasses showed higher DM after 4 h fermentation. The CP and ASH contents in fermented bagasse 3 were the highest, while the contents of NDF and ADF in fermented bagasse 3 were the lowest among all the groups. The effective degradability of DM, CP, NDF, and ADF was highest in fermented bagasse 3 among the evaluated bagasse feed, followed by fermented bagasse 2 > fermented bagasse 1 > bagasse. Overall, fermented bagasse 3 was better than the control and other treated bagasses, thus fermented bagasse 3 is a hopeful source for ruminant diet of beef cattle.

Yeasts Have Evolved Divergent Enzyme Strategies To Deconstruct and Metabolize Xylan

Together with bacteria and filamentous fungi, yeasts actively take part in the global carbon cycle. Over 100 yeast species have been shown to grow on the major plant polysaccharide xylan, which requires an arsenal of carbohydrate active enzymes. However, which enzymatic strategies yeasts use to deconstruct xylan and what specific biological roles they play in its conversion remain unclear. In fact, genome analyses reveal that many xylan-metabolizing yeasts lack expected xylanolytic enzymes. Guided by bioinformatics, we have here selected three xylan-metabolizing ascomycetous yeasts for in-depth characterization of growth behavior and xylanolytic enzymes. The savanna soil yeast Blastobotrys mokoenaii displays superior growth on xylan thanks to an efficient secreted glycoside hydrolase family 11 (GH11) xylanase; solving its crystal structure revealed a high similarity to xylanases from filamentous fungi. The termite gut-associated Scheffersomyces lignosus, in contrast grows more slowly, and its xylanase activity was found to be mainly cell surface-associated. The wood-isolated Wickerhamomyces canadensis, surprisingly, could not utilize xylan as the sole carbon source without the addition of xylooligosaccharides or exogenous xylanases or even co-culturing with B. mokoenaii, suggesting that W. canadensis relies on initial xylan hydrolysis by neighboring cells. Furthermore, our characterization of a novel W. canadensis GH5 subfamily 49 (GH5_49) xylanase represents the first demonstrated activity in this subfamily. Our collective results provide new information on the variable xylanolytic systems evolved by yeasts and their potential roles in natural carbohydrate conversion. IMPORTANCE Microbes that take part in the degradation of the polysaccharide xylan, the major hemicellulose component in plant biomass, are equipped with specialized enzyme machineries to hydrolyze the polymer into monosaccharides for further metabolism. However, despite being found in virtually every habitat, little is known of how yeasts break down and metabolize xylan and what biological role they may play in its turnover in nature. Here, we have explored the enzymatic xylan deconstruction strategies of three underexplored yeasts from diverse environments, Blastobotrys mokoenaii from soil, Scheffersomyces lignosus from insect guts, and Wickerhamomyces canadensis from trees, and we show that each species has a distinct behavior regarding xylan conversion. These findings may be of high relevance for future design and development of microbial cell factories and biorefineries utilizing renewable plant biomass.

Inhibition of enzyme hydrolysis of cellulose by phenols from hydrothermally pretreated sugarcane straw

Relatively few studies have addressed the characterization of sugarcane straw (SCS) for production of fermentable sugars through enzyme hydrolysis. Straw is a major co-product of the sugarcane harvest in Brazil that has potential to sustainably increase cellulosic feedstocks in Brazil by 50%. Pretreatment of 10% w/v straw with liquid hot water (LHW) at 180 °C for 50 min (severity, S_o, of 4.05), solubilizes hemicellulose, preserves glucan, and generates 4.49 g/L soluble phenolic compounds in the resulting liquid. Extracts from washing pretreated solids with excess hot water followed by acetone resulted in 1.10 and 0.83 g/L phenolics, respectively. Acetone-derived extracts were more inhibitory and decreased glucose yield for enzyme hydrolysis of Solka Floc (a lignin-free cellulose) by 42%. In comparison, pretreated straw washed with hot water or acetone was readily hydrolyzed to 92% and 97% by cellulase enzyme. Hydrothermally treated SCS has the potential to provide a valuable and added source of fermentable sugars suitable for bioprocessing into biofuels and bioproducts when cellulase enzyme inhibitors are removed after pretreatment.

Screening method for Enzyme-based liquefaction of corn stover pellets at high solids

Liquefaction of high solid loadings of unpretreated corn stover pellets has been demonstrated with rheology of the resulting slurries enabling mixing and movement within biorefinery bioreactors. However, some forms of pelleted stover do not readily liquefy, so it is important to screen out lots of unsuitable pellets before processing is initiated. This work reports a laboratory assay that rapidly assesses whether pellets have the potential for enzyme-based liquefaction at high solids loadings. Twenty-eight pelleted corn stover (harvested at the same time and location) were analyzed using 20 mL enzyme solutions (3 FPU cellulase/ g biomass) at 30 % w/v solids loading. Imaging together with measurement of reducing sugars were performed over 24-hours. Some samples formed concentrated slurries of 300 mg/mL (dry basis) in the small-scale assay, which was later confirmed in an agitated bioreactor. Also, the laboratory assay showed potential for optimizing enzyme formulations that could be employed for slurry formation.

Bioconversion of Some Agro-Residues into Organic Acids by Cellulolytic Rock-Phosphate-Solubilizing Aspergillus japonicus

Biological-based conversion of agricultural residues into bioactive compounds may be considered to be the basis for various vital industries. However, finding a suitable microorganism is a challenge in the bioconversion process. Therefore, this study was conducted to find local fungal isolates able to convert a combination of plant biomass residues into organic acids (OAs). Based on their cellulase and phytase activities and rock phosphate (RP) solubilization potential, an efficient 15 fungal isolates (named F1 to F15) were selected and identified by both morphological and molecular methods using the 18S rRNA sequencing technique. The best fungal isolate (F15) was identified as Aspergillus japonicus. After 4 weeks of incubation below solid-state fermentation (SSF) with a mix of sugarcane bagasse and faba bean straw (3:7), with 7.5% (v/w) fungal inoculum to the growth medium, the biodegradation process by the fungus reached its peak, i.e., maximum cellulolytic activity and RP solubilization ability. Under such fermentation conditions, seven organic acids were detected using HPLC, in the following order: ascorbic acid > oxalic acid > formic acid > malic acid > succinic acid > lactic acid > citric acid. Based on the results, Aspergillus japonicus (F15) could produce OAs and cellulose enzymes, and could be considered a new single-step bio-converter of sugarcane bagasse and faba bean straw residues into OAs. Furthermore, this fungus could be a new source of fungal cellulose, and could present a practical approach to reducing environmental contamination. Additional work is encouraged for more optimization of fermentation conditions.

