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Vieira MM, Valadares FL, Velasco J, da Silva SS, Segato F, Chandel AK. Analysis of Aureobasidium pullulans LB83 secretome reveals distinct carbohydrate active enzymes for biomass saccharification. Prep Biochem Biotechnol 2024; 54:729-735. [PMID: 37966162 DOI: 10.1080/10826068.2023.2279109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Aureobasidium pullulans LB83 is a versatile biocatalyst that produces a plethora of bioactive products thriving on a variety of feedstocks under the varying culture conditions. In our last study using this microorganism, we found cellulase activity (FPase, 2.27 U/ml; CMCase, 7.42 U/ml) and other plant cell wall degrading enzyme activities grown on sugarcane bagasse and soybean meal as carbon source and nitrogen, respectively. In the present study, we provide insights on the secretome analysis of this enzymatic cocktail. The secretome analysis of A. pullulans LB83 by Liquid Chromatography coupled to Mass Spectroscopy (LC-MS/MS) revealed 38 classes of Carbohydrate Active enZymes (CAZymes) of a total of 464 identified proteins. These CAZymes consisted of 21 glycoside hydrolases (55.26%), 12 glycoside hydrolases harboring carbohydrate-binding module (31.58%), 4 carbohydrate esterases (10.53%) and one glycosyl transferase (2.63%). To the best of our knowledge, this is the first report on the secretome analysis of A. pullulans LB83.
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Affiliation(s)
- Matheus Maitan Vieira
- Department of Biotechnology, Engineering School of Lorena- University of São Paulo, Lorena, Brazil
| | - Fernanda Lima Valadares
- Department of Biotechnology, Engineering School of Lorena- University of São Paulo, Lorena, Brazil
| | - Josman Velasco
- Department of Biotechnology, Engineering School of Lorena- University of São Paulo, Lorena, Brazil
| | - Silvio S da Silva
- Department of Biotechnology, Engineering School of Lorena- University of São Paulo, Lorena, Brazil
| | - Fernando Segato
- Department of Biotechnology, Engineering School of Lorena- University of São Paulo, Lorena, Brazil
| | - Anuj K Chandel
- Department of Biotechnology, Engineering School of Lorena- University of São Paulo, Lorena, Brazil
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Zheng F, Basit A, Wang J, Zhuang H, Chen J, Zhang J. Characterization of a novel acidophilic, ethanol tolerant and halophilic GH12 β-1,4-endoglucanase from Trichoderma asperellum ND-1 and its synergistic hydrolysis of lignocellulosic biomass. Int J Biol Macromol 2024; 254:127650. [PMID: 38287580 DOI: 10.1016/j.ijbiomac.2023.127650] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 10/10/2023] [Accepted: 10/23/2023] [Indexed: 01/31/2024]
Abstract
A novel acidophilic GH5 β-1,4-endoglucanase (TaCel12) from Trichoderma asperellum ND-1 was efficiently expressed in Pichia pastoris (a 1.5-fold increase). Deglycosylated TaCel12 migrated as a single band (26.5 kDa) in SDS-PAGE. TaCel12 was acidophilic with a pH optimum of 4.0 and displayed great pH stability (>80 % activity over pH 3.0-5.0). TaCel12 exhibited considerable activity towards sodium carboxymethyl cellulose and sodium alginate with Vmax values of 197.97 μmol/min/mg and 119.06 μmol/min/mg, respectively. Moreover, TaCel12 maintained >80 % activity in the presence of 20 % ethanol and 4.28 M NaCl. Additionally, Mn2+, Pb2+ and Cu2+ negatively affected TaCel12 activity, while the presence of 5 mM Co2+ significantly increased the enzyme activity. Analysis of action mode revealed that TaCel12 required at least four glucose (cellotetraose) residues for hydrolysis to yield cellobiose and cellotriose. Site-directed mutagenesis results suggested that Glu133 and Glu217 of TaCel12 are crucial catalytic residues, with Asp116 displaying an auxiliary function. Production of soluble sugars from lignocellulose is a crucial step in bioethanol development, and it is noteworthy that TaCel12 could synergistically yield fermentable sugars from corn stover and bagasse, respectively. Thus TaCel12 with excellent properties will be considered a potential biocatalyst for applications in various industries, especially for lignocellulosic biomass conversion.
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Affiliation(s)
- Fengzhen Zheng
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310021, China.
| | - Abdul Basit
- Department of Microbiology, University of Jhang, Jhang 35200, Pakistan
| | - Jiaqiang Wang
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310021, China
| | - Huan Zhuang
- Department of ENT and Head & Neck Surgery, The Children's Hospital Zhejiang University School of Medicine, Zhejiang, Hangzhou 310051, China
| | - Jun Chen
- Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310021, China
| | - Jianfen Zhang
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310021, China
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Bulgari D, Alias C, Peron G, Ribaudo G, Gianoncelli A, Savino S, Boureghda H, Bouznad Z, Monti E, Gobbi E. Solid-State Fermentation of Trichoderma spp.: A New Way to Valorize the Agricultural Digestate and Produce Value-Added Bioproducts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3994-4004. [PMID: 36735958 PMCID: PMC9999421 DOI: 10.1021/acs.jafc.2c07388] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 01/18/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
In this study, the agricultural digestate from anaerobic biogas production mixed with food wastes was used as a substrate to grow Trichoderma reesei RUT-C30 and Trichoderma atroviride Ta13 in solid-state fermentation (SSF) and produce high-value bioproducts, such as bioactive molecules to be used as ingredients for biostimulants. The Trichoderma spp. reached their maximum growth after 6 and 3 SSF days, respectively. Both Trichoderma species were able to produce cellulase, esterase, and citric and malic acids, while T. atroviride also produced gibberellins and oxylipins as shown by ultraperformance liquid chromatography with quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) profiling. Experimental evaluation of germination parameters highlighted a significant promotion of tomato seed germination and root elongation induced by T. atroviride crude extracts from SSF. This study suggests an innovative sustainable use of the whole digestate mixed with agro-food waste as a valuable substrate in fungal biorefineries. Here, it has been applied to produce plant growth-promoting fungi and bioactive molecules for sustainable agriculture.
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Affiliation(s)
- Daniela Bulgari
- Agri-Food
and Environmental Microbiology Platform, Department of Molecular and
Translational Medicine, University of Brescia, Viale Europa, 11, 25123Brescia, Italy
| | - Carlotta Alias
- Agri-Food
and Environmental Microbiology Platform, Department of Molecular and
Translational Medicine, University of Brescia, Viale Europa, 11, 25123Brescia, Italy
- B+LabNet-Environmental
Sustainability Lab, University of Brescia, Via Branze 45, 25123Brescia, Italy
| | - Gregorio Peron
- Proteomics
Platform, AgroFood Lab, Department of Molecular and Translational
Medicine, University of Brescia, Viale Europa, 11, 25123Brescia, Italy
| | - Giovanni Ribaudo
- Proteomics
Platform, AgroFood Lab, Department of Molecular and Translational
Medicine, University of Brescia, Viale Europa, 11, 25123Brescia, Italy
| | - Alessandra Gianoncelli
- Proteomics
Platform, AgroFood Lab, Department of Molecular and Translational
Medicine, University of Brescia, Viale Europa, 11, 25123Brescia, Italy
| | - Salvatore Savino
- Unit
of Biotechnology, Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123Brescia, Italy
| | - Houda Boureghda
- Department
of Botany, Laboratory of Phytopathology and Molecular Biology, Ecole Nationale Supérieure Agronomique (ENSA), El Harrach, Algiers16200, Algeria
| | - Zouaoui Bouznad
- Department
of Botany, Laboratory of Phytopathology and Molecular Biology, Ecole Nationale Supérieure Agronomique (ENSA), El Harrach, Algiers16200, Algeria
| | - Eugenio Monti
- Unit
of Biotechnology, Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123Brescia, Italy
| | - Emanuela Gobbi
- Agri-Food
and Environmental Microbiology Platform, Department of Molecular and
Translational Medicine, University of Brescia, Viale Europa, 11, 25123Brescia, Italy
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Zheng F, Basit A, Zhuang H, Chen J, Zhang J, Chen W. Biochemical characterization of a novel acidophilic β-xylanase from Trichoderma asperellum ND-1 and its synergistic hydrolysis of beechwood xylan. Front Microbiol 2022; 13:998160. [PMID: 36199370 PMCID: PMC9527580 DOI: 10.3389/fmicb.2022.998160] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022] Open
Abstract
Acidophilic β-xylanases have attracted considerable attention due to their excellent activity under extreme acidic environments and potential industrial utilizations. In this study, a novel β-xylanase gene (Xyl11) of glycoside hydrolase family 11, was cloned from Trichoderma asperellum ND-1 and efficiently expressed in Pichia pastoris (a 2.0-fold increase). Xyl11 displayed a maximum activity of 121.99 U/ml at pH 3.0 and 50°C, and exhibited strict substrate specificity toward beechwood xylan (Km = 9.06 mg/ml, Vmax = 608.65 μmol/min/mg). The Xyl11 retained over 80% activity at pH 2.0–5.0 after pretreatment at 4°C for 1 h. Analysis of the hydrolytic pattern revealed that Xyl11 could rapidly convert xylan to xylobiose via hydrolysis activity as well as transglycosylation. Moreover, the results of site-directed mutagenesis suggested that the Xyl11 residues, Glu127, Glu164, and Glu216, are essential catalytic sites, with Asp138 having an auxiliary function. Additionally, a high degree of synergy (15.02) was observed when Xyl11 was used in association with commercial β-xylosidase. This study provided a novel acidophilic β-xylanase that exhibits excellent characteristics and can, therefore, be considered a suitable candidate for extensive applications, especially in food and animal feed industries.
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Affiliation(s)
- Fengzhen Zheng
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou, China
- *Correspondence: Fengzhen Zheng,
| | - Abdul Basit
- Department of Microbiology, University of Jhang, Jhang, Pakistan
| | - Huan Zhuang
- Department of ENT and Head & Neck Surgery, The Children’s Hospital Zhejiang University School of Medicine, Zhejiang, Hangzhou, China
| | - Jun Chen
- Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou, China
| | - Jianfen Zhang
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou, China
| | - Weiqing Chen
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou, China
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Whole-Genome Sequence and Comparative Analysis of Trichoderma asperellum ND-1 Reveal Its Unique Enzymatic System for Efficient Biomass Degradation. Catalysts 2022. [DOI: 10.3390/catal12040437] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The lignocellulosic enzymes of Trichoderma asperellum have been intensely investigated toward efficient conversion of biomass into high-value chemicals/industrial products. However, lack of genome data is a remarkable hurdle for hydrolase systems studies. The secretory enzymes of newly isolated T. asperellum ND-1 during lignocellulose degradation are currently poorly known. Herein, a high-quality genomic sequence of ND-1, obtained by both Illumina HiSeq 2000 sequencing platforms and PacBio single-molecule real-time, has an assembly size of 35.75 Mb comprising 10,541 predicted genes. Secretome analysis showed that 895 proteins were detected, with 211 proteins associated with carbohydrate-active enzymes (CAZymes) responsible for biomass hydrolysis. Additionally, T. asperellum ND-1, T. atroviride IMI 206040, and T. virens Gv-298 shared 801 orthologues that were not identified in T. reesei QM6a, indicating that ND-1 may play critical roles in biological-control. In-depth analysis suggested that, compared with QM6a, the genome of ND-1 encoded a unique enzymatic system, especially hemicellulases and chitinases. Moreover, after comparative analysis of lignocellulase activities of ND-1 and other fungi, we found that ND-1 displayed higher hemicellulases (particularly xylanases) and comparable cellulases activities. Our analysis, combined with the whole-genome sequence information, offers a platform for designing advanced T. asperellum ND-1 strains for industrial utilizations, such as bioenergy production.
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Corrêa TLR, Román EKB, da Silva Cassoli J, dos Santos LV, Pereira GAG. Secretome analysis of Trichoderma reesei RUT-C30 and Penicillium oxalicum reveals their synergic potential to deconstruct sugarcane and energy cane biomasses. Microbiol Res 2022; 260:127017. [DOI: 10.1016/j.micres.2022.127017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/18/2022] [Accepted: 03/29/2022] [Indexed: 11/28/2022]
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Yahya A, Khalid NA, Salleh MM. Biocompost from Oil Producing Plants. BIOREFINERY OF OIL PRODUCING PLANTS FOR VALUE‐ADDED PRODUCTS 2022:605-629. [DOI: 10.1002/9783527830756.ch30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Insights into the Lignocellulose-Degrading Enzyme System of Humicola grisea var. thermoidea Based on Genome and Transcriptome Analysis. Microbiol Spectr 2021; 9:e0108821. [PMID: 34523973 PMCID: PMC8557918 DOI: 10.1128/spectrum.01088-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Humicola grisea var. thermoidea is a thermophilic ascomycete and important enzyme producer that has an efficient enzymatic system with a broad spectrum of thermostable carbohydrate-active (CAZy) enzymes. These enzymes can be employed in lignocellulose biomass deconstruction and other industrial applications. In this work, the genome of H. grisea var. thermoidea was sequenced. The acquired sequence reads were assembled into a total length of 28.75 Mbp. Genome features correlate with what was expected for thermophilic Sordariomycetes. The transcriptomic data showed that sugarcane bagasse significantly upregulated genes related to primary metabolism and polysaccharide deconstruction, especially hydrolases, at both pH 5 and pH 8. However, a number of exclusive and shared genes between the pH values were found, especially at pH 8. H. grisea expresses an average of 211 CAZy enzymes (CAZymes), which are capable of acting in different substrates. The top upregulated genes at both pH values represent CAZyme-encoding genes from different classes, including acetylxylan esterase, endo-1,4-β-mannosidase, exoglucanase, and endoglucanase genes. For the first time, the arsenal that the thermophilic fungus H. grisea var. thermoidea possesses to degrade the lignocellulosic biomass is shown. Carbon source and pH are of pivotal importance in regulating gene expression in this organism, and alkaline pH is a key regulatory factor for sugarcane bagasse hydrolysis. This work paves the way for the genetic manipulation and robust biotechnological applications of this fungus. IMPORTANCE Most studies regarding the use of fungi as enzyme producers for biomass deconstruction have focused on mesophile species, whereas the potential of thermophiles has been evaluated less. This study revealed, through genome and transcriptome analyses, the genetic repertoire of the biotechnological relevant thermophile fungus Humicola grisea. Comparative genomics helped us to further understand the biology and biotechnological potential of H. grisea. The results demonstrate that this fungus possesses an arsenal of carbohydrate-active (CAZy) enzymes to degrade the lignocellulosic biomass. Indeed, it expresses more than 200 genes encoding CAZy enzymes when cultivated in sugarcane bagasse. Carbon source and pH are key factors for regulating the gene expression in this organism. This work shows, for the first time, the great potential of H. grisea as an enzyme producer and a gene donor for biotechnological applications and provides the base for the genetic manipulation and robust biotechnological applications of this fungus.
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Comparative Secretomics Analysis Reveals the Major Components of Penicillium oxalicum 16 and Trichoderma reesei RUT-C30. Microorganisms 2021; 9:microorganisms9102042. [PMID: 34683363 PMCID: PMC8538001 DOI: 10.3390/microorganisms9102042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/16/2021] [Accepted: 09/24/2021] [Indexed: 11/23/2022] Open
Abstract
In this study, the major secretome components of Penicillium oxalicum 16 and Trichoderma reesei RUT-C30 under wheat bran (WB) and rice straw (RS) solid-state fermentation were systematically analyzed. The activities of the major components, e.g., cellulase, hemicellulase, and amylase, were consistent with their abundance in the secretomes. P. oxalicum 16 secreted more abundant glycoside hydrolases than T. reesei RUT-C30. The main up-regulated proteins from the induction of WB, compared with that from RS, were amylase, pectinase, and protease, whereas the main down-regulated enzymes were cellulase, hemicellulase, swollenin, and lytic polysaccharide monooxygenase (LPMO). Specifically, WB induced more β-1,4-glucosidases, namely, S8B0F3 (UniProt ID), and A0A024RWA5 than RS, but RS induced more β-1,4-exoglucanases and β-1,4-endoglucanases, namely, A0A024RXP8, A024SH76, S7B6D6, S7ZP52, A024SH20, A024S2H5, S8BGM3, S7ZX22, and S8AIJ2. The P. oxalicum 16 xylanases S8AH74 and S7ZA57 were the major components responsible for degrading soluble xylan, and S8BDN2 probably acted on solid-state hemicellulose instead of soluble xylan. The main hemicellulase component of T. reesei RUT-C30 in RS was the xyloglucanase A0A024S9Z6 with an abundance of 16%, but T. reesei RUT-C30 lacked the hemicellulase mannanase and had a small amount of the hemicellulase xylanase. P. oxalicum 16 produced more amylase than T. reesei RUT-C30, and the results suggest amylase S7Z6T2 may degrade soluble starch. The percentage of the glucoamylase S8B6D7 did not significantly change, and reached an average abundance of 5.5%. The major auxiliary degradation enzymes of P. oxalicum 16 were LPMOs S7Z716 and S7ZPW1, whereas those of T. reesei RUT-C30 were swollenin and LPMOs A0A024SM10, A0A024SFJ2, and A0A024RZP7.
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Ogunyewo OA, Upadhyay P, Rajacharya GH, Okereke OE, Faas L, Gómez LD, McQueen-Mason SJ, Yazdani SS. Accessory enzymes of hypercellulolytic Penicillium funiculosum facilitate complete saccharification of sugarcane bagasse. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:171. [PMID: 34446097 PMCID: PMC8394629 DOI: 10.1186/s13068-021-02020-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/15/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND Sugarcane bagasse (SCB) is an abundant feedstock for second-generation bioethanol production. This complex biomass requires an array of carbohydrate active enzymes (CAZymes), mostly from filamentous fungi, for its deconstruction to monomeric sugars for the production of value-added fuels and chemicals. In this study, we evaluated the repertoire of proteins in the secretome of a catabolite repressor-deficient strain of Penicillium funiculosum, PfMig188, in response to SCB induction and examined their role in the saccharification of SCB. RESULTS A systematic approach was developed for the cultivation of the fungus with the aim of producing and understanding arrays of enzymes tailored for saccharification of SCB. To achieve this, the fungus was grown in media supplemented with different concentrations of pretreated SCB (0-45 g/L). The profile of secreted proteins was characterized by enzyme activity assays and liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 280 proteins were identified in the secretome of PfMig188, 46% of them being clearly identified as CAZymes. Modulation of the cultivation media with SCB up to 15 g/L led to sequential enhancement in the secretion of hemicellulases and cell wall-modifying enzymes, including endo-β-1,3(4)-glucanase (GH16), endo-α-1,3-glucanase (GH71), xylanase (GH30), β-xylosidase (GH5), β-1,3-galactosidase (GH43) and cutinase (CE5). There was ~ 122% and 60% increases in β-xylosidase and cutinase activities, respectively. There was also a 36% increase in activities towards mixed-linked glucans. Induction of these enzymes in the secretome improved the saccharification performance to 98% (~ 20% increase over control), suggesting their synergy with core cellulases in accessing the recalcitrant region of SCB. CONCLUSION Our findings provide an insight into the enzyme system of PfMig188 for degradation of complex biomass such as SCB and highlight the importance of adding SCB to the culture medium to optimize the secretion of enzymes specific for the saccharification of sugarcane bagasse.
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Affiliation(s)
- Olusola A Ogunyewo
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Pooja Upadhyay
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Girish H Rajacharya
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Omoaruemike E Okereke
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
- Biotechnology Advanced Research Centre, Sheda Science and Technology Complex (SHESTCO), Abuja, Nigeria
| | - Laura Faas
- Department of Biology, Centre for Novel Agricultural Products, CNAP, University of York, York, YO10 5DD, UK
| | - Leonardo D Gómez
- Department of Biology, Centre for Novel Agricultural Products, CNAP, University of York, York, YO10 5DD, UK
| | - Simon J McQueen-Mason
- Department of Biology, Centre for Novel Agricultural Products, CNAP, University of York, York, YO10 5DD, UK
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.
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Sethupathy S, Morales GM, Li Y, Wang Y, Jiang J, Sun J, Zhu D. Harnessing microbial wealth for lignocellulose biomass valorization through secretomics: a review. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:154. [PMID: 34225772 PMCID: PMC8256616 DOI: 10.1186/s13068-021-02006-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/26/2021] [Indexed: 05/10/2023]
Abstract
The recalcitrance of lignocellulosic biomass is a major constraint to its high-value use at industrial scale. In nature, microbes play a crucial role in biomass degradation, nutrient recycling and ecosystem functioning. Therefore, the use of microbes is an attractive way to transform biomass to produce clean energy and high-value compounds. The microbial degradation of lignocelluloses is a complex process which is dependent upon multiple secreted enzymes and their synergistic activities. The availability of the cutting edge proteomics and highly sensitive mass spectrometry tools make possible for researchers to probe the secretome of microbes and microbial consortia grown on different lignocelluloses for the identification of hydrolytic enzymes of industrial interest and their substrate-dependent expression. This review summarizes the role of secretomics in identifying enzymes involved in lignocelluloses deconstruction, the development of enzyme cocktails and the construction of synthetic microbial consortia for biomass valorization, providing our perspectives to address the current challenges.
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Affiliation(s)
- Sivasamy Sethupathy
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Gabriel Murillo Morales
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yixuan Li
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yongli Wang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianxiong Jiang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianzhong Sun
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Daochen Zhu
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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Lopes DCB, Carraro CB, Silva RN, de Paula RG. Molecular Characterization of Xyloglucanase cel74a from Trichoderma reesei. Int J Mol Sci 2021; 22:ijms22094545. [PMID: 33925273 PMCID: PMC8123685 DOI: 10.3390/ijms22094545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022] Open
Abstract
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.
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Affiliation(s)
- Douglas Christian Borges Lopes
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto 14049-900, SP, Brazil; (D.C.B.L.); (C.B.C.); (R.G.d.P.)
| | - Cláudia Batista Carraro
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto 14049-900, SP, Brazil; (D.C.B.L.); (C.B.C.); (R.G.d.P.)
| | - Roberto Nascimento Silva
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto 14049-900, SP, Brazil; (D.C.B.L.); (C.B.C.); (R.G.d.P.)
- Correspondence:
| | - Renato Graciano de Paula
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto 14049-900, SP, Brazil; (D.C.B.L.); (C.B.C.); (R.G.d.P.)
- Department of Physiological Sciences, Health Sciences Centre, Federal University of Espirito Santo, Vitoria 29047-105, ES, Brazil
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Brandt SC, Brognaro H, Ali A, Ellinger B, Maibach K, Rühl M, Wrenger C, Schlüter H, Schäfer W, Betzel C, Janssen S, Gand M. Insights into the genome and secretome of Fusarium metavorans DSM105788 by cultivation on agro-residual biomass and synthetic nutrient sources. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:74. [PMID: 33743779 PMCID: PMC7981871 DOI: 10.1186/s13068-021-01927-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The transition to a biobased economy involving the depolymerization and fermentation of renewable agro-industrial sources is a challenge that can only be met by achieving the efficient hydrolysis of biomass to monosaccharides. In nature, lignocellulosic biomass is mainly decomposed by fungi. We recently identified six efficient cellulose degraders by screening fungi from Vietnam. RESULTS We characterized a high-performance cellulase-producing strain, with an activity of 0.06 U/mg, which was identified as a member of the Fusarium solani species complex linkage 6 (Fusarium metavorans), isolated from mangrove wood (FW16.1, deposited as DSM105788). The genome, representing nine potential chromosomes, was sequenced using PacBio and Illumina technology. In-depth secretome analysis using six different synthetic and artificial cellulose substrates and two agro-industrial waste products identified 500 proteins, including 135 enzymes assigned to five different carbohydrate-active enzyme (CAZyme) classes. The F. metavorans enzyme cocktail was tested for saccharification activity on pre-treated sugarcane bagasse, as well as untreated sugarcane bagasse and maize leaves, where it was complemented with the commercial enzyme mixture Accellerase 1500. In the untreated sugarcane bagasse and maize leaves, initial cell wall degradation was observed in the presence of at least 196 µg/mL of the in-house cocktail. Increasing the dose to 336 µg/mL facilitated the saccharification of untreated sugarcane biomass, but had no further effect on the pre-treated biomass. CONCLUSION Our results show that F. metavorans DSM105788 is a promising alternative pre-treatment for the degradation of agro-industrial lignocellulosic materials. The enzyme cocktail promotes the debranching of biopolymers surrounding the cellulose fibers and releases reduced sugars without process disadvantages or loss of carbohydrates.
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Affiliation(s)
- Sophie C Brandt
- Faculty of Mathematics, Computer Science and Natural Science, Department of Biology, Biozentrum Klein Flottbek, Molecular Phytopathology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Hévila Brognaro
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, CEP, 05508-000, Brazil
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146, Hamburg, Germany
| | - Arslan Ali
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146, Hamburg, Germany
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, University Road, Karachi, 75270, Pakistan
- Institute of Clinical Chemistry and Laboratory Medicine Diagnostic Center, Campus Research. Martinistr. 52, N27, 20246, Hamburg, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Department ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany
| | - Katharina Maibach
- Department Biology and Chemistry, Algorithmic Bioinformatics, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35392, Gießen, Germany
| | - Martin Rühl
- Department Biology and Chemistry, Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Gießen, Germany
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, CEP, 05508-000, Brazil
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146, Hamburg, Germany
| | - Hartmut Schlüter
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146, Hamburg, Germany
- Institute of Clinical Chemistry and Laboratory Medicine Diagnostic Center, Campus Research. Martinistr. 52, N27, 20246, Hamburg, Germany
| | - Wilhelm Schäfer
- Faculty of Mathematics, Computer Science and Natural Science, Department of Biology, Biozentrum Klein Flottbek, Molecular Phytopathology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146, Hamburg, Germany
| | - Stefan Janssen
- Department Biology and Chemistry, Algorithmic Bioinformatics, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35392, Gießen, Germany
| | - Martin Gand
- Faculty of Mathematics, Computer Science and Natural Science, Department of Biology, Biozentrum Klein Flottbek, Molecular Phytopathology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany.
- Department Biology and Chemistry, Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Gießen, Germany.
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Díaz GV, Coniglio RO, Alvarenga AE, Zapata PD, Villalba LL, Fonseca MI. Secretomic analysis of cheap enzymatic cocktails of Aspergillus niger LBM 134 grown on cassava bagasse and sugarcane bagasse. Mycologia 2020; 112:663-676. [PMID: 32574526 DOI: 10.1080/00275514.2020.1763707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
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.
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Affiliation(s)
- Gabriela Verónica Díaz
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - Romina Olga Coniglio
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - Adriana Elizabet Alvarenga
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - Pedro Darío Zapata
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - Laura Lidia Villalba
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - María Isabel Fonseca
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
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Mohamad Sobri MF, Abd-Aziz S, Abu Bakar FD, Ramli N. In-Silico Characterization of Glycosyl Hydrolase Family 1 β-Glucosidase from Trichoderma asperellum UPM1. Int J Mol Sci 2020; 21:ijms21114035. [PMID: 32512945 PMCID: PMC7311958 DOI: 10.3390/ijms21114035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/22/2020] [Accepted: 04/30/2020] [Indexed: 11/16/2022] Open
Abstract
β-glucosidases (Bgl) are widely utilized for releasing non-reducing terminal glucosyl residues. Nevertheless, feedback inhibition by glucose end product has limited its application. A noticeable exception has been found for β-glucosidases of the glycoside hydrolase (GH) family 1, which exhibit tolerance and even stimulation by glucose. In this study, using local isolate Trichoderma asperellum UPM1, the gene encoding β-glucosidase from GH family 1, hereafter designated as TaBgl2, was isolated and characterized via in-silico analyses. A comparison of enzyme activity was subsequently made by heterologous expression in Escherichia coli BL21(DE3). The presence of N-terminal signature, cis-peptide bonds, conserved active site motifs, non-proline cis peptide bonds, substrate binding, and a lone conserved stabilizing tryptophan (W) residue confirms the identity of Trichoderma sp. GH family 1 β-glucosidase isolated. Glucose tolerance was suggested by the presence of 14 of 22 known consensus residues, along with corresponding residues L167 and P172, crucial in the retention of the active site's narrow cavity. Retention of 40% of relative hydrolytic activity on ρ-nitrophenyl-β-D-glucopyranoside (ρNPG) in a concentration of 0.2 M glucose was comparable to that of GH family 1 β-glucosidase (Cel1A) from Trichoderma reesei. This research thus underlines the potential in the prediction of enzymatic function, and of industrial importance, glucose tolerance of family 1 β-glucosidases following relevant in-silico analyses.
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Affiliation(s)
- Mohamad Farhan Mohamad Sobri
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia; (M.F.M.S.); (S.A.-A.)
- School of Bioprocess Engineering, Universiti Malaysia Perlis, Kompleks Pusat Pengajian Jejawi 3, Arau 02600, Perlis, Malaysia
| | - Suraini Abd-Aziz
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia; (M.F.M.S.); (S.A.-A.)
| | - Farah Diba Abu Bakar
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600 UKM, Selangor, Malaysia;
| | - Norhayati Ramli
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia; (M.F.M.S.); (S.A.-A.)
- Correspondence: ; Tel.: +60-3-9769-1948
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An endoxylanase rapidly hydrolyzes xylan into major product xylobiose via transglycosylation of xylose to xylotriose or xylotetraose. Carbohydr Polym 2020; 237:116121. [PMID: 32241400 DOI: 10.1016/j.carbpol.2020.116121] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 12/18/2022]
Abstract
Here, we proposed an effective strategy to enhance a novel endoxylanase (Taxy11) activity and elucidated an efficient catalysis mechanism to produce xylooligosaccharides (XOSs). Codon optimization and recruitment of natural propeptide in Pichia pastoris resulted in achievement of Taxy11 activity to 1405.65 ± 51.24 U/mL. Analysis of action mode reveals that Taxy11 requires at least three xylose (xylotriose) residues for hydrolysis to yield xylobiose. Results of site-directed mutagenesis indicate that residues Glu119, Glu210, and Asp53 of Taxy11 are key catalytic sites, while Asp203 plays an auxiliary role. The novel mechanism whereby Taxy11 catalyzes conversion of xylan or XOSs into major product xylobiose involves transglycosylation of xylose to xylotriose or xylotetraose as substrate, to form xylotetraose or xylopentaose intermediate, respectively. Taxy11 displayed highly hydrolytic activity toward corncob xylan, producing 50.44 % of xylobiose within 0.5 h. This work provides a cost-effective and sustainable way to produce value-added biomolecules XOSs (xylobiose-enriched) from agricultural waste.
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Shinkawa S, Mitsuzawa S. Feasibility study of on-site solid-state enzyme production by Aspergillus oryzae. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:31. [PMID: 32127918 PMCID: PMC7045521 DOI: 10.1186/s13068-020-1669-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/28/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND The development of biorefinery systems that use lignocellulosic biomass as a renewable carbon source to produce fuels and chemicals is attracting increasing attention. The process cost of enzymatic saccharification of biomass is a major challenge for commercialization. To decrease this cost, researchers have proposed on-site solid-state fermentation (SSF). This study investigated the feasibility of using Aspergillus oryzae as a host microorganism for SSF recombinant enzyme production with ammonia-treated rice straw as model biomass. Eight A. oryzae strains were tested, all of which are used in the food industry. We evaluated the effects of acetic acid, a fermentation inhibitor. We also developed a platform strain for targeted recombinant enzyme production by gene engineering technologies. RESULTS The SSF validation test showed variation in the visibility of mycelium growth and secreted protein in all eight A. oryzae strains. The strains used to produce shoyu and miso grew better under test conditions. The ammonia-treated rice straw contained noticeable amounts of acetic acid. This acetic acid enhanced the protein production by A. oryzae in a liquid-state fermentation test. The newly developed platform strain successfully secreted three foreign saccharifying enzymes. CONCLUSIONS A. oryzae is a promising candidate as a host microorganism for on-site SSF recombinant enzyme production, which bodes well for the future development of a more cost-efficient saccharifying enzyme production system.
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Affiliation(s)
- Satoru Shinkawa
- Fundamental Technology Center, Honda R&D Co., Ltd., 1-4-1 Chuo, Wako-shi, Saitama, 351-0113 Japan
- Present Address: Honda Research Institute Japan Co., Ltd., 8-1 Honcho, Wako-shi, Saitama, 351-0188 Japan
| | - Shigenobu Mitsuzawa
- Fundamental Technology Center, Honda R&D Co., Ltd., 1-4-1 Chuo, Wako-shi, Saitama, 351-0113 Japan
- Present Address: Honda Research Institute Japan Co., Ltd., 8-1 Honcho, Wako-shi, Saitama, 351-0188 Japan
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18
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Cellulases Production by a Trichoderma sp. Using Food Manufacturing Wastes. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9204419] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The cost of cellulase enzymes is a main contributor to the operational cost of a biorefinery producing ethanol from lignocellulosic material. Therefore, onsite production of enzymes using low-value substrates might be an option to make a bio-based facility more economical, while improving environmental sustainability. Food manufacturing wastes (FMWs), such as olive mill solids, tomato pomace, and grape pomace, are some of the main wastes produced by the food industry in Chile. FMWs are mostly composed of lignocellulosic material, which is primarily made of cellulose. A fungal strain obtained from olive stones was identified as a Trichoderma sp. and characterized by molecular and morphological techniques. This strain was able to grow on three FMWs in both liquid and solid cultures. In liquid cultures, cellulase and β-glucosidase activities from the culture supernatants were quantified. Identification of extracellular proteins using mass spectrometry revealed the presence of endoglucanases, exoglucanases, and β-glucosidases. Cellulase production from agroindustrial residues could be an excellent opportunity to utilize FMWs as well as decrease enzyme production costs in biorefinery processes.
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Novy V, Nielsen F, Seiboth B, Nidetzky B. The influence of feedstock characteristics on enzyme production in Trichoderma reesei: a review on productivity, gene regulation and secretion profiles. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:238. [PMID: 31624500 PMCID: PMC6781402 DOI: 10.1186/s13068-019-1571-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/20/2019] [Indexed: 05/21/2023]
Abstract
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.
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Affiliation(s)
- Vera Novy
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Graz, Austria
- Present Address: Department of Wood Science, Faculty of Forestry, The University of British Columbia, Vancouver, Canada
| | - Fredrik Nielsen
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Graz, Austria
- Present Address: Department of Wood Science, Faculty of Forestry, The University of British Columbia, Vancouver, Canada
| | - Bernhard Seiboth
- Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (acib) GmbH, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Graz, Austria
- Austrian Centre of Industrial Biotechnology (acib) GmbH, Graz, Austria
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20
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Ezeilo UR, Lee CT, Huyop F, Zakaria II, Wahab RA. Raw oil palm frond leaves as cost-effective substrate for cellulase and xylanase productions by Trichoderma asperellum UC1 under solid-state fermentation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 243:206-217. [PMID: 31096173 DOI: 10.1016/j.jenvman.2019.04.113] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/26/2019] [Accepted: 04/27/2019] [Indexed: 06/09/2023]
Abstract
Production of cellulases and xylanase by a novel Trichoderma asperellum UC1 (GenBank accession no. MF774876) under solid state fermentation (SSF) of raw oil palm frond leaves (OPFL) was optimized. Under optimum fermentation parameters (30 °C, 60-80% moisture content, 2.5 × 106 spores/g inoculum size) maximum CMCase, FPase, β-glucosidase and xylanase activity were recorded at 136.16 IU/g, 26.03 U/g, 130.09 IU/g and 255.01 U/g, respectively. Cellulases and xylanase were produced between a broad pH range of pH 6.0-12.0. The enzyme complex that comprised of four endo-β-1,4-xylanases and endoglucanases, alongside exoglucanase and β-glucosidase showed thermophilic and acidophilic characteristics at 50-60 °C and pH 3.0-4.0, respectively. Glucose (16.87 mg/g) and fructose (18.09 mg/g) were among the dominant sugar products from the in situ hydrolysis of OPFL, aside from cellobiose (105.92 mg/g) and xylose (1.08 mg/g). Thermal and pH stability tests revealed that enzymes CMCase, FPase, β-glucosidase and xylanase retained 50% residual activities for up to 15.18, 4.06, 17.47 and 15.16 h of incubation at 60 °C, as well as 64.59, 25.14, 68.59 and 19.20 h at pH 4.0, respectively. Based on the findings, it appeared that the unique polymeric structure of raw OPFL favored cellulases and xylanase productions.
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Affiliation(s)
- Uchenna R Ezeilo
- Faculty of Bioscience and Medical Engineering, Department of Biotechnology and Medical Engineering, Universiti Teknologi Malaysia, 81310, UTM Johor Bahru, Malaysia; Department of Chemistry/Biochemistry, Federal University Ndufu-Alike Ikwo, PMB, 1010, Ebonyi State, Nigeria; Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310, UTM Johor Bahru, Malaysia
| | - Chew Tin Lee
- School of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310, Johor Bahru, Malaysia; Innovation Centre in Agritechnology for Advanced Bioprocessing, UTM Pagoh, Hub Pendidikan Tinggi Pagoh, 84600, Pagoh, Johor. Malaysia
| | - Fahrul Huyop
- Faculty of Bioscience and Medical Engineering, Department of Biotechnology and Medical Engineering, Universiti Teknologi Malaysia, 81310, UTM Johor Bahru, Malaysia; Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310, UTM Johor Bahru, Malaysia
| | - Iffah Izzati Zakaria
- Natural Products and Drug Discovery Center, Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institute of Biotechnology Malaysia, Ministry of Science, Technology and Innovation, Block 5-A, Halaman Bukit Gambir, 11700, Pulau Pinang, Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310, UTM Johor Bahru, Malaysia; Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310, UTM Johor Bahru, Malaysia.
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Wang Q, Chen L, Fang C, Wang H, Shi Y, Zhao Y. The overexpression of one single cbh gene making Trichoderma asperellum T-1 a better cellulase producer. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01458-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Lignocellulolytic characterization and comparative secretome analysis of a Trichoderma erinaceum strain isolated from decaying sugarcane straw. Fungal Biol 2019; 123:330-340. [PMID: 30928041 DOI: 10.1016/j.funbio.2019.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 01/18/2019] [Accepted: 01/24/2019] [Indexed: 11/21/2022]
Abstract
The fungus Trichoderma reesei is employed in the production of most enzyme cocktails used by the lignocellulosic biofuels industry today. Despite significant improvements, the cost of the required enzyme preparations remains high, representing a major obstacle for the industrial production of these alternative fuels. In this study, a new Trichoderma erinaceum strain was isolated from decaying sugarcane straw. The enzyme cocktail secreted by the new isolate during growth in pretreated sugarcane straw-containing medium presented higher specific activities of β-glucosidase, endoxylanase, β-xylosidase and α-galactosidase than the cocktail of a wild T. reesei strain and yielded more glucose in the hydrolysis of pretreated sugarcane straw. A proteomic analysis of the two strains' secretomes identified a total of 86 proteins, of which 48 were exclusive to T. erinaceum, 35 were exclusive to T. reesei and only 3 were common to both strains. The secretome of T. erinaceum also displayed a higher number of carbohydrate-active enzymes than that of T. reesei (37 and 27 enzymes, respectively). Altogether, these results reveal the significant potential of the T. erinaceum species for the production of lignocellulases, both as a possible source of enzymes for the supplementation of industrial cocktails and as a candidate chassis for enzyme production.
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Zheng F, Liu J, Basit A, Miao T, Jiang W. Insight to Improve α-L-Arabinofuranosidase Productivity in Pichia pastoris and Its Application on Corn Stover Degradation. Front Microbiol 2018; 9:3016. [PMID: 30631307 PMCID: PMC6315152 DOI: 10.3389/fmicb.2018.03016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/22/2018] [Indexed: 12/20/2022] Open
Abstract
α-L-arabinofuranosidase (ARA) with enhanced specific activity and in large amounts, is needed for a variety of industrial applications. To improve ARA production with engineered methylotrophic yeast Pichia pastoris, a genetically modified ara gene from Aspergillus niger ND-1 was investigated. Through codon optimization and rational replacement of α-factor signal peptide with the native propeptide (MFSRRNLVALGLAATVSA), ARA production was improved from 2.61 ± 0.13 U/mL to 14.37 ± 0.22 U/mL in shaking flask culture (a 5.5-fold increase). Results of N-terminal sequencing showed that secreted active ARA of recombinant strain p-oARA had theoretical initial five amino acids (GPCDI) comparable to the mature sequences of α-oARA (EAEAG) and αp-oARA (NLVAL). The kinetic values have been determined for ARA of recombinant strain p-oARA (Vmax = 747.55 μmol/min/mg, Km = 5.36 mmol/L), optimal activity temperature 60°C and optimal pH 4.0. Scaling up of ARA production by p-oARA in a 7.5-L fermentor resulted in remarkably high extracellular ARA specific activity (479.50 ± 12.83 U/mg) at 168 h, and maximal production rate 164.47 ± 4.40 U/mL. In studies of corn stover degradation activity, degree of synergism for ARA and xylanase was 32.4% and enzymatic hydrolysis yield for ARA + xylanase addition was 15.9% higher than that of commercial cellulase, indicating significant potential of ARA for catalytic conversion of corn stover to fermentable sugars for biofuel production.
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Affiliation(s)
- Fengzhen Zheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Junquan Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Abdul Basit
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ting Miao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wei Jiang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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Borin GP, Carazzolle MF, Dos Santos RAC, Riaño-Pachón DM, Oliveira JVDC. Gene Co-expression Network Reveals Potential New Genes Related to Sugarcane Bagasse Degradation in Trichoderma reesei RUT-30. Front Bioeng Biotechnol 2018; 6:151. [PMID: 30406095 PMCID: PMC6204389 DOI: 10.3389/fbioe.2018.00151] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/03/2018] [Indexed: 12/11/2022] Open
Abstract
The biomass-degrading fungus Trichoderma reesei has been considered a model for cellulose degradation, and it is the primary source of the industrial enzymatic cocktails used in second-generation (2G) ethanol production. However, although various studies and advances have been conducted to understand the cellulolytic system and the transcriptional regulation of T. reesei, the whole set of genes related to lignocellulose degradation has not been completely elucidated. In this study, we inferred a weighted gene co-expression network analysis based on the transcriptome dataset of the T. reesei RUT-C30 strain aiming to identify new target genes involved in sugarcane bagasse breakdown. In total, ~70% of all the differentially expressed genes were found in 28 highly connected gene modules. Several cellulases, sugar transporters, and hypothetical proteins coding genes upregulated in bagasse were grouped into the same modules. Among them, a single module contained the most representative core of cellulolytic enzymes (cellobiohydrolase, endoglucanase, β-glucosidase, and lytic polysaccharide monooxygenase). In addition, functional analysis using Gene Ontology (GO) revealed various classes of hydrolytic activity, cellulase activity, carbohydrate binding and cation:sugar symporter activity enriched in these modules. Several modules also showed GO enrichment for transcription factor activity, indicating the presence of transcriptional regulators along with the genes involved in cellulose breakdown and sugar transport as well as other genes encoding proteins with unknown functions. Highly connected genes (hubs) were also identified within each module, such as predicted transcription factors and genes encoding hypothetical proteins. In addition, various hubs contained at least one DNA binding site for the master activator Xyr1 according to our in silico analysis. The prediction of Xyr1 binding sites and the co-expression with genes encoding carbohydrate active enzymes and sugar transporters suggest a putative role of these hubs in bagasse cell wall deconstruction. Our results demonstrate a vast range of new promising targets that merit additional studies to improve the cellulolytic potential of T. reesei strains and to decrease the production costs of 2G ethanol.
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Affiliation(s)
- Gustavo Pagotto Borin
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biologia, Universidade de Campinas (UNICAMP), Campinas, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | | | | | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biologia, Universidade de Campinas (UNICAMP), Campinas, Brazil
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Guo H, Wang XD, Lee DJ. Proteomic researches for lignocellulose-degrading enzymes: A mini-review. BIORESOURCE TECHNOLOGY 2018; 265:532-541. [PMID: 29884341 DOI: 10.1016/j.biortech.2018.05.101] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 05/14/2023]
Abstract
Protective action of lignin/hemicellulose networks and crystalline structures of embedded cellulose render lignocellulose material resistant to external enzymatic attack. To eliminate this bottleneck, research has been conducted in which advanced proteomic techniques are applied to identify effective commercial hydrolytic enzymes. This mini-review summarizes researches on lignocellulose-degrading enzymes, the mechanisms of the responses of various lignocellulose-degrading strains and microbial communities to various carbon sources and various biomass substrates, post-translational modifications of lignocellulose-degrading enzymes, new lignocellulose-degrading strains, new lignocellulose-degrading enzymes and a new method of secretome analysis. The challenges in the practical use of enzymatic hydrolysis process to realize lignocellulose biorefineries are discussed, along with the prospects for the same.
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Affiliation(s)
- Hongliang Guo
- College of Food Engineering, Harbin University of Commerce, Harbin 150076, China
| | - Xiao-Dong Wang
- Research Center of Engineering Thermophysics, North China Electric Power University, Beijing 102206, China; School of Energy Power and Mechanical Engineering, North China Electric Power University, Beijing 102206, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan.
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de Gouvêa PF, Bernardi AV, Gerolamo LE, de Souza Santos E, Riaño-Pachón DM, Uyemura SA, Dinamarco TM. Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse. BMC Genomics 2018; 19:232. [PMID: 29614953 PMCID: PMC5883313 DOI: 10.1186/s12864-018-4627-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sugarcane bagasse has been proposed as a lignocellulosic residue for second-generation ethanol (2G) produced by breaking down biomass into fermentable sugars. The enzymatic cocktails for biomass degradation are mostly produced by fungi, but low cost and high efficiency can consolidate 2G technologies. A. fumigatus plays an important role in plant biomass degradation capabilities and recycling. To gain more insight into the divergence in gene expression during steam-exploded bagasse (SEB) breakdown, this study profiled the transcriptome of A. fumigatus by RNA sequencing to compare transcriptional profiles of A. fumigatus grown on media containing SEB or fructose as the sole carbon source. Secretome analysis was also performed using SDS-PAGE and LC-MS/MS. RESULTS The maximum activities of cellulases (0.032 U mL-1), endo-1,4-β--xylanase (10.82 U mL-1) and endo-1,3-β glucanases (0.77 U mL-1) showed that functional CAZymes (carbohydrate-active enzymes) were secreted in the SEB culture conditions. Correlations between transcriptome and secretome data identified several CAZymes in A. fumigatus. Particular attention was given to CAZymes related to lignocellulose degradation and sugar transporters. Genes encoding glycoside hydrolase classes commonly expressed during the breakdown of cellulose, such as GH-5, 6, 7, 43, 45, and hemicellulose, such as GH-2, 10, 11, 30, 43, were found to be highly expressed in SEB conditions. Lytic polysaccharide monooxygenases (LPMO) classified as auxiliary activity families AA9 (GH61), CE (1, 4, 8, 15, 16), PL (1, 3, 4, 20) and GT (1, 2, 4, 8, 20, 35, 48) were also differentially expressed in this condition. Similarly, the most important enzymes related to biomass degradation, including endoxylanases, xyloglucanases, β-xylosidases, LPMOs, α-arabinofuranosidases, cellobiohydrolases, endoglucanases and β-glucosidases, were also identified in the secretome. CONCLUSIONS This is the first report of a transcriptome and secretome experiment of Aspergillus fumigatus in the degradation of pretreated sugarcane bagasse. The results suggest that this strain employs important strategies for this complex degradation process. It was possible to identify a set of genes and proteins that might be applied in several biotechnology fields. This knowledge can be exploited for the improvement of 2G ethanol production by the rational design of enzymatic cocktails.
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Affiliation(s)
- Paula Fagundes de Gouvêa
- Faculty of Philosophy, Sciences and Literature of Ribeirão Preto, Chemistry Department, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Aline Vianna Bernardi
- Faculty of Philosophy, Sciences and Literature of Ribeirão Preto, Chemistry Department, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Luis Eduardo Gerolamo
- Faculty of Philosophy, Sciences and Literature of Ribeirão Preto, Chemistry Department, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Emerson de Souza Santos
- Faculty of Pharmaceutical Science, Department of Clinical, Toxicological and Bromatological Analysis, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Diego Mauricio Riaño-Pachón
- Brazilian Bioethanol Science and Technology Laboratory, Campinas, São Paulo, Brazil
- Current address: Laboratory of Regulatory Systems Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Sergio Akira Uyemura
- Faculty of Pharmaceutical Science, Department of Clinical, Toxicological and Bromatological Analysis, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Taisa Magnani Dinamarco
- Faculty of Philosophy, Sciences and Literature of Ribeirão Preto, Chemistry Department, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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Quantitative multiplexed profiling of Penicillium funiculosum secretome grown on polymeric cellulase inducers and glucose. J Proteomics 2018; 179:150-160. [PMID: 29597011 DOI: 10.1016/j.jprot.2018.03.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/16/2018] [Accepted: 03/20/2018] [Indexed: 11/22/2022]
Abstract
Filamentous fungi respond to the need to secure utilisable carbon from their growth milieu by secreting unique extracellular proteins depending upon the types of polymeric substrates. We have here profiled the variations in the secretome pattern of a non-model hypercellulolytic fungus - Penicillium funiculosum, grown in minimal media containing four different polymeric cellulase inducers, i.e., Avicel, wheat bran, ammonium-pretreated wheat straw and Avicel & wheat bran, and glucose over its early and late log phases of growth. Of the 137 secreted proteins validated at 1% FDR, we identified the quantified proteins in three clusters as early, persistently or lately expressed. The type of carbon substrate present in the culture media significantly affected the levels of cellulolytic enzymes expression by the fungus. The top abundant proteins quantified in the secretome for Avicel and wheat bran were cellobiohydrolaseI [GH7-CBM1], cellobiohydrolaseII [GH6-CBM1], β-glucosidase [GH3], arabinofuranosidase [GH51] and β-xylosidase [GH3], with bicupin being highest in case of wheat straw. Our results further suggested that the fungus secreted the extracellular proteins in waves, such that the initial responders act to hydrolyse the composite substrates in the culture environment before the second wave of proteins which tend to be more tailored to the specific substrate in the cultivating media. BIOLOGICAL SIGNIFICANCE In this article, we have comprehensively examined the dynamics of the secretome of a non-model hypercellulolytic fungus produced in response to model and composite cellulase inducers. Our study has provided additional insights into how the fungus enzyme machinery responds to the presence of different polymeric cellulase inducers over the two different growth phases (early growth and late growth phase). The comprehensive typing and quantification of the different proteins present in the secretomes of the cellulolytic fungal strains in response to diverse nutrient sources hold many prospects in understanding the fungus unique enzyme machinery and dynamics for the downstream biotechnological applications.
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Li YH, Zhang XY, Zhang F, Peng LC, Zhang DB, Kondo A, Bai FW, Zhao XQ. Optimization of cellulolytic enzyme components through engineering Trichoderma reesei and on-site fermentation using the soluble inducer for cellulosic ethanol production from corn stover. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:49. [PMID: 29483942 PMCID: PMC5824536 DOI: 10.1186/s13068-018-1048-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/12/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Cellulolytic enzymes produced by Trichoderma reesei are widely studied for biomass bioconversion, and enzymatic components vary depending on different inducers. In our previous studies, a mixture of glucose and disaccharide (MGD) was developed and used to induce cellulase production. However, the enzymatic profile induced by MGD is still not defined, and further optimization of the enzyme cocktail is also required for efficient ethanol production from lignocellulosic biomass. RESULTS In this study, cellulolytic enzymes produced by T. reesei Rut C30 using MGD and alkali-pretreated corn stover (APCS) as inducer were compared. Cellular secretome in response to each inducer was analyzed, which revealed a similar enzyme profile. However, significant difference in the content of cellulases and xylanase was detected. Although MGD induction enhanced β-glucosidase production, its activity was still not sufficient for biomass hydrolysis. To overcome such a disadvantage, aabgl1 encoding β-glucosidase in Aspergillus aculeatus was heterologously expressed in T. reesei Rut C30 under the control of the pdc1 promoter. The recombinant T. reesei PB-3 strain showed an improved β-glucosidase activity of 310 CBU/mL in the fed-batch fermentation, 71-folds higher than that produced by the parent strain. Meanwhile, cellulase activity of 50 FPU/mL was detected. Subsequently, the crude enzyme was applied for hydrolyzing corn stover with a solid loading of 20% through separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation, respectively, for ethanol production. Better performance was observed in the SHF process, through which a total of 119.9 g/L glucose was released within 12 h for concomitant ethanol production of 54.2 g/L. CONCLUSIONS The similar profile of cellulolytic enzymes was detected under the induction of MGD and APCS, but higher amount of cellulases was present in the crude enzyme induced by MGD. However, β-glucosidase activity induced by MGD was not sufficient for hydrolyzing lignocellulosic biomass. High titers of cellulases and β-glucosidase were achieved simultaneously by heterologous expression of aabgl1 in T. reesei and fed-batch fermentation through feeding MGD. We demonstrated that on-site cellulase production by T. reesei PB-3 has a potential for efficient biomass saccharification and ethanol production from lignocellulosic biomass.
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Affiliation(s)
- Yong-Hao Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
- Present Address: School of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing, 401331 China
| | - Xiao-Yue Zhang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116023 China
| | - Fei Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Liang-Cai Peng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Da-Bing Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, 657-8501 Japan
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
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Cologna NDMD, Gómez-Mendoza DP, Zanoelo FF, Giannesi GC, Guimarães NCDA, Moreira LRDS, Filho EXF, Ricart CAO. Exploring Trichoderma and Aspergillus secretomes: Proteomics approaches for the identification of enzymes of biotechnological interest. Enzyme Microb Technol 2018; 109:1-10. [DOI: 10.1016/j.enzmictec.2017.08.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 12/13/2022]
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30
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Reina R, García-Sánchez M, Liers C, García-Romera I, Aranda E. An Overview of Fungal Applications in the Valorization of Lignocellulosic Agricultural By-Products: The Case of Two-Phase Olive Mill Wastes. Fungal Biol 2018. [DOI: 10.1007/978-3-319-77386-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wang Q, Chen L, Yu D, Lin H, Shen Q, Zhao Y. Excellent waste biomass-degrading performance of Trichoderma asperellum T-1 during submerged fermentation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 609:1329-1339. [PMID: 28793402 DOI: 10.1016/j.scitotenv.2017.07.212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/23/2017] [Accepted: 07/23/2017] [Indexed: 06/07/2023]
Abstract
The random disposal and incineration of agricultural residues cause resources waste and environmental pollution. The potential of waste biomass for the production of alternative liquid fuels is increasing and the bioconversion of lignocellulose to fermentable monomeric sugars is essential for second-generation biofuel production. Here, natural and pretreated switch grass or rice straw were fermented by both Trichoderma asperellum T-1 and Trichoderma reesei QM6a, with the fermentation results highlighted the potential of T. asperellum T-1 in the degradation of natural waste lignocellulosic materials. In fermenting different substrates, the filter paper activity, β-glucosidase activity, xylanase activity and carboxymethyl cellulase activity of T-1 can respectively reach 1.88, 8.00, 7.15 and 20.52 times that of QM6a. Although acid pretreatment could improve the enzyme activities of both T-1 and QM6a, its effect on T-1 was much smaller than that on QM6a. Moreover, strain T-1 fermented the natural rice straw better than the pretreated rice straw. Therefore, T-1 is considered to be more suitable for the degradation of natural biomass, especially for the degradation of rice straw. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and scanning electron microscopy (SEM) showed that the cellulase series secreted by T. asperellum T-1 was more abundant, and its substrate deconstruction ability was stronger than T. reesei QM6a. All these results suggest the potential of T. asperellum T-1 in the degradation of natural waste lignocellulosic material, with practical benefits in terms of cost and pollution reduction.
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Affiliation(s)
- Qun Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, Research Institute of Eco-environmental Science, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Liang Chen
- Zhejiang Gongshang University, Hangzhou 310018, China
| | - Daobing Yu
- School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin'an 311300, China
| | - Hui Lin
- Institute of Environment Resource and Soil Fertilizer, Zhejiang Academy of Agriculture Science, Hangzhou 310021, China
| | - Qi Shen
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuhua Zhao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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32
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Berrin JG, Rosso MN, Abou Hachem M. Fungal secretomics to probe the biological functions of lytic polysaccharide monooxygenases. Carbohydr Res 2017; 448:155-160. [DOI: 10.1016/j.carres.2017.05.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/12/2017] [Accepted: 05/12/2017] [Indexed: 11/29/2022]
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33
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Characterization of novel Trichoderma hemicellulase and its use to enhance downstream processing of lignocellulosic biomass to simple fermentable sugars. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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A Chrysoporthe cubensis enzyme cocktail produced from a low-cost carbon source with high biomass hydrolysis efficiency. Sci Rep 2017. [PMID: 28634326 PMCID: PMC5478631 DOI: 10.1038/s41598-017-04262-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Low cost and high efficiency cellulolytic cocktails can consolidate lignocellulosic ethanol technologies. Sugarcane bagasse (SCB) is a low cost agro-industrial residue, and its use as a carbon source can reduce the costs of fungi cultivation for enzyme production. Chrysoporthe cubensis grown under solid state fermentation (SSF) with wheat bran has potential to produce efficient enzymatic extracts for SCB saccharification. This fungus was grown under submersed fermentation (SmF) and SSF with in natura SCB, pretreated with acid or alkali and with others carbon sources. In natura SCB induced the highest carboxymethylcellulase (CMCase), xylanase, β-xylosidase, α-galactosidase and mannanase activities by C. cubensis under SSF. In natura and washed SCB, inducers of enzyme production under SSF, did not induce high cellulases and hemicellulases production by C. cubensis in SmF. The C. cubensis enzymatic extract produced under SSF with in natura SCB as a carbon source was more efficient for lignocelulolic biomass hydrolysis than extracts produced under SSF with wheat bran and commercial cellulolytic extract. Chrysoporthe cubensis showed high potential for cellulases and hemicellulases production, especially when grown under SSF with in natura SCB as carbon source.
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Santos CA, Ferreira-Filho JA, O'Donovan A, Gupta VK, Tuohy MG, Souza AP. Production of a recombinant swollenin from Trichoderma harzianum in Escherichia coli and its potential synergistic role in biomass degradation. Microb Cell Fact 2017; 16:83. [PMID: 28511724 PMCID: PMC5432999 DOI: 10.1186/s12934-017-0697-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/05/2017] [Indexed: 01/09/2023] Open
Abstract
Background Fungal swollenins (SWOs) constitute a class of accessory proteins that are homologous to canonical plant expansins. Expansins and expansin-related proteins are well known for acting in the deagglomeration of cellulose structure by loosening macrofibrils. Consequently, SWOs can increase the accessibility and efficiency of the other enzymes involved in the saccharification of cellulosic substrates. Thus, SWOs are promising targets for improving the hydrolysis of plant biomass and for use as an additive to enhance the efficiency of an enzyme cocktail designed for the production of biofuels. Results Here, we report the initial characterization of an SWO from Trichoderma harzianum (ThSwo) that was successfully produced using Escherichia coli as a host. Initially, transcriptome and secretome data were used to compare swo gene expression and the amount of secreted ThSwo. The results from structural modeling and phylogenetic analysis of the ThSwo protein showed that ThSwo does preserve some structural features of the plant expansins and family-45 glycosyl hydrolase enzymes, but it evolutionarily diverges from both of these protein classes. Recombinant ThSwo was purified at a high yield and with high purity and showed secondary folding similar to that of a native fungal SWO. Bioactivity assays revealed that the purified recombinant ThSwo created a rough and amorphous surface on Avicel and displayed a high synergistic effect with a commercial xylanase from T. viride, enhancing its hydrolytic performance up to 147 ± 7%. Conclusions Many aspects of the structure and mechanism of action of fungal SWOs remain unknown. In the present study, we produced a recombinant, active SWO from T. harzianum using a prokaryotic host and confirmed its potential synergistic role in biomass degradation. Our work paves the way for further studies evaluating the structure and function of this protein, especially regarding its use in biotechnology. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0697-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Clelton A Santos
- Molecular Glycobiotechnology Group, Department of Biochemistry, National University of Ireland Galway, Galway, Ireland.,Center for Molecular Biology and Genetic Engineering, University of Campinas, Campinas, SP, Brazil
| | - Jaire A Ferreira-Filho
- Center for Molecular Biology and Genetic Engineering, University of Campinas, Campinas, SP, Brazil
| | - Anthonia O'Donovan
- Molecular Glycobiotechnology Group, Department of Biochemistry, National University of Ireland Galway, Galway, Ireland.,Technology Centre for Biorefining and Bioenergy, Orbsen Building, National University of Ireland, Galway, Ireland
| | - Vijai K Gupta
- Molecular Glycobiotechnology Group, Department of Biochemistry, National University of Ireland Galway, Galway, Ireland.,Technology Centre for Biorefining and Bioenergy, Orbsen Building, National University of Ireland, Galway, Ireland.,Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, School of Science, Tallinn University of Technology, Tallinn, Estonia
| | - Maria G Tuohy
- Molecular Glycobiotechnology Group, Department of Biochemistry, National University of Ireland Galway, Galway, Ireland.,Technology Centre for Biorefining and Bioenergy, Orbsen Building, National University of Ireland, Galway, Ireland
| | - Anete P Souza
- Center for Molecular Biology and Genetic Engineering, University of Campinas, Campinas, SP, Brazil. .,Department of Plant Biology, Biology Institute, University of Campinas, Campinas, SP, Brazil.
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da Silva Delabona P, Rodrigues GN, Zubieta MP, Ramoni J, Codima CA, Lima DJ, Farinas CS, da Cruz Pradella JG, Seiboth B. The relation between xyr1 overexpression in Trichoderma harzianum and sugarcane bagasse saccharification performance. J Biotechnol 2017; 246:24-32. [DOI: 10.1016/j.jbiotec.2017.02.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 01/09/2017] [Accepted: 02/02/2017] [Indexed: 01/16/2023]
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Liu J, Zhu N, Yang J, Yang Y, Wang R, Liu L, Yuan H. Lipopeptide produced from Bacillus sp. W112 improves the hydrolysis of lignocellulose by specifically reducing non-productive binding of cellulases with and without CBMs. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:301. [PMID: 29255484 PMCID: PMC5729243 DOI: 10.1186/s13068-017-0993-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 12/05/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Surfactants have attracted increasing interest for their capability to improve the enzymatic hydrolysis of lignocellulosic biomass. Compared to chemical surfactants, biosurfactants have a broader prospect for industrial applications because they are more environmentally friendly and more effective in some researches. Commercial cellulase preparations are mainly composed of endoglucanases (EGs) and cellobiohydrolases (CBHs) that possess carbohydrate-binding modules (CBMs). However, the effects of lipopeptide-type biosurfactants on enzymatic saccharification of lignocellulose and adsorption behaviors of cellulases with CBMs remain unclear. RESULTS In this study, we found that Bacillus sp. W112 could produce a lipopeptide-type biosurfactant from untreated biomass, such as wheat bran and Jerusalem artichoke tuber. The lipopeptide could enhance the enzymatic hydrolysis of dilute acid pretreated Giant Juncao grass (DA-GJG) by fungal and bacterial enzymes. The enhancement increased over a range of temperatures from 30 to 50 °C. Lipopeptide was shown to be more effective in promoting DA-GJG saccharification than chemical surfactants at low dosages, with a best stimulatory degree of 20.8% at 2% loading of the substrates (w/w). Lipopeptide increased the thermostability of EG and CBH in commercial cellulase cocktails. Moreover, the dual effects of lipopeptide on the adsorption behaviors of cellulases were found. It specifically lowered the non-productive binding of cellulases to lignin and increased the binding of cellulases to cellulose. In addition, we investigated the influence of lipopeptide on the adsorption behaviors of CBHs with CBMs for the first time. Our results showed that lipopeptide reduced the adsorption of CBM-deleted CBH to DA-GJG to a greater extent than that of intact CBH while the non-productive binding of intact CBH to lignin was reduced more, indicating that lipopeptide decreased the binding of CBMs onto lignin but not their combination with cellulose. CONCLUSIONS In this study, we found that lipopeptide from Bacillus sp. W112 promoted the enzymatic hydrolysis of DA-GJG at relative low loadings. The stimulatory effect could be attributed to increasing the cellulase thermostability, reducing non-productive adsorption of cellulases with CBMs caused by lignin and enhancing the binding of cellulases to cellulose.
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Affiliation(s)
- Jiawen Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ning Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jinshui Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yi Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ruonan Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Liang Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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Inoue H, Kitao C, Yano S, Sawayama S. Production of β-xylosidase from Trichoderma asperellum KIF125 and its application in efficient hydrolysis of pretreated rice straw with fungal cellulase. World J Microbiol Biotechnol 2016; 32:186. [DOI: 10.1007/s11274-016-2145-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/16/2016] [Indexed: 01/11/2023]
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The Post-genomic Era of Trichoderma reesei: What's Next? Trends Biotechnol 2016; 34:970-982. [PMID: 27394390 DOI: 10.1016/j.tibtech.2016.06.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/09/2016] [Accepted: 06/13/2016] [Indexed: 11/21/2022]
Abstract
The ascomycete Trichoderma reesei is one of the most well studied cellulolytic microorganisms. This fungus is widely used in the biotechnology industry, mainly in the production of biofuels. Due to its importance, its genome was sequenced in 2008, opening new avenues to study this microorganism. In this 'post-genomic' era, a transcriptomic and proteomic era has emerged. Here, we present an overview of new findings in the gene expression regulation network of T. reesei. We also discuss new rational strategies to obtain mutants that produce hydrolytic enzymes with a higher yield, using metabolic engineering. Finally, we present how synthetic biology strategies can be used to create engineered promoters to efficiently synthesize enzymes for biomass degradation to produce bioethanol.
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Florencio C, Cunha FM, Badino AC, Farinas CS, Ximenes E, Ladisch MR. Secretome analysis of Trichoderma reesei and Aspergillus niger cultivated by submerged and sequential fermentation processes: Enzyme production for sugarcane bagasse hydrolysis. Enzyme Microb Technol 2016; 90:53-60. [PMID: 27241292 DOI: 10.1016/j.enzmictec.2016.04.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/25/2016] [Accepted: 04/26/2016] [Indexed: 10/21/2022]
Abstract
Cellulases and hemicellulases from Trichoderma reesei and Aspergillus niger have been shown to be powerful enzymes for biomass conversion to sugars, but the production costs are still relatively high for commercial application. The choice of an effective microbial cultivation process employed for enzyme production is important, since it may affect titers and the profile of protein secretion. We used proteomic analysis to characterize the secretome of T. reesei and A. niger cultivated in submerged and sequential fermentation processes. The information gained was key to understand differences in hydrolysis of steam exploded sugarcane bagasse for enzyme cocktails obtained from two different cultivation processes. The sequential process for cultivating A. niger gave xylanase and β-glucosidase activities 3- and 8-fold higher, respectively, than corresponding activities from the submerged process. A greater protein diversity of critical cellulolytic and hemicellulolytic enzymes were also observed through secretome analyses. These results helped to explain the 3-fold higher yield for hydrolysis of non-washed pretreated bagasse when combined T. reesei and A. niger enzyme extracts from sequential fermentation were used in place of enzymes obtained from submerged fermentation. An enzyme loading of 0.7 FPU cellulase activity/g glucan was surprisingly effective when compared to the 5-15 times more enzyme loadings commonly reported for other cellulose hydrolysis studies. Analyses showed that more than 80% consisted of proteins other than cellulases whose role is important to the hydrolysis of a lignocellulose substrate. Our work combined proteomic analyses and enzymology studies to show that sequential and submerged cultivation methods differently influence both titers and secretion profile of key enzymes required for the hydrolysis of sugarcane bagasse. The higher diversity of feruloyl esterases, xylanases and other auxiliary hemicellulolytic enzymes observed in the enzyme mixtures from the sequential fermentation could be one major reason for the more efficient enzyme hydrolysis that results when using the combined secretomes from A. niger and T. reesei.
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Affiliation(s)
- Camila Florencio
- Laboratory of Renewable Resources Engineering, Department of Agricultural and Biological Engineering, Purdue University, IN 47907, West Lafayette, IN, USA; Graduate Program of Biotechnology, Federal University of Sao Carlos, 13565-905, Sao Carlos, SP, Brazil; Embrapa Instrumentation, 1452 XV de Novembro Street, 13560-970, Sao Carlos, SP, Brazil
| | - Fernanda M Cunha
- Embrapa Instrumentation, 1452 XV de Novembro Street, 13560-970, Sao Carlos, SP, Brazil; Graduate Program of Chemical Engineering, Federal University of Sao Carlos, 13565-905, Sao Carlos, SP, Brazil
| | - Alberto C Badino
- Graduate Program of Biotechnology, Federal University of Sao Carlos, 13565-905, Sao Carlos, SP, Brazil; Graduate Program of Chemical Engineering, Federal University of Sao Carlos, 13565-905, Sao Carlos, SP, Brazil
| | - Cristiane S Farinas
- Graduate Program of Biotechnology, Federal University of Sao Carlos, 13565-905, Sao Carlos, SP, Brazil; Embrapa Instrumentation, 1452 XV de Novembro Street, 13560-970, Sao Carlos, SP, Brazil; Graduate Program of Chemical Engineering, Federal University of Sao Carlos, 13565-905, Sao Carlos, SP, Brazil
| | - Eduardo Ximenes
- Laboratory of Renewable Resources Engineering, Department of Agricultural and Biological Engineering, Purdue University, IN 47907, West Lafayette, IN, USA
| | - Michael R Ladisch
- Laboratory of Renewable Resources Engineering, Department of Agricultural and Biological Engineering, Purdue University, IN 47907, West Lafayette, IN, USA.
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A. L. Rocha V, N. Maeda R, Pereira N, F. Kern M, Elias L, Simister R, Steele-King C, Gómez LD, McQueen-Mason SJ. Characterization of the cellulolytic secretome ofTrichoderma harzianumduring growth on sugarcane bagasse and analysis of the activity boosting effects of swollenin. Biotechnol Prog 2016; 32:327-36. [DOI: 10.1002/btpr.2217] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/02/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Vanessa A. L. Rocha
- LADEBIO, Centre of Biofuels, Oil and its Derivatives, School of Chemistry; Department of Biochemical Engineering, Centre of Technology, Federal University of Rio De Janeiro; Rio De Janeiro 21941-909 Brazil
| | - Roberto N. Maeda
- LADEBIO, Centre of Biofuels, Oil and its Derivatives, School of Chemistry; Department of Biochemical Engineering, Centre of Technology, Federal University of Rio De Janeiro; Rio De Janeiro 21941-909 Brazil
| | - Nei Pereira
- LADEBIO, Centre of Biofuels, Oil and its Derivatives, School of Chemistry; Department of Biochemical Engineering, Centre of Technology, Federal University of Rio De Janeiro; Rio De Janeiro 21941-909 Brazil
| | - Marcelo F. Kern
- MasonCNAP, Dept. of Biology; University of York; Wentworth Way, York YO10 5DD U.K
| | - Luisa Elias
- MasonCNAP, Dept. of Biology; University of York; Wentworth Way, York YO10 5DD U.K
| | - Rachael Simister
- MasonCNAP, Dept. of Biology; University of York; Wentworth Way, York YO10 5DD U.K
| | - Clare Steele-King
- MasonCNAP, Dept. of Biology; University of York; Wentworth Way, York YO10 5DD U.K
| | - Leonardo D. Gómez
- MasonCNAP, Dept. of Biology; University of York; Wentworth Way, York YO10 5DD U.K
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Zhu N, Liu J, Yang J, Lin Y, Yang Y, Ji L, Li M, Yuan H. Comparative analysis of the secretomes of Schizophyllum commune and other wood-decay basidiomycetes during solid-state fermentation reveals its unique lignocellulose-degrading enzyme system. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:42. [PMID: 26900401 PMCID: PMC4761152 DOI: 10.1186/s13068-016-0461-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/11/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND The genome of Schizophyllum commune encodes a diverse repertoire of degradative enzymes for plant cell wall breakdown. Recent comparative genomics study suggests that this wood decayer likely has a mode of biodegradation distinct from the well-established white-rot/brown-rot models. However, much about the extracellular enzyme system secreted by S. commune during lignocellulose deconstruction remains unknown and the underlying mechanism is poorly understood. In this study, extracellular proteins of S. commune colonizing Jerusalem artichoke stalk were analyzed and compared with those of two white-rot fungi Phanerochaete chrysosporium and Ceriporiopsis subvermispora and a brown-rot fungus Gloeophyllum trabeum. RESULTS Under solid-state fermentation (SSF) conditions, S. commune displayed considerably higher levels of hydrolytic enzyme activities in comparison with those of P. chrysosporium, C. subvermispora and G. trabeum. During biodegradation process, this fungus modified the lignin polymer in a way which was consistent with a hydroxyl radical attack, similar to that of G. trabeum. The crude enzyme cocktail derived from S. commune demonstrated superior performance over a commercial enzyme preparation from Trichoderma longibrachiatum in the hydrolysis of pretreated lignocellulosic biomass at low enzyme loadings. Secretomic analysis revealed that compared with three other fungi, this species produced a higher diversity of carbohydrate-degrading enzymes, especially hemicellulases and pectinases acting on polysaccharide backbones and side chains, and a larger set of enzymes potentially supporting the generation of hydroxyl radicals. In addition, multiple non-hydrolytic proteins implicated in enhancing polysaccharide accessibility were identified in the S. commune secretome, including lytic polysaccharide monooxygenases (LPMOs) and expansin-like proteins. CONCLUSIONS Plant lignocellulose degradation by S. commune involves a hydroxyl radical-mediated mechanism for lignocellulose modification in parallel with the synergistic system of various polysaccharide-degrading enzymes. Furthermore, the complex enzyme system of S. commune holds significant potential for application in biomass saccharification. These discoveries will help unveil the diversity of natural lignocellulose-degrading mechanisms, and advance the design of more efficient enzyme mixtures for the deconstruction of lignocellulosic feedstocks.
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Affiliation(s)
- Ning Zhu
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Jiawen Liu
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Jinshui Yang
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Yujian Lin
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Yi Yang
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Lei Ji
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Meng Li
- />National Energy R&D Center for Non-food Biomass, China Agricultural University, 100193 Beijing, China
| | - Hongli Yuan
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
- />National Energy R&D Center for Non-food Biomass, China Agricultural University, 100193 Beijing, China
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Zhao S, Yan YS, He QP, Yang L, Yin X, Li CX, Mao LC, Liao LS, Huang JQ, Xie SB, Nong QD, Zhang Z, Jing L, Xiong YR, Duan CJ, Liu JL, Feng JX. Comparative genomic, transcriptomic and secretomic profiling of Penicillium oxalicum HP7-1 and its cellulase and xylanase hyper-producing mutant EU2106, and identification of two novel regulatory genes of cellulase and xylanase gene expression. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:203. [PMID: 27688806 PMCID: PMC5035457 DOI: 10.1186/s13068-016-0616-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 09/14/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND The filamentous fungus Penicillium oxalicum is a potential alternative to Trichoderma reesei for industrial production of a complete cellulolytic enzyme system for a bio-refinery. Comparative omics approaches can support rational genetic engineering and/or breeding of filamentous fungi with improved cellulase production capacity. In this study, comparative genomic, transcriptomic and secretomic profiling of P. oxalicum HP7-1 and its cellulase and xylanase hyper-producing mutant EU2106 were employed to screen for novel regulators of cellulase and xylanase gene expression. RESULTS The 30.62 Mb P. oxalicum HP7-1 genome was sequenced, and 9834 protein-coding genes were annotated. Re-sequencing of the mutant EU2106 genome identified 274 single nucleotide variations and 12 insertion/deletions. Comparative genomic, transcriptomic and secretomic profiling of HP7-1 and EU2106 revealed four candidate regulators of cellulase and xylanase gene expression. Deletion of these candidate genes and measurement of the enzymatic activity of the resultant mutants confirmed the identity of three regulatory genes. POX02484 and POX08522, encoding a putative Zn(II)2Cys6 DNA-binding domain and forkhead protein, respectively, were found to be novel, while PoxClrB is an ortholog of ClrB, a key transcriptional regulator of cellulolytic enzyme gene expression in filamentous fungi. ΔPOX02484 and ΔPOX08522 mutants exhibited significantly reduced β-glucosidase activity, increased carboxymethylcellulose cellulase and xylanase activities, and altered transcription level of cellulase and xylanase genes compared with the parent strain ΔPoxKu70, with Avicel as the sole carbon source. CONCLUSIONS Two novel genes, POX02484 and POX08522, were found and characterized to regulate the expression of cellulase and xylanase genes in P. oxalicum. These findings are important for engineering filamentous fungi to improve cellulase and xylanase production.
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Affiliation(s)
- Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Yu-Si Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Qi-Peng He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Lin Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Xin Yin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Cheng-Xi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Li-Chun Mao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Lu-Sheng Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Jin-Qun Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Shang-Bo Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Qing-Dong Nong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Zheng Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Lei Jing
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Ya-Ru Xiong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Cheng-Jie Duan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Jun-Liang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
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Madende M, Osthoff G, Patterton HG, Patterton HE, Martin P, Opperman DJ. Characterization of casein and alpha lactalbumin of African elephant (Loxodonta africana) milk. J Dairy Sci 2015; 98:8308-18. [PMID: 26454297 DOI: 10.3168/jds.2014-9195] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 08/14/2015] [Indexed: 11/19/2022]
Abstract
The current research reports partial characterization of the caseins and α-lactalbumin (α-LA) of the African elephant with proposed unique structure-function properties. Extensive research has been carried out to understand the structure of the casein micelles. Crystallographic structure elucidation of caseins and casein micelles is not possible. Consequently, several models have been developed in an effort to describe the casein micelle, specifically of cow milk. Here we report the characterization of African elephant milk caseins. The κ-caseins and β-caseins were investigated, and their relative ratio was found to be approximately 1:8.5, whereas α-caseins were not detected. The gene sequence of β-casein in the NCBI database was revisited, and a different sequence in the N-terminal region is proposed. Amino acid sequence alignment and hydropathy plots showed that the κ-casein of African elephant milk is similar to that of other mammals, whereas the β-casein is similar to the human protein, and displayed a section of unique AA composition and additional hydrophilic regions compared with bovine caseins. Elephant milk is destabilized by 62% alcohol, and it is speculated that the β-casein characteristics may allow maintenance of the colloidal nature of the casein micelle, a role that was previously only associated with κ-casein. The oligosaccharide content of milk was reported to be low in dairy animals but high in some other species such as humans and elephants. In the milk of the African elephant, lactose and oligosaccharides both occur at high levels. These levels are typically related to the content of α-LA in the mammary gland and thus point to a specialized carbohydrate synthesis, where the whey protein α-LA plays a role. We report the characterization of African elephant α-LA. Homology modeling of the α-LA showed that it is structurally similar to crystal structures of other mammalian species, which in turn may be an indication that its functional properties, such as lactose synthesis, should not be impaired.
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Affiliation(s)
- M Madende
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, PO Box 339, Bloemfontein 9300, Republic of South Africa
| | - G Osthoff
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, PO Box 339, Bloemfontein 9300, Republic of South Africa.
| | - H-G Patterton
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, PO Box 339, Bloemfontein 9300, Republic of South Africa
| | - H E Patterton
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, PO Box 339, Bloemfontein 9300, Republic of South Africa
| | - P Martin
- UMR1313 Génétique Animale et Biologie Integrative, Institut National de la Recherche Agronomique, Domaine de Vilvert - Bâtiment 221, 78350 Jouy-en-Josas, France
| | - D J Opperman
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, PO Box 339, Bloemfontein 9300, Republic of South Africa
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Ogunmolu FE, Kaur I, Gupta M, Bashir Z, Pasari N, Yazdani SS. Proteomics Insights into the Biomass Hydrolysis Potentials of a Hypercellulolytic Fungus Penicillium funiculosum. J Proteome Res 2015; 14:4342-58. [PMID: 26288988 DOI: 10.1021/acs.jproteome.5b00542] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The quest for cheaper and better enzymes needed for the efficient hydrolysis of lignocellulosic biomass has placed filamentous fungi in the limelight for bioprospecting research. In our search for efficient biomass degraders, we identified a strain of Penicillium funiculosum whose secretome demonstrates high saccharification capabilities. Our probe into the secretome of the fungus through qualitative and label-free quantitative mass spectrometry based proteomics studies revealed a high abundance of inducible CAZymes and several nonhydrolytic accessory proteins. The preferential association of these proteins and the attending differential biomass hydrolysis gives an insight into their interactions and clues about possible roles of novel hydrolytic and nonhydrolytic proteins in the synergistic deconstruction of lignocellulosic biomass. Our study thus provides the first comprehensive insight into the repertoire of proteins present in a high-performing secretome of a hypercellulolytic Penicillium funiculosum, their relative abundance in the secretome, and the interaction dynamics of the various protein groups in the secretome. The gleanings from the stoichiometry of these interactions hold a prospect as templates in the design of cost-effective synthetic cocktails for the optimal hydrolysis of biomass.
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Affiliation(s)
- Funso Emmanuel Ogunmolu
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
| | - Inderjeet Kaur
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
| | - Mayank Gupta
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
| | - Zeenat Bashir
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
| | - Nandita Pasari
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
| | - Syed Shams Yazdani
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
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Zafra G, Absalón AE, Cortés-Espinosa DV. Morphological changes and growth of filamentous fungi in the presence of high concentrations of PAHs. Braz J Microbiol 2015; 46:937-41. [PMID: 26413081 PMCID: PMC4568862 DOI: 10.1590/s1517-838246320140575] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/28/2014] [Indexed: 11/21/2022] Open
Abstract
In this study, we evaluated the effect of low and high molecular weight polycyclic
aromatic hydrocarbons (PAHs), i.e., Phenanthrene, Pyrene and
Benzo[a]pyrene, on the radial growth and morphology of the PAH-degrading fungal
strains Aspergillus nomius H7 and Trichoderma
asperellum H15. The presence of PAHs in solid medium produced significant
detrimental effects on the radial growth of A. nomius H7 at 4,000
and 6,000 mg L−1 and changes in mycelium pigmentation, abundance and
sporulation ability at 1,000–6,000 mg L−1. In contrast, the radial growth
of T. asperellum H15 was not affected at any of the doses tested,
although sporulation was observed only up to 4,000 mg L−1 and as with the
H7 strain, some visible changes in sporulation patterns and mycelium pigmentation
were observed. Our results suggest that fungal strains exposed to high doses of PAHs
significantly vary in their growth rates and sporulation characteristics in response
to the physiological and defense mechanisms that affect both pigment production and
conidiation processes. This finding is relevant for obtaining a better understanding
of fungal adaptation in PAH-polluted environments and for developing and implementing
adequate strategies for the remediation of contaminated soils.
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Affiliation(s)
- German Zafra
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Tlaxcala, México
| | - Angel E Absalón
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Tlaxcala, México
| | - Diana V Cortés-Espinosa
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Tlaxcala, México
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Comparative Secretome Analysis of Trichoderma reesei and Aspergillus niger during Growth on Sugarcane Biomass. PLoS One 2015; 10:e0129275. [PMID: 26053961 PMCID: PMC4460134 DOI: 10.1371/journal.pone.0129275] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/06/2015] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Our dependence on fossil fuel sources and concern about the environment has generated a worldwide interest in establishing new sources of fuel and energy. Thus, the use of ethanol as a fuel is advantageous because it is an inexhaustible energy source and has minimal environmental impact. Currently, Brazil is the world's second largest producer of ethanol, which is produced from sugarcane juice fermentation. However, several studies suggest that Brazil could double its production per hectare by using sugarcane bagasse and straw, known as second-generation (2G) bioethanol. Nevertheless, the use of this biomass presents a challenge because the plant cell wall structure, which is composed of complex sugars (cellulose and hemicelluloses), must be broken down into fermentable sugar, such as glucose and xylose. To achieve this goal, several types of hydrolytic enzymes are necessary, and these enzymes represent the majority of the cost associated with 2G bioethanol processing. Reducing the cost of the saccharification process can be achieved via a comprehensive understanding of the hydrolytic mechanisms and enzyme secretion of polysaccharide-hydrolyzing microorganisms. In many natural habitats, