A simple and accurate method for specific quantification of biomass in mixed cultures of filamentous fungi by quantitative PCR / Un método simple y preciso para la cuantificación específica de biomasa en cultivos mixtos de hongos filamentosos por PCR cuantitativa

Abstract Production of lignocellulolytic enzymes by filamentous fungi have a great potential at industrial level due to their widespread applications. Mixed fungal cultures and particularly mixed fungal biofilms constitute a promising fermentation system for an enhanced enzyme production. However, it has not been addressed how much of this enhancement depends on the mixed biomass proportion. In this sense, the aim of this study was to develop a method to specifically and accurately quantify mixed fungal biomass. For this purpose, mixed biofilm cultures composed of Aspergillus niger and Trichoderma reesei, two filamentous fungi used industrially for cellulase production, were collected from 48 to 120 h of growth; mycelia were pulverized, and DNA was extracted for qPCR assays with specific primers for each fungus. Primers were designed from non-conserved regions of sequences of actin and β-tubulin genes of both A. niger and T. reesei. Specificity of these primers was tested in silico and experimentally. A statistically significant correlation was obtained between qPCR-calculated biomass and dry weight biomass data. By this method, it was possible to detect changes on mycelia proportions in biofilms over time, suggesting a competitive interaction between these two fungi. In conclusion, this method allows a specific and accurate quantification of mixed fungal biomass and could be also applied to different mixed culture systems for studying microbial interactions.

Resumen La producción de enzimas lignocelulolíticas por hongos filamentosos tiene un gran potencial a nivel industrial debido a sus diversas aplicaciones. Los cultivos fúngicos mixtos y particularmente las biopelículas fúngicas mixtas constituyen un sistema de fermentación prometedor para una mayor producción enzimática. Sin embargo, no se ha abordado cuánto de esta mejora depende de la proporción de biomasa mixta. En este sentido, el objetivo de este estudio fue desarrollar un método para cuantificar de forma específica y precisa la biomasa fúngica mixta. Para este propósito, se recolectaron cultivos mixtos de biopelículas de 48 a 120 h de crecimiento compuestos por Aspergillus niger y Trichoderma reesei, dos hongos filamentosos utilizados industrialmente para la producción de celulasas; el micelio se pulverizó y el ADN se extrajo para ensayos de qPCR con cebadores específicos para cada hongo. Los cebadores se diseñaron a partir de regiones no conservadas de las secuencias de los genes de actina y β-tubulina de A. niger y T. reesei. La especificidad de estos cebadores se probó in silico y experimentalmente. Se obtuvo una correlación estadísticamente significativa entre la biomasa calculada mediante qPCR y los datos de biomasa en peso seco. Mediante este método, fue posible detectar cambios en las proporciones de los micelios en las biopelículas a lo largo del tiempo, lo que sugiere una interacción competitiva entre estos dos hongos. En conclusión, este método permite una cuantificación específica y precisa de la biomasa fúngica mixta y también podría aplicarse a diferentes sistemas de cultivo mixto para estudiar interacciones microbianas.

Enhance of Cellulase Production and Biomass Degradation by Transformation of the Trichoderma reesei RUT-C30∆ zface1 Strain

Abstract The second-generation bioethanol employs lignocellulosic materials degraded by microbial cellulases in their production. The fungus Trichoderma reesei is one of the main microorganisms producing cellulases, and its genetic modification can lead to the optimization in obtaining hydrolytic enzymes. This work carried out the deletion of the sequence that encodes the zinc finger motif of the transcription factor ACE1 (cellulase expression repressor I) of the fungus T. reesei RUT-C30. The transformation of the RUT-C30 lineage was confirmed by amplification of the 989 bp fragment relative to the selection marker, and by the absence of the zinc finger region amplification in mutants, named T. reesei RUT-C30Δzface1. The production of cellulases by mutants was compared to RUT-C30 and measured with substrates carboxymethylcellulose (CMC), microcrystalline cellulose (Avicel®) and Whatman filter paper (PF). The results demonstrated that RUT-C30Δzface1 has cellulolytic activity increased 3.2-fold in Avicel and 2.1-fold in CMC and PF. The mutants presented 1.4-fold higher sugar released in the hydrolysis of the biomass assays. These results suggest that the partial deletion of ace1 gene is an important strategy in achieving bioethanol production on an industrial scale at a competitive price in the fuel market.

Artificial zinc finger protein mediated cellulase production in Trichoderma reesei Rut-C30 / 生物工程学报

Trichoderma reesei Rut-C30 is widely used in industrial cellulase production, and development of cellulase hyper-producer is of great importance for economic lignocellulosic biorefinery. In this study, T. reesei Rut-C30 was engineered with an artificial zinc finger proteins (AZFPs) library. Two mutants T. reesei M1 and M2 with improved cellulase production were obtained. Compared to the parent strain, the filter paper activity (FPase) of T. reesei M1 and M2 increased 100% and 53%, respectively. In addition, the total amount of extracellular protein from the M1 mutant increased 69%, whereas the endo-β-glucanase (CMCase) activity of the M2 mutant is 64% higher compared to the parental strain. Furthermore, RT-qPCR analysis showed that the major cellulase genes exhibited significantly increased expression in both mutants, but different patterns were observed in the two mutants. On the other hand, the cellulase transcriptional repressor ace1 was down-regulated in both mutants, but the transcription level of the activator xyr1 was only up-regulated in the strain M1. These results demonstrated that different AZFPs exert diverse regulatory mechanisms on cellulase production in T. reesei. Analysis of the target genes of AZFPs from T. reesei M1 and M2 will not only benefit further exploration of the regulatory mechanisms of cellulase biosynthesis in T. reesei, but also enable development of cellulase hyper-producing strains by metabolic engineering.

Production of thermostable ß-glucosidase and CMCase by Penicillium sp: LMI01 isolated from the Amazon region

Background: Cellulolytic enzymes of microbial origin have great industrial importance because of their wide application in various industrial sectors. Fungi are considered the most efficient producers of these enzymes. Bioprospecting survey to identify fungal sources of biomass-hydrolyzing enzymes from a high-diversity environment is an important approach to discover interesting strains for bioprocess uses. In this study, we evaluated the production of endoglucanase (CMCase) and ß-glucosidase, enzymes from the lignocellulolytic complex, produced by a native fungus. Penicillium sp. LMI01 was isolated from decaying plant material in the Amazon region, and its performance was compared with that of the standard isolate Trichoderma reesei QM9414 under submerged fermentation conditions. Results: The effectiveness of LMI01 was similar to that of QM9414 in volumetric enzyme activity (U/mL); however, the specific enzyme activity (U/mg) of the former was higher, corresponding to 24.170 U/mg of CMCase and 1.345 U/mg of ß-glucosidase. The enzymes produced by LMI01 had the following physicochemical properties: CMCase activity was optimal at pH 4.2 and the ß-glucosidase activity was optimal at pH 6.0. Both CMCase and ß-glucosidase had an optimum temperature at 60°C and were thermostable between 50 and 60°C. The electrophoretic profile of the proteins secreted by LMI01 indicated that this isolate produced at least two enzymes with CMCase activity, with approximate molecular masses of 50 and 35 kDa, and ß-glucosidases with molecular masses between 70 and 100 kDa. Conclusions: The effectiveness and characteristics of these enzymes indicate that LMI01 can be an alternative for the hydrolysis of lignocellulosic materials and should be tested in commercial formulations.

Produção de xilanases por fermentação em estado sólido de farelo de trigo utilizando consórcios fúngicos / Production of xylanases by solid state fermentation of wheat bran using fungal consortia

A fim de se agregar valor ao resíduo farelo de trigo gerado em indústrias do setor alimentício avaliou-se, no presente trabalho, o potencial deste subproduto como substrato para produção de enzima xilanase no cultivo em estado sólido, utilizando consórcios fúngicos bem como os fungos Aspergillus oryzae CCT nº 0975 (ATCC9362) eTrichoderma reesei CCT nº 2768 - QM 9414. Para tanto utilizou-se o farelo de trigo, não lavado e não autoclavado, como fonte de carbono e energia na fermentação em estado sólido pelo fungo Aspergillus oryzae que apresentou maior produção do percentual de proteína nas 72 horas de cultivo. Depois de realizado um Delineamento Composto Central Rotacional (DCCR) - planejamento fatorial 23,com três repetições no ponto central e seis pontos axiais - partiu-se para otimização dos fatores que foram considerados significativos no processo: umidade, pH e granulometria. Os fatores foram considerados significativos pela A NOVA com o nível de 95% de confiança e com o resultado otimizado de atividade enzimática de (1.84 ± 0.01) UI/mL utilizando pH 3,3, granulometria de 900,0 µm e umidade de 40%. O caldo enzimático obtido foi considerado eficiente na modificação de tipificação de farinhas de trigo pelo estudo dos parâmetros reológicos do falling number e alveografia sendo estável por cerca de 3 meses

This study aimed to find alternatives for wheat bran disposal destination generated in food industry sector,thus contributing to the reduction of the resultant impact of residue depo-sition in the environment. The poten-tial of the wheat bran as a substrate for xylanase production by solid-state fermentation using fungal con-sortiums as well as Aspergillus ory-zae (ATCC9362) and Trichoderma reesei (2768) was valued. The use of non-washed and non-autoclaved wheat bran as carbon and energy source in solid-state fermentation by A. oryzae fungus showed greater per-centage of produced protein after 72 h of cultivation. The use of a central composite rotatable design(CCRD), 23 factorial planning with three rep-etitions at the central point as well as six axial points, coupled with Sur-face Response Methodology (SRM) allowed to assay the influence of hu-midity, pH, and grain size (indepen-dent variables or factors) on the xy-lanase activity(dependent variable or response) as well as to optimize the best conditions for the enzyme production. The results showed that all factors and their combinations were significant at 95% confidence level. The optimized xylanase activi-ty was (1.84 ± 0.01) UI/mL, obtained at 40% humidity and pH 3.3 with a grain size of 900.0 µm. The produced broth was stable for 3 months and approximately had 50% of the initial xylanase activity at 4°C. SDS-PAGE assay showed that xylanase has 30 kDa molar mass. The obtained en-zymatic broth was efficient to modify wheat flours as shown by the falling number rheologic parameters and alveography assay

Gene optimization and efficient expression of Trichoderma reesei Cel5A in Pichia pastoris / 生物工程学报

Deficient activity of endo-1,4-beta-glucanase II (Cel5A) secreted by Trichoderma reesei is one of the challenges involved in effective cellulase saccharification of cellulosic substrates. Therefore, we expressed Cel5A in Pichia pastoris by constructing a recombinant strain. With the gene optimization based on codon bias, and the construction of expression vector pPIC9K-eg2, the optimized gene was electro-transformed into P. pastoris GS115 to form transformants. Then, a high Cel5A activity producing recombinant, namely P. pastoris GS115-EG Ⅱ, was selected on G-418 resistant plates, followed by shake-flask cultivation. Enzyme characterization showed that the recombinant Cel5A reacted optimally at pH 4.5 and 60 ℃, with 50 kDa of molecular weight, preferentially degrading amorphous cellulose. Recombinant Cel5A was not significantly different from the native T. reesei Cel5A. Moreover, a shake-flask fermentation of the recombinant strain was optimized as below: incubation temperature 28 ℃, initial pH 5.0, inoculum volume 2%, methanol addition (per 24 h) 1.5% (V/V), sorbitol addition (per 24 h) 4 g/L and Tween 80 4 g/L. Under above optimized condition, the recombinant produced 24.0 U/mL of the Cel5A after 192 h fermentation. When incubated in a 5 L fermentation, Cel5A enzyme activity reached 270.9 U/mL at 180 h, with 4.16 g/L of the total protein. The study indicates that the recombinant strain P. pastoris GS115-EG Ⅱ is extremely suitable for heterologous expression of T. reesei cellulase Cel5A. And the recombinant Cel5A can be used as an alternative to the native T. reesei Cel5A in development of a commercially relevant enzyme based biorefinery process.

Induction and regulation of cellulase expression in filamentous fungi: a review / 生物工程学报

Production of bioenergy and bio-based chemicals by using fermentable sugars released from low-cost renewable lignocellulosic biomass has received great attention. Efficient cellulolytic enzymes are crucial for lignocellulose bioconversion, but high cellulase production cost is limiting the bioconversion efficiency of cellulosic biomass and industrial applications of lignocellulose biorefinery. Studies on induction and regulation of cellulase in filamentous fungi will help to further develop superior fungal strains for efficient cellulase production and reduce cellulase production cost. With the advances in high-throughput sequencing and gene manipulation technology using fungal strains, an in-depth understanding of cellulase induction and regulation mechanisms of enzyme expression has been achieved. We reviewed recent progresses in the induction and regulation of cellulase expression in several model filamentous fungi, emphasizing sugar transporters, transcription factors and chromatin remodeling. Future prospects in application of artificial zinc finger proteins for cellulase induction and regulation in filamentous fungi were discussed.

Producción de celulasas y biomasa del hongo Trichoderma reesei utilizando lodo papelero como fuente de carbono / Production of cellulase enzymes and biomass of the fungus Trichoderma reesei using paper sludge as carbon source

La producción del papel en Venezuela genera una gran cantidad de desechos de fibras de celulosa no utilizables (lodo papelero), produciéndose problemas ambientales y de almacenamiento. La búsqueda de usos para este lodo papelero disminuiría los problemas generados. En este trabajo, se utilizó al hongo Trichoderma reesei para la realización de fermentaciones líquidas y el estudio del efecto de sales minerales, tamaño de partícula del lodo y pretratamientos ácidos y básicos, sobre la producción de azúcares reductores y la actividad celulasa. También se realizaron fermentaciones sólidas para obtener biomasa (esporas) del hongo. Los resultados indicaron que el uso de lodo higiénico, sales minerales y la reducción del tamaño de partícula, mejoran el rendimiento en azúcares reductores (AR). La máxima actividad celulasa obtenida, medida con carboximetilcelulosa, fue de 2,6 mg AR/L/h. Se determinó que con el pretratamiento ácido se obtienen mayores cantidades de AR (17 mg/L) que con el básico (7,4 mg/L). Se demostró que T. reesei puede crecer en fermentaciones sólidas a expensas del lodo papelero generando hasta 1,24x10(8) esporas por gramo de lodo seco. Se requiere estandarizar y escalar estas técnicas para usar al lodo papelero como materia prima en este tipo de procesos industriales.

Paper production in Venezuela generates large amounts of cellulose fibers (paper sludge), producing environmental and storage problems. Finding uses for this papermaking sludge would decrease the problems caused. In this work the fungus Trichoderma reesei was used on submerged fermentation to study the effect of mineral salts, particle size and acid-alkali pretreatment of sludge on production of reducing sugars (RS) and cellulase activity. Solid fermentations were also conducted to obtain biomass (spores) of the fungus. The results indicated that the use of sanitized sludge, mineral salts and smaller particles, increased the production of reducing sugars (RS). The maximum cellulase activity, measured with carboxymethylcellulose, was RS 2.6 mg/L/h. Acid pretreatment was the best in rendering RS (17 mg/L) in comparison with alkali treatment (7.4 mg/L). It was also demonstrated that T. reesei can grow on paper sludge producing biomass (spores) with a yield of 1,24x10(8) spores/g of dry sludge. It is necessary to standardize and scale range these procedures in order to be able to use paper sludge to industrialize these processes.

Bioethanol production from rice straw residues

A rice straw -cellulose utilizing mold was isolated from rotted rice straw residues. The efficient rice straw degrading microorganism was identified as Trichoderma reesei. The results showed that different carbon sources in liquid culture such as rice straw, carboxymethyl cellulose, filter paper, sugar cane bagasse, cotton stalk and banana stalk induced T. reesei cellulase production whereas glucose or Potato Dextrose repressed the synthesis of cellulase. T. reesei cellulase was produced by the solid state culture on rice straw medium. The optimal pH and temperature for T. reesei cellulase production were 6 and 25 ºC, respectively. Rice straw exhibited different susceptibilities towards cellulase to their conversion to reducing sugars. The present study showed also that, the general trend of rice straw bioconversion with cellulase was more than the general trend by T. reesei. This enzyme effectively led to enzymatic conversion of acid, alkali and ultrasonic pretreated cellulose from rice straw into glucose, followed by fermentation into ethanol. The combined method of acid pretreatment with ultrasound and subsequent enzyme treatment resulted the highest conversion of lignocellulose in rice straw to sugar and consequently, highest ethanol concentration after 7 days fermentation with S. cerevisae yeast. The ethanol yield in this study was about 10 and 11 g.L-¹.

Optimization of solid state fermentation conditions for the production of cellulase by Trichoderma reesei.

Cellulase production studies have been carried out using the fungal strain Trichoderma reesei NCIM 992 by using three different lignocellulosic materials by solid state fermentation (SSF). The effect of basic fermentation parameters (pH, temperature, moisture content, particle size of substrate and moistening agent) on enzyme production was studied. Maximum cellulase production was 2.63 U ml-1 using wheat bran as substrate. The optimal conditions for cellulase production for wheat bran were found to be: initial moisture content-70%, initial medium pH-5.0, temperature-30oC, moistening agents (MSS) and particle size of substrate (500 @m).The optimal incubation time for production was six days. Results indicate the scope for further optimization of the production conditions to obtain higher cellulase titres using the strain under SSF.

Evaluation of Potential Fungal Species for the in situ Simultaneous Saccharification and Fermentation (SSF) of Cellulosic Material

Three fungal species were evaluated for their abilities to saccharify pure cellulose. The three species chosen represented three major wood-rot molds; brown rot (Gloeophyllum trabeum), white rot (Phanerochaete chrysosporium) and soft rot (Trichoderma reesei). After solid state fermentation of the fungi on the filter paper for four days, the saccharified cellulose was then fermented to ethanol by using Saccharomyces cerevisiae. The efficiency of the fungal species in saccharifying the filter paper was compared against a low dose (25 FPU/g cellulose) of a commercial cellulase. Total sugar, cellobiose and glucose were monitored during the fermentation period, along with ethanol, acetic acid and lactic acid. Results indicated that the most efficient fungal species in saccharifying the filter paper was T. reesei with 5.13 g/100 g filter paper of ethanol being produced at days 5, followed by P. chrysosporium at 1.79 g/100 g filter paper. No ethanol was detected for the filter paper treated with G. trabeum throughout the five day fermentation stage. Acetic acid was only produced in the sample treated with T. reesei and the commercial enzyme, with concentration 0.95 and 2.57 g/100 g filter paper, respectively at day 5. Lactic acid production was not detected for all the fungal treated filter paper after day 5. Our study indicated that there is potential in utilizing in situ enzymatic saccharification of biomass by using T. reesei and P. chrysosporium that may lead to an economical simultaneous saccharification and fermentation process for the production of fuel ethanol.

Influence of buffer systems on Trichoderma reesei Rut C-30 morphology and cellulase production

The cellulase enzyme production is a key issue in the enzymatic hydrolysis of lignocellulosic materials. Since fungal morphology influences the productivity of fungal fermentations, it is of major importance to well know the fungal behavior during culture for cellulase production. In this work, the influence of medium supplementation, with different buffer systems at two different concentrations and pH conditions, on the morphology of T. reesei Rut C-30 and cellulase production, was investigated. A medium without buffer was used as control. The results suggest that fungal morphology is significantly dependent on the addition of different buffer systems to the nutrient broth. The mycelial morphology shows a clear transition from clumped to pelleted forms in cultures with variation of buffer systems and concentration. The higher filter paper activity was obtained using 100 mM succinate buffer, at pH 4.8, in the medium supplementation, corresponding to a dispersed mycelial morphology.

A Secretive Pichia pastoris Expression Vector for Direct PCR Product Cloning / 中国生物工程杂志

A secretive expression vector of Pichia pastoris system which can be used for the direct cloning of PCR products was constructed,and was verified through the expression of recombinant cellobiohydrolase II in Pichia pastoris.A randomly selected fragment was amplified with properly designed primers by PCR.The XhoI and Eam1105Ⅰ restriction sites were included in the 5'end of the fragment,and the Eam1105Ⅰ and XbaI restriction sites were included in its 3'end.The PCR amplified product was inserted into the P.pastoris expression plasmid pPICZ?A through XhoI and XbaI restriction sites and the resultant plasmid was digested with Eam1105Ⅰ,and lastly the big fragment was recovered,generating the P.pastoris expressive Tvector pPICZ?T.Then the cellobiohydrolase II of T.reesei was successfully expressed in P.pastoris with this expressive Tvector.Such results indicated that the constructed expression Tvector was convenient for PCR product cloning,and was effective for heterologous protein expression in P.pastoris.On the other hand,the application of the expression Tvector avoided the introduction of additional amino acids at the Nterminus of the expressed protein,which generally occurred when normal expression vectors were used in secretive expression system.

Expression of the Trichoderma reesei Endoglucanse IV in Pichia pastoris / 微生物学通报

In this work,the Pichia pastoris expression system was applied to express the T.reesei EGⅣ.The eg4 gene was isolated from rice hull induced T.reesei culture through RT-PCR,and was ligated with the Pichia expression vector pPICZ?A,resulting in the recombinant plasmid pPICZ?A-eg4.The recombinant plasmid pPICZ?A-eg4 was then linearized and transformed into P.pastoris GS115,and the eg4 gene was in frame integrated into the Pichia genome through homologous recombination,resulting the recombinant strain P.pastoris-EGⅣ1.With methanol induction,the recombinant strain P.pastoris-EGⅣ1 expressed and secreated EGⅣ into the culture supernatant with CMC activity of 2.11U/mL.The SDS-PAGE analysis showed that the apparent molecular weight of expressed protein was about 50kD,slightly less than that produced by T.reesei.

Sequential release of cellulose enzymes during germination of Trichoderma reesei spores.

The pattern of release of extracellular cellulase during the germination of Trichoderma reesei spores has been examined. The four enzymes namely, filter paper degrading enzyme, β-1,4 endoglucanase, β-glucosidase and xylanase appear sequentially in the culture broth during germination of the spores. The order of enzyme appearance is not altered by the type of carbon source in the germination medium. Measureable quantities of filter paper degrading enzyme is detected only after the outgrowth has occurred. A possible mechanism of spore germination and induction of the enzymes by insoluble cellulose is suggested.