Lignocellulolytic enzymes from Aspergillus allahabadii for efficient bioconversion of rice straw into fermentable sugars and biogas

The study was aimed at developing lignocellulolytic strain capable of efficient hydrolysis of mild alkali deacetylated (MAD) rice straw. The valorisation of lignin rich black liquor obtained during pre-treatment of rice straw into biogas was also evaluated. Study reports highly proficient cellulolytic Aspergillus allahabadii strain harbouring a spectrum of CAZymes based on comparative genome wide analysis that was subjected to strain breeding for developing a hyper producing strain. The secretome analysis showed up-modulation and several folds increase in the CAZyme activities in the culture extracts of the developed strain MAN 40 when compared to parent. The cellulolytic cocktail of the developed strain showed 1.52 folds higher saccharification of MAD rice straw when compared to Cellic CTec 3. Moreover, in-situ addition of cellulases derived from developed strains resulted in ∼3.7 folds higher methane production during anaerobic digestion of mixture of lignin rich black liquor and differently treated rice straw.

Deletion of AA9 Lytic Polysaccharide Monooxygenases Impacts A. nidulans Secretome and Growth on Lignocellulose

Lytic polysaccharide monooxygenases (LPMOs) are oxidative enzymes found in viruses, archaea, and bacteria as well as eukaryotes, such as fungi, algae and insects, actively contributing to the degradation of different polysaccharides. In Aspergillus nidulans, LPMOs from family AA9 (AnLPMO9s), along with an AA3 cellobiose dehydrogenase (AnCDH1), are cosecreted upon growth on crystalline cellulose and lignocellulosic substrates, indicating their role in the degradation of plant cell wall components. Functional analysis revealed that three target LPMO9s (AnLPMO9C, AnLPMO9F and AnLPMO9G) correspond to cellulose-active enzymes with distinct regioselectivity and activity on cellulose with different proportions of crystalline and amorphous regions. AnLPMO9s deletion and overexpression studies corroborate functional data. The abundantly secreted AnLPMO9F is a major component of the extracellular cellulolytic system, while AnLPMO9G was less abundant and constantly secreted, and acts preferentially on crystalline regions of cellulose, uniquely displaying activity on highly crystalline algae cellulose. Single or double deletion of AnLPMO9s resulted in about 25% reduction in fungal growth on sugarcane straw but not on Avicel, demonstrating the contribution of LPMO9s for the saprophytic fungal lifestyle relies on the degradation of complex lignocellulosic substrates. Although the deletion of AnCDH1 slightly reduced the cellulolytic activity, it did not affect fungal growth indicating the existence of alternative electron donors to LPMOs. Additionally, double or triple knockouts of these enzymes had no accumulative deleterious effect on the cellulolytic activity nor on fungal growth, regardless of the deleted gene. Overexpression of AnLPMO9s in a cellulose-induced secretome background confirmed the importance and applicability of AnLPMO9G to improve lignocellulose saccharification. IMPORTANCE Fungal lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that boost plant biomass degradation in combination with glycoside hydrolases. Secretion of LPMO9s arsenal by Aspergillus nidulans is influenced by the substrate and time of induction. These findings along with the biochemical characterization of novel fungal LPMO9s have implications on our understanding of their concerted action, allowing rational engineering of fungal strains for biotechnological applications such as plant biomass degradation. Additionally, the role of oxidative players in fungal growth on plant biomass was evaluated by deletion and overexpression experiments using a model fungal system.

Morphologically favorable mutant of Trichoderma reesei for low viscosity cellulase production

Metabolite production by filamentous fungi hampered because of high viscosity generated during growth. Low viscosity fermentation by mold is one of the preferred ways of large scale enzymes production. Cellulolytic enzymes play a key role during the process of lignocellulosic biomass conversion. In this study a mutant RC-23-1 was isolated through mutagenesis (diethyl sulfate followed by UV) of T. reesei RUT-C30. RC-23-1 not only gave higher cellulase production but also generated lower viscosity during enzyme production. Viscosity of mutant growth was more than three times lower than parent strain. RC-23-1 shows unique, yeast like colony morphology on solid media and small pellet like growth in liquid media. This mutant did not spread like mold on solid media. This mutant produces cellulases constitutively when grown in sugars. Using only glucose, the cellulase production was 4.1 FPU/ml. Among polysaccharides (avicel, xylan and pectin), avicel gave maximum of 6.2 FPU/ml and pretreated biomass (rice straw, wheat straw and sugarcane bagasse) produced 5.1-5.8 FPU/ml. At 7L scale reactor, fed-batch process was designed for cellulase production using different carbon and nitrogen sources. Maximum yield of cellulases was 182 FPU/g of lactose consumed was observed in fed-batch process. The produced enzyme used for hydrolysis of acid pretreated rice straw (20% solid loading) and maximum of 60 % glucan conversion was observed. RC-23-1 mutant is good candidate for large scale cellulase production and could be a model strain to study mold to yeast-like transformation. This article is protected by copyright. All rights reserved.

Bio-based composite granules with simultaneous biocontrol and phosphorus fertilization roles: outcomes from a lab-scale in-vitro assessment

The use of phosphate rocks as low-solubility phosphorus fertilizers has been promoted to reduce the environmental impacts of agriculture, but adequate nutrient uptake by plants depends on solubilization of the rock, driven by soil microorganisms. Here, investigation was made of the microbial solubilization of low-solubility phosphate rocks, together with simultaneous bioprotective action involving the biocontrol of microorganisms. The aim was to enhance function and value by delivering two effects using a single bio-based product, in accordance with the concept of a "bioreactor-in-a-granule" system. A composite structure was developed, based on a starch matrix, comprising a combination of Trichoderma asperelloides, as a biocontrol agent, and Aspergillus niger, as an acidulant. A significant increase of up to 150% in P solubilization was achieved, indicating the positive effect of the microorganism-composite interaction. In vitro assays showed that the ability of T. asperelloides to inhibit Fusarium oxysporum mycelial growth was maintained in the presence of A. niger. Moreover, the estimated cost of the composite granule (0.35 US$/kg of product on a dry basis) revealed competitive. The results indicated that the association of T. asperelloides and A. niger is an effective way to increase nutrient availability and to inhibit plant pathogens, opening up possibilities for the design of multifunctional bio-based fertilizer composites. This article is protected by copyright. All rights reserved.

From fungal secretomes to enzymes cocktails: The path forward to bioeconomy

Bioeconomy is seen as a way to mitigate the carbon footprint of human activities by reducing at least part of the fossil resources-based economy. In this new paradigm of sustainable development, the use of enzymes as biocatalysts will play an increasing role to provide services and goods. In industry, most of multicomponent enzyme cocktails are of fungal origin. Filamentous fungi secrete complex enzyme sets called "secretomes" that can be utilized as enzyme cocktails to valorize different types of bioresources. In this review, we highlight recent advances in the study of fungal secretomes using improved computational and experimental secretomics methods, the progress in the understanding of industrially important fungi, and the discovery of new enzymatic mechanisms and interplays to degrade renewable resources rich in polysaccharides (e.g. cellulose). We review current biotechnological applications focusing on the benefits and challenges of fungal secretomes for industrial applications with some examples of commercial cocktails of fungal origin containing carbohydrate-active enzymes (CAZymes) and we discuss future trends.

Use of a Sequential Fermentation Method for the Production of Aspergillus tamarii URM4634 Protease and a Kinetic/Thermodynamic Study of the Enzyme

Microbial proteases are commonly produced by submerged (SmF) or solid-state fermentation (SSF), whose combination results in an unconventional method, called sequential fermentation (SF), which has already been used only to produce cellulolytic enzymes. In this context, the aim of the present study was the development of a novel SF method for protease production using wheat bran as a substrate. Moreover, the kinetic and thermodynamic parameters of azocasein hydrolysis were estimated, thus providing a greater understanding of the catalytic reaction. In SF, an approximately 9-fold increase in protease activity was observed compared to the conventional SmF method. Optimization of glucose concentration and medium volume by statistical means allowed us to achieve a maximum protease activity of 180.17 U mL−1. The obtained enzyme had an optimum pH and temperature of 7.0 and 50 °C, respectively. Kinetic and thermodynamic parameters highlighted that such a neutral protease is satisfactorily thermostable at 50 °C, a temperature commonly used in many applications in the food industry. The results obtained suggested not only that SF could be a promising alternative to produce proteases, but also that it could be adapted to produce several other enzymes.

Purification and characterization of a highly-stable fungal xylanase from Aspergillus tubingensis cultivated on palm wastes through combined solid-state and submerged fermentation

Fungal xylanase was produced from lignocellulosic palm wastes through combined solid-state fermentation (SSF) and submerged fermentation (SmF) by Aspergillus tubingensis TSIP9 in a helical-impeller equipped bioreactor. The combined SSF-SmF promoted the xylanase production by 15 and 70% higher than SSF and SmF, respectively. Sequential purification yielded 7.4-fold purified xylanase with 9.07% recovery. The maximum activities of crude and purified xylanase were observed at the same pH of 5.0 and the same temperature of 50 °C while purified xylanase is more active and highly stable at a wider pH range of 3-8 and temperature of 30-60 °C. The half-life of purified xylanase at various temperatures was also much improved by 2-8 folds compared to crude xylanase. Michaelis-Menten constants, V_max and K_m, for purified xylanase are 2,602.8 U/mg and 32.4 mg/mL, respectively. Purified xylanase activity was most enhanced with Ca²⁺ followed by Zn²⁺ and Fe²⁺ at 10 mM while significantly inhibited by Co²⁺, Cu²⁺, Pb²⁺, and Ag⁺. This study has shown the effectiveness of combined SSF-SmF for xylanase production and superior properties of purified xylanase for industrial processes.

Molecular Characterization of Xyloglucanase cel74a from Trichoderma reesei

BACKGROUND

The filamentous fungus Trichoderma reesei is used on an industrial scale to produce enzymes of biotechnological interest. This fungus has a complex cellulolytic system involved in the degradation of lignocellulosic biomass. However, several aspects related to the regulation of the expression of holocellulolytic genes and the production of cellulases by this fungus are still understood.

METHODS

Here, we constructed a null mutant strain for the xyloglucanase cel74a gene and performed the characterization of the Δcel74a strain to evaluate the genetic regulation of the holocellulases during sugarcane bagasse (SCB) cultivation.

RESULTS

Our results demonstrate that the deletion of xyloglucanase cel74a may impact the regulation of holocellulase expression during SCB cultivation. The expression of cellulases cel7a, cel7b, and cel6a was reduced in Δcel74a strain, while the hemicellulases xyn1 and xyn2 were increased in the presence of SCB. The cel74a mutation also affected the xyloglucan hydrolysis patterns. In addition, CEL74A activity was modulated in the presence of calcium, suggesting that this ion may be required for efficient degradation of xyloglucan.

CONCLUSIONS

CEL74A affects the regulation of holocellulolytic genes and the efficient degradation of SCB in T. reesei. This data makes a significant contribution to our understanding of the carbon utilization of fungal strains as a whole.

An overview of Trichoderma reesei co-cultures for the production of lignocellulolytic enzymes

Biorefineries are core facilities for implementing a sustainable circular bioeconomy. These facilities rely on microbial enzymes to hydrolyze lignocellulosic substrates into fermentable sugars. Fungal co-cultures mimic the process of natural biodegradation and have been shown to increase certain enzyme activities. Trichoderma reesei and its many mutant strains are major cellulase producers and are heavily utilized as a source of carbohydrate-active enzymes. Several reports have demonstrated that T. reesei co-cultures present higher enzyme activities compared with its monocultures, especially in the context of β-glucosidase activity. The performance of T. reesei during co-culturing has been assessed with several fungal partners, including Aspergillus niger, one of the most recurrent partners. Various aspects of co-cultivation still need further investigation, especially regarding the molecular interactions between fungi in controlled environments and the optimization of the resulting enzyme cocktails. Since plenty of genetic and physiological data on T. reesei is available, the species is an outstanding candidate for future co-culture investigations. Co-cultures are still a developing field for industrial enzyme production, and many aspects of the technique need further improvement before real applications. KEY POINTS: • T. reesei co-cultures are an alternative for producing lignocellulolytic enzymes. • Several reports suggest an increase in certain enzyme activities in co-cultures. • More in-depth investigations of co-cultures are necessary for advancing this field.

Secretomic insight into the biomass hydrolysis potential of the phytopathogenic fungus Chrysoporthe cubensis

The phytopathogenic fungus Chrysoporthe cubensis has a great capacity to produce highly efficient enzymes for the hydrolysis of lignocellulosic biomass. The bioinfosecretome of C. cubensis was identified by computational predictions of secreted proteins combined with protein analysis using 1D-LC-MS/MS. The in silico secretome predicted 562 putative genes capable of encoding secreted proteins, including 273 CAZymes. Proteomics analysis confirmed the existence of 313 proteins, including 137 CAZymes classified as Glycosyl Hydrolases (GH), Polysaccharide Lyases (PL), Carbohydrate Esterases (CE) and Auxiliary Activities enzymes (AA), which indicates the presence of classical and oxidative cellulolytic mechanisms. The enzymes diversity in the extract shows fungal versatility to act in complex biomasses. This study provides an insight into the lignocellulose-degradation mechanisms by C. cubensis and allows the identification of the enzymes that are potentially useful in improving industrial process of bioconversion of lignocellulose. SIGNIFICANCE: Chrysoporthe cubensis is an important deadly canker pathogen of commercially cultivated Eucalyptus species. The effective depolymerisation of the recalcitrant plant cell wall performed by this fungus is closely related to its high potential of lignocellulolytic enzymes secretion. Since the degradation of biomass occurs in nature almost exclusively by enzyme secretion systems, it is reasonable to suggest that the identification of C. cubensis lignocellulolytic enzymes is relevant in contributing to new sustainable alternatives for industrial solutions. As far as we know, this work is the first accurate proteomic evaluation of the enzymes secreted by this species of fungus. The integration of the gel-based proteomic approach, the bioinformatic prediction of the secretome and the analyses of enzymatic activity are powerful tools in the evaluation of biotechnological potential of C. cubensis in producing carbohydrate-active enzymes. In addition, analysis of the C. cubensis secretome grown in wheat bran draws attention to this plant pathogen and its extracellular enzymatic machinery, especially regarding the identification of promising new enzymes for industrial applications. The results from this work allowed for explanation and reinforce previous research that revealed C. cubensis as a strong candidate to produce enzymes to hydrolyse sugarcane bagasse and similar substrates.

Production of cellulases by Aureobasidium pullulans LB83: optimization, characterization, and hydrolytic potential for the production of cellulosic sugars

Aureobasidium pullulans LB83 was evaluated for cellulase production under submerged fermentation conditions. Different process variables such as carbon sources (corn cob, sugarcane bagasse, and sugarcane straw), synthetic (urea, ammonium sulfate, and peptone), and non-synthetic (soybean meal, rice, and corn meal) nitrogen sources and inoculum size were evaluated by one parameter at-a-time strategy. Aureobasidium pullulans LB83 showed maximum cellulase activity (FPase, 2.27 U/mL; CMCase, 7.42 U/mL) on sugarcane bagasse. Among the nitrogen sources, soybean meal as a non-synthetic nitrogen sources showed a maximum cellulase activity (FPase 2.45 U/mL; CMCase, 6.86 U/mL) after 60 hr. The inoculum size of 1.6 × 106 CFU/mL had the maximum FPase and CMCase activities of 3.14 and 8.74 U/mL, respectively. For the enzymatic hydrolysis, both the commercial cellulase (10 FPU/g of Cellic CTec 2 (#A) and 10 FPU/g of crude enzyme extract (CEE) (#B), and varying ratio of CTec 2 and CEE in combination #C (5 FPU/g of CTec 2 + 5 FPU/g CEE), combination #D (2.5 FPU/g of CTec 2 + 7.5 FPU/g CEE), and combination #E (7.5 FPU/g of CTec 2 + 2.5 FPU/g CEE) were assessed for enzymatic hydrolysis of delignified sugarcane bagasse. Enzyme combination #C showed maximum hydrolysis yield of 92.40%. The study shows the hydrolytic potential of cellulolytic enzymes from A. pullulans LB83 for lignocellulosic sugars production from delignified sugarcane bagasse.

Eco-friendly Transformation of Waste Biomass to Biofuels

Background:

The development of viable alternative fuel sources is assuming a new urgency in the face of climate change and environmental degradation linked to the escalating consumption of fossil fuels. Lignocellulosic biomass is composed primarily of high-energy structural components such as cellulose, hemicellulose and lignin. The transformation of lignocellulosic biomass to biofuels requires the application of both pretreatment and conversion technologies.

Methods:

Several pretreatment technologies (e.g. physical, chemical and biological) are used to recover cellulose, hemicellulose and lignin from biomass and begin the transformation into biofuels. This paper reviews the thermochemical (e.g. pyrolysis, gasification and liquefaction), hydrothermal (e.g. subcritical and supercritical water gasification and hydrothermal liquefaction), and biological (e.g. fermentation) conversion pathways that are used to further transform biomass feedstocks into fuel products.

Results:

Through several thermochemical and biological conversion technologies, lignocellulosic biomass and other organic residues can produce biofuels such as bio-oils, biochar, syngas, biohydrogen, bioethanol and biobutanol, all of which have the potential to replace hydrocarbon-based fossil fuels.

Conclusions:

This review paper describes the conversion technologies used in the transformation of biomass into viable biofuels. Biofuels produced from lignocellulosic biomass and organic wastes are a promising potential clean energy source with the potential to be carbon-neutral or even carbonnegative.

Secretomic analysis of cheap enzymatic cocktails of Aspergillus niger LBM 134 grown on cassava bagasse and sugarcane bagasse

Currently, agroindustrial wastes are little used for generating value-added products; hence, their use of these waste to produce enzymatic cocktails for the conversion of lignocellulosic biomass to fermentable sugars is a very interesting alternative in the second-generation bioethanol process. The Ascomycota fungus Aspergillus niger LBM 134 produces hydrolytic enzymes in large proportions. In this work, A. niger LBM 134 was grown on sugarcane and cassava bagasses under optimized conditions. To identify the extracellular enzymes involved in the degradation of these agroindustrial wastes, the secretomes of the culture supernatants of the fungus were analyzed and validated by biochemical assays of the enzymatic activities. A. niger LBM 134 secreted higher quantities of xylanases and accessory hemicellulases when it grew on sugarcane bagasse, whereas more cellulases, amylases, and pectinases were secreted when it grew on cassava bagasse. These findings suggest two promising enzyme cocktails for the hydrolysis of lignocellulose carbohydrate polymers to fermentable sugars. These bioinformatic analysis were functional validates through enzymatic biochemical assays that confirm the biotechnological potential of A. niger LBM 134 for the bioconversion of hemicellulosic substrates such as sugarcane and cassava bagasses.

Studies of Cellulose and Starch Utilization and the Regulatory Mechanisms of Related Enzymes in Fungi

Polysaccharides are biopolymers made up of a large number of monosaccharides joined together by glycosidic bonds. Polysaccharides are widely distributed in nature: Some, such as peptidoglycan and cellulose, are the components that make up the cell walls of bacteria and plants, and some, such as starch and glycogen, are used as carbohydrate storage in plants and animals. Fungi exist in a variety of natural environments and can exploit a wide range of carbon sources. They play a crucial role in the global carbon cycle because of their ability to break down plant biomass, which is composed primarily of cell wall polysaccharides, including cellulose, hemicellulose, and pectin. Fungi produce a variety of enzymes that in combination degrade cell wall polysaccharides into different monosaccharides. Starch, the main component of grain, is also a polysaccharide that can be broken down into monosaccharides by fungi. These monosaccharides can be used for energy or as precursors for the biosynthesis of biomolecules through a series of enzymatic reactions. Industrial fermentation by microbes has been widely used to produce traditional foods, beverages, and biofuels from starch and to a lesser extent plant biomass. This review focuses on the degradation and utilization of plant homopolysaccharides, cellulose and starch; summarizes the activities of the enzymes involved and the regulation of the induction of the enzymes in well-studied filamentous fungi.

Effect of Lignin Content on Cellulolytic Saccharification of Liquid Hot Water Pretreated Sugarcane Bagasse

Lignin contributes to the rigid structure of the plant cell wall and is partially responsible for the recalcitrance of lignocellulosic materials to enzymatic digestion. Overcoming this recalcitrance is one the most critical issues in a sugar-flat form process. This study addresses the effect of low lignin sugarcane bagasse on enzymatic hydrolysis after liquid hot water pretreatment at 190 °C and 20 min (severity factor: 3.95). The hydrolysis of bagasse from a sugarcane line selected for a relatively low lignin content, gave an 89.7% yield of cellulose conversion to glucose at 40 FPU/g glucan versus a 68.3% yield from a comparably treated bagasse from the high lignin bred line. A lower enzyme loading of 5 FPU/g glucan (equivalent to 3.2 FPU/g total solids) resulted in 31.4% and 21.9% conversion yields, respectively, for low and high lignin samples, suggesting the significance of lignin content in the saccharification process. Further increases in the enzymatic conversion of cellulose to glucose were achieved when the bagasse sample was pre-incubated with a lignin blocking agent, e.g., bovine serum albumin (50 mg BSA/g glucan) at 50 °C for 1 h prior to an actual saccharification. In this work, we have demonstrated that even relatively small differences in lignin content can result in considerably increased sugar production, which supports the dissimilarity of bagasse lignin content and its effects on cellulose digestibility. The increased glucose yields with the addition of BSA helped to decrease the inhibition of non-productive absorption of cellulose enzymes onto lignin and solid residual lignin fractions.

Oxygen radical based on non-thermal atmospheric pressure plasma alleviates lignin-derived phenolic toxicity in yeast

BACKGROUND

Vanillin is the main byproduct of alkaline-pretreated lignocellulosic biomass during the process of fermentable-sugar production and a potent inhibitor of ethanol production by yeast. Yeast cells are usually exposed to vanillin during the industrial production of bioethanol from lignocellulosic biomass. Therefore, vanillin toxicity represents a major barrier to reducing the cost of bioethanol production.

RESULTS

In this study, we analysed the effects of oxygen-radical treatment on vanillin molecules. Our results showed that vanillin was converted to vanillic acid, protocatechuic aldehyde, protocatechuic acid, methoxyhydroquinone, 3,4-dihydroxy-5-methoxybenzaldehyde, trihydroxy-5-methoxybenzene, and their respective ring-cleaved products, which displayed decreased toxicity relative to vanillin and resulted in reduced vanillin-specific toxicity to yeast during ethanol fermentation. Additionally, after a 16-h incubation, the ethanol concentration in oxygen-radical-treated vanillin solution was 7.0-fold greater than that from non-treated solution, with similar results observed using alkaline-pretreated rice straw slurry with oxygen-radical treatment.

CONCLUSIONS

This study analysed the effects of oxygen-radical treatment on vanillin molecules in the alkaline-pretreated rice straw slurry, thereby finding that this treatment converted vanillin to its derivatives, resulting in reduced vanillin toxicity to yeast during ethanol fermentation. These findings suggest that a combination of chemical and oxygen-radical treatment improved ethanol production using yeast cells, and that oxygen-radical treatment of plant biomass offers great promise for further improvements in bioethanol-production processes.

The Indispensable Role of Histone Methyltransferase PoDot1 in Extracellular Glycoside Hydrolase Biosynthesis of Penicillium oxalicum

Histone methylation is associated with transcription regulation, but its role for glycoside hydrolase (GH) biosynthesis is still poorly understood. We identified the histone H3 lysine 79 (H3K79)-specific methyltransferase PoDot1 in Penicillium oxalicum. PoDot1 affects conidiation by regulating the transcription of key regulators (BrlA, FlbC, and StuA) of asexual development and is required in normal hyphae septum and branch formation by regulating the transcription of five septin-encoding genes, namely, aspA, aspB, aspC, aspD, and aspE. Tandem affinity purification/mass spectrometry showed that PoDot1 has no direct interaction with transcription machinery, but it affects the expressions of extracellular GH genes extensively. The expression of genes (amy15A, amy13A, cel7A/cbh1, cel61A, chi18A, cel3A/bgl1, xyn10A, cel7B/eg1, cel5B/eg2, and cel6A/cbh2) that encode the top 10 GHs was remarkably downregulated by Podot1 deletion (ΔPodot1). Consistent with the decrease in gene transcription level, the activities of amylases and cellulases were significantly decreased in ΔPodot1 mutants in agar (solid) and fermentation (liquid) media. The repression of GH gene expressions caused by PoDot1 deletion was not mediated by key transcription factors, such as AmyR, ClrB, CreA, and XlnR, but was accompanied by defects in global demethylated H3K79 (H3K79me2) and trimethylated H3K79 (H3K79me3). The impairment of H3K79me2 on specific GH gene loci was observed due to PoDot1 deletion. The results implies that defects of H3K79 methylation is the key reason of the downregulated transcription level of GH-encoding genes and reveals the indispensable role of PoDot1 in extracellular GH biosynthesis.

The influence of feedstock characteristics on enzyme production in Trichoderma reesei: a review on productivity, gene regulation and secretion profiles

Biorefineries, designed for the production of lignocellulose-based chemicals and fuels, are receiving increasing attention from the public, governments, and industries. A major obstacle for biorefineries to advance to commercial scale is the high cost of the enzymes required to derive the fermentable sugars from the feedstock used. As summarized in this review, techno-economic studies suggest co-localization and integration of enzyme manufacturing with the cellulosic biorefinery as the most promising alternative to alleviate this problem. Thus, cultivation of Trichoderma reesei, the principal producer of lignocellulolytic enzymes, on the lignocellulosic biomass processed on-site can reduce the cost of enzyme manufacturing. Further, due to a complex gene regulation machinery, the fungus can adjust the gene expression of the lignocellulolytic enzymes towards the characteristics of the feedstock, increasing the hydrolytic efficiency of the produced enzyme cocktail. Despite extensive research over decades, the underlying regulatory mechanisms are not fully elucidated. One aspect that has received relatively little attention in literature is the influence the characteristics of a lignocellulosic substrate, i.e., its chemical and physical composition, has on the produced enzyme mixture. Considering that the fungus is dependent on efficient enzymatic degradation of the lignocellulose for continuous supply of carbon and energy, a relationship between feedstock characteristics and secretome composition can be expected. The aim of this review was to systematically collect, appraise, and aggregate data and integrate results from studies analyzing enzyme production by T. reesei on insoluble cellulosic model substrates and lignocellulosic biomass. The results show that there is a direct effect of the substrate's complexity (rated by structure, composition of the lignin-carbohydrate complex, and recalcitrance in enzymatic saccharification) on enzyme titers and the composition of specific activities in the secretome. It further shows that process-related factors, such as substrate loading and cultivation set-up, are direct targets for increasing enzyme yields. The literature on transcriptome and secretome composition further supports the proposed influence of substrate-related factors on the expression of lignocellulolytic enzymes. This review provides insights into the interrelation between the characteristics of the substrate and the enzyme production by T. reesei, which may help to advance integrated enzyme manufacturing of substrate-specific enzymes cocktails at scale.

Recent advances in plasmid-based tools for establishing novel microbial chassis

A key challenge for domesticating alternative cultivable microorganisms with biotechnological potential lies in the development of innovative technologies. Within this framework, a myriad of genetic tools has flourished, allowing the design and manipulation of complex synthetic circuits and genomes to become the general rule in many laboratories rather than the exception. More recently, with the development of novel technologies such as DNA automated synthesis/sequencing and powerful computational tools, molecular biology has entered the synthetic biology era. In the beginning, most of these technologies were established in traditional microbial models (known as chassis in the synthetic biology framework) such as Escherichia coli and Saccharomyces cerevisiae, enabling fast advances in the field and the validation of fundamental proofs of concept. However, it soon became clear that these organisms, although extremely useful for prototyping many genetic tools, were not ideal for a wide range of biotechnological tasks due to intrinsic limitations in their molecular/physiological properties. Over the last decade, researchers have been facing the great challenge of shifting from these model systems to non-conventional chassis with endogenous capacities for dealing with specific tasks. The key to address these issues includes the generation of narrow and broad host plasmid-based molecular tools and the development of novel methods for engineering genomes through homologous recombination systems, CRISPR/Cas9 and other alternative methods. Here, we address the most recent advances in plasmid-based tools for the construction of novel cell factories, including a guide for helping with "build-your-own" microbial host.

Designing cellulolytic enzyme systems for biorefinery: From nature to application

Cellulolytic enzymes play a key role on conversion of lignocellulosic plant biomass to biofuels and biochemicals in sugar platform biorefineries. In this review, we survey composite carbohydrate-active enzymes (CAZymes) among groups of cellulolytic fungi and bacteria that exist under aerobic and anaerobic conditions. Recent advances in designing effective cellulase mixtures are described, starting from the most complex microbial consortium-based enzyme preparations, to single-origin enzymes derived from intensively studied cellulase producers such as Trichoderma reesei, Talaromyces cellulolyticus, and Penicellium funiculosum, and the simplest minimal enzyme systems comprising selected sets of mono-component enzymes tailor-made for specific lignocellulosic substrates. We provide a comprehensive update on studies in developing high-performance cellulases for biorefineries.

Carbon sources and XlnR-dependent transcriptional landscape of CAZymes in the industrial fungus Talaromyces versatilis: when exception seems to be the rule

Background

Research on filamentous fungi emphasized the remarkable redundancy in genes encoding hydrolytic enzymes, the similarities but also the large differences in their expression, especially through the role of the XlnR/XYR1 transcriptional activator. The purpose of this study was to evaluate the specificities of the industrial fungus Talaromyces versatilis, getting clues into the role of XlnR and the importance of glucose repression at the transcriptional level, to provide further levers for cocktail production.

Results

By studying a set of 62 redundant genes representative of several categories of enzymes, our results underlined the huge plasticity of transcriptional responses when changing nutritional status. As a general trend, the more heterogeneous the substrate, the more efficient to trigger activation. Genetic modifications of xlnR led to significant reorganisation of transcriptional patterns. Just a minimal set of genes actually fitted in a simplistic model of regulation by a transcriptional activator, and this under specific substrates. On the contrary, the diversity of xlnR⁺ versus ΔxlnR responses illustrated the existence of complex and unpredicted patterns of co-regulated genes that were highly dependent on the culture condition, even between genes that encode members of a functional category of enzymes. They notably revealed a dual, substrate-dependant repressor-activator role of XlnR, with counter-intuitive transcripts regulations that targeted specific genes. About glucose, it appeared as a formal repressive sugar as we observed a massive repression of most genes upon glucose addition to the mycelium grown on wheat straw. However, we also noticed a positive role of this sugar on the basal expression of a few genes, (notably those encoding cellulases), showing again the strong dependence of these regulatory mechanisms upon promoter and nutritional contexts.

Conclusions

The diversity of transcriptional patterns appeared to be the rule, while common and stable behaviour, both within gene families and with fungal literature, the exception. The setup of a new biotechnological process to reach optimized, if not customized expression patterns of enzymes, hence appeared tricky just relying on published data that can lead, in the best scenario, to approximate trends. We instead encourage preliminary experimental assays, carried out in the context of interest to reassess gene responses, as a mandatory step before thinking in (genetic) strategies for the improvement of enzyme production in fungi.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1062-8) contains supplementary material, which is available to authorized users.

One-pot strategy for on-site enzyme production, biomass hydrolysis, and ethanol production using the whole solid-state fermentation medium of mixed filamentous fungi

The efficient use of renewable lignocellulosic feedstocks to obtain biofuels and other bioproducts is a key requirement for a sustainable biobased economy. This requires novel and effective strategies to reduce the cost contribution of the cellulolytic enzymatic cocktails needed to convert the carbohydrates into simple sugars, in order to make large-scale commercial processes economically competitive. Here, we propose the use of the whole solid-state fermentation (SSF) medium of mixed filamentous fungi as an integrated one-pot strategy for on-site enzyme production, biomass hydrolysis, and ethanol production. Ten different individual and mixed cultivations of commonly used industrial filamentous fungi (Aspergillus niger, Aspergillus oryzae, Trichoderma harzianum, and Trichoderma reesei) were performed under SSF and the whole media (without the extraction step) were used in the hydrolysis of pretreated sugarcane bagasse. The cocultivation of T. reesei with A. oryzae increased the amount of glucose released by around 50%, compared with individual cultivations. The release of glucose and reducing sugars achieved using the whole SSF medium was around 3-fold higher than obtained with the enzyme extract. The addition of soybean protein (0.5% w/w) during the hydrolysis reaction further significantly improved the saccharification performance by blocking the lignin and avoiding unproductive adsorption of enzymes. The results of the alcoholic fermentation validated the overall integrated process, with a volumetric ethanol productivity of 4.77 g/L.h, representing 83.5% of the theoretical yield. These findings demonstrate the feasibility of the proposed one-pot integrated strategy using the whole SSF medium of mixed filamentous fungi for on-site enzymes production, biomass hydrolysis, and ethanol production. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:671-680, 2018.

A closed-loop strategy for endoglucanase production using sugarcane bagasse liquefied by a home-made enzymatic cocktail

Use of the same lignocellulosic biomass as feedstock for enzymes and ethanol production has been suggested as a lower cost option in future biorefineries. Here, we propose a closed-loop strategy to produce the cellulolytic enzymes required for biomass hydrolysis using sugarcane bagasse liquefied by a home-made enzymatic cocktail as carbon source and inducer. The fed-batch liquefaction conditions were firstly evaluated using commercial enzymes. Subsequently, the effects of different liquefied materials and solids loadings on endoglucanase production by Aspergillus niger cultivated in submerged fermentation were investigated. The liquefied bagasse produced using the home-made cocktail was more favorable for endoglucanase production, resulting in improvement up to 17%, compared to bagasse liquefied by commercial enzymes. The results indicated that liquefied bagasse produced by home-made enzymatic cocktail could provide a cost-effective carbon source and inducer for cellulolytic enzyme production, and could contribute to closing loops within the biorefinery, thus reducing costs and minimizing waste.

Characterization of cellulase from Aspergillus tubingensis NKBP-55 for generation of fermentable sugars from agricultural residues

The aim of this work was to characterize cellulase from Aspergillus tubingensis NKBP-55 for generation of fermentable sugars from agricultural residues. The strain produced high titres of cellulase (750 U/gds) on copra meal in solid state fermentation (SSF). The enzyme preparation also showed hemicellulolytic activities (U/gds) viz. endo-mannanase (1023), endo-xylanase (167), β-glucosidase (72) and α-galactosidase (54). Zymography revealed presence of six cellulases, six mannanases and one β-glucosidase. It effectively degraded sugarcane bagasse (SCB) and rice straw (RS) releasing xylose, glucose and cellobiose. One cellulase (Cat 1, Mr ∼65 kDa) was purified and characterized. It retained more than 50% activity at 70 °C after 150 mins and its activity was enhanced in the presence of Mn²⁺ ions (130%) and β-mercaptoethanol (140%). FTIR and ¹³C CP/MAS NMR analysis of the enzyme treated SCB and RS revealed degradation of cellulose and hemicellulose, while ¹H and ¹³C liquid state NMR experiments confirmed release of glucose.

On-Site Production of Cellulolytic Enzymes by the Sequential Cultivation Method

The conversion of renewable lignocellulosic biomass into fuels, chemicals, and high-value materials using the biochemical platform has been considered the most sustainable alternative for the implementation of future biorefineries. However, the high cost of the cellulolytic enzymatic cocktails used in the saccharification step significantly affects the economics of industrial large-scale conversion processes. The on-site production of enzymes, integrated to the biorefinery plant, is being considered as a potential strategy that could be used to reduce costs. In such approach, the microbial production of enzymes can be carried out using the same lignocellulosic biomass as feedstock for fungal development and biofuels production. Most of the microbial cultivation processes for the production of industrial enzymes have been developed using the conventional submerged fermentation. Recently, a sequential solid-state followed by submerged fermentation has been described as a potential alternative cultivation method for cellulolytic enzymes production. This chapter presents the detailed procedure of the sequential cultivation method, which could be employed for the on-site production of the cellulolytic enzymes required to convert lignocellulosic biomass into simple sugars.

A novel bifunctional acetyl xylan esterase/arabinofuranosidase from Penicillium chrysogenum P33 enhances enzymatic hydrolysis of lignocellulose

BACKGROUND

Xylan, the major constituent of hemicellulose, is composed of β-(1,4)-linked xylopyranosyl units that for the backbone, with side chains formed by other chemical moieties such as arabinose, galactose, mannose, ferulic acid and acetyl groups. Acetyl xylan esterases and α-L-arabinofuranosidases are two important accessory enzymes that remove side chain residues from xylan backbones and may act in synergy with other xylanolytic enzymes. Compared with enzymes possessing a single catalytic activity, multifunctional enzymes can achieve lignocellulosic biomass hydrolysis using a less complex mixture of enzymes.

RESULTS

Here, we cloned an acetyl xylan esterase (PcAxe) from Penicillium chrysogenum P33 and expressed it in Pichia pastoris GS115. The optimal pH and temperature of the recombinant PcAxe (rPcAxe) for 4-nitrophenyl acetate were 7.0 and 40 °C, respectively. rPcAxe is stable across a broad pH range, retaining 100% enzyme activity om pH 6-9 after a 1 h incubation. The enzyme tolerates the presence of a wide range of metal ions. Sequence alignment revealed a GH62 domain exhibiting α-L-arabinofuranosidase activity with pH and temperature optima of pH 7.0 and 50 °C, in addition to the expected esterase domain. rPcAxe displayed significant synergy with a recombinant xylanase, with a degree of synergy of 1.35 for the hydrolysis of delignified corn stover. Release of glucose was increased by 51% from delignified corn stover when 2 mg of a commercial cellulase was replaced by an equivalent amount of rPcAxe, indicating superior hydrolytic efficiency.

CONCLUSIONS

The novel bifunctional enzyme PcAxe was identified in P. chrysogenum P33. rPcAxe includes a carbohydrate esterase domain and a glycosyl hydrolase family 62 domain. This is the first detailed report on a novel bifunctional enzyme possessing acetyl xylan esterase and α-L-arabinofuranosidase activities. These findings expand our current knowledge of glycoside hydrolases and pave the way for the discovery of similar novel enzymes.

Potential of Mangrove-Associated Endophytic Fungi for Production of Carbohydrolases with High Saccharification Efficiency

The endophytic fungi represent a potential source of microorganisms for enzyme production. However, there have been only few studies exploiting their potential for the production of enzymes of industrial interest, such as the (hemi)cellulolytic enzymatic cocktail required in the hydrolysis of lignocellulosic biomass. Here, a collection of endophytic fungi isolated from mangrove tropical forests was evaluated for the production of carbohydrolases and performance on the hydrolysis of cellulose. For that, 41 endophytic strains were initially screened using a plate assay containing crystalline cellulose as the sole carbon source and the selected strains were cultivated under solid-state fermentation for endoglucanase, β-glucosidase, and xylanase enzyme quantification. The hydrolysis of a cellulosic material with the enzymes from endophytic strains of the Aspergillus genus resulted in glucose and conversion values more than twofold higher than the reference strains (Aspergillus niger F12 and Trichoderma reesei Rut-C30). Particularly, the enzymes from strains A. niger 56 (3) and A. awamori 82 (4) showed a distinguished saccharification performance, reaching cellulose conversion values of about 35% after 24 h. Linking hydrolysis performance to the screening steps played an important role towards finding potential fungal strains for producing enzymatic cocktails with high saccharification efficiency. These results indicate the potential of mangrove-associated endophytic fungi for production of carbohydrolases with efficient performance in the hydrolysis of biomass, thus contributing to the implementation of future biorefineries.

Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei

Background

Second generation (2G) ethanol is produced by breaking down lignocellulosic biomass into fermentable sugars. In Brazil, sugarcane bagasse has been proposed as the lignocellulosic residue for this biofuel production. The enzymatic cocktails for the degradation of biomass-derived polysaccharides are mostly produced by fungi, such as Aspergillus niger and Trichoderma reesei. However, it is not yet fully understood how these microorganisms degrade plant biomass. In order to identify transcriptomic changes during steam-exploded bagasse (SEB) breakdown, we conducted a RNA-seq comparative transcriptome profiling of both fungi growing on SEB as carbon source.

Results

Particular attention was focused on CAZymes, sugar transporters, transcription factors (TFs) and other proteins related to lignocellulose degradation. Although genes coding for the main enzymes involved in biomass deconstruction were expressed by both fungal strains since the beginning of the growth in SEB, significant differences were found in their expression profiles. The expression of these enzymes is mainly regulated at the transcription level, and A. niger and T. reesei also showed differences in TFs content and in their expression. Several sugar transporters that were induced in both fungal strains could be new players on biomass degradation besides their role in sugar uptake. Interestingly, our findings revealed that in both strains several genes that code for proteins of unknown function and pro-oxidant, antioxidant, and detoxification enzymes were induced during growth in SEB as carbon source, but their specific roles on lignocellulose degradation remain to be elucidated.

Conclusions

This is the first report of a time-course experiment monitoring the degradation of pretreated bagasse by two important fungi using the RNA-seq technology. It was possible to identify a set of genes that might be applied in several biotechnology fields. The data suggest that these two microorganisms employ different strategies for biomass breakdown. This knowledge can be exploited for the rational design of enzymatic cocktails and 2G ethanol production improvement.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3857-5) contains supplementary material, which is available to authorized users.

Soybean protein as a cost-effective lignin-blocking additive for the saccharification of sugarcane bagasse

Addition of surfactants, polymers, and non-catalytic proteins can improve the enzymatic hydrolysis of lignocellulosic materials by blocking the exposed lignin surfaces, but involves extra expense. Here, soybean protein, one of the cheapest proteins available, was evaluated as an alternative additive for the enzymatic hydrolysis of pretreated sugarcane bagasse. The effect of the enzyme source was investigated using enzymatic cocktails from A. niger and T. reesei cultivated under solid-state, submerged, and sequential fermentation. The use of soybean protein led to approximately 2-fold increases in hydrolysis, relative to the control, for both A. niger and T. reesei enzymatic cocktails from solid-state fermentation. The effect was comparable to that of BSA. Moreover, the use of soybean protein and a 1:1 combination of A. niger and T. reesei enzymatic cocktails resulted in 54% higher glucose release, compared to the control. Soybean protein is a potential cost-effective additive for use in the biomass conversion process.

Secretome data from Trichoderma reesei and Aspergillus niger cultivated in submerged and sequential fermentation methods

The cultivation procedure and the fungal strain applied for enzyme production may influence levels and profile of the proteins produced. The proteomic analysis data presented here provide critical information to compare proteins secreted by Trichoderma reesei and Aspergillus niger when cultivated through submerged and sequential fermentation processes, using steam-explosion sugarcane bagasse as inducer for enzyme production. The proteins were organized according to the families described in CAZy database as cellulases, hemicellulases, proteases/peptidases, cell-wall-protein, lipases, others (catalase, esterase, etc.), glycoside hydrolases families, predicted and hypothetical proteins. Further detailed analysis of this data is provided in “Secretome analysis of Trichoderma reesei and Aspergillus niger cultivated by submerged and sequential fermentation process: enzyme production for sugarcane bagasse hydrolysis” C. Florencio, F.M. Cunha, A.C Badino, C.S. Farinas, E. Ximenes, M.R. Ladisch (2016) [1].

Expression and chromatin structures of cellulolytic enzyme gene regulated by heterochromatin protein 1

BACKGROUND

Heterochromatin protein 1 (HP1, homologue HepA in Penicillium oxalicum) binding is associated with a highly compact chromatin state accompanied by gene silencing or repression. HP1 loss leads to the derepression of gene expression. We investigated HepA roles in regulating cellulolytic enzyme gene expression, as an increasingly number of studies have suggested that cellulolytic enzyme gene expression is not only regulated by transcription factors, but is also affected by the chromatin status.

RESULTS

Among the genes that exhibited significant differences between the hepA deletion strain (ΔhepA) and the wild type (WT), most (95.0 %) were upregulated in ΔhepA compared with WT. The expression of the key transcription factor for cellulolytic enzyme gene (e.g., repressor CreA and activator ClrB) increased significantly. However, the deletion of hepA led to downregulation of prominent extracellular cellulolytic enzyme genes. Among the top 10 extracellular glycoside hydrolases (Amy15A, Amy13A, Cel7A/CBHI, Cel61A, Chi18A, Cel3A/BGLI, Xyn10A, Cel7B/EGI, Cel5B/EGII, and Cel6A/CBHII), in which secretion amount is from the highest to the tenth in P. oxalicum secretome, eight genes, including two amylase genes (amy15A and amy13A), all five cellulase genes (cel7A/cbh1, cel6A/cbh2, cel7B/eg1, cel5B/eg2, and cel3A/bgl1), and the cellulose-active LPMO gene (cel61A) expression were downregulated. Results of chromatin accessibility real-time PCR (CHART-PCR) showed that the chromatin of all three tested upstream regions opened specifically because of the deletion of hepA in the case of two prominent cellulase genes cel7A/cbh1 and cel7B/eg1. However, the open chromatin status did not occur along with the activation of cellulolytic enzyme gene expression. The overexpression of hepA upregulated the cellulolytic enzyme gene expression without chromatin modification. The overexpression of hepA remarkably activated the cellulolytic enzyme synthesis, not only in WT (~150 % filter paper activity (FPA) increase), but also in the industry strain RE-10 (~20-30 % FPA increase).

CONCLUSIONS

HepA is required for chromatin condensation of prominent cellulase genes. However, the opening of chromatin mediated by the deletion of hepA was not positively correlated with cellulolytic enzyme gene activation. HepA is actually a positive regulator for cellulolytic enzyme gene expression and could be a promising target for genetic modification to improve cellulolytic enzyme synthesis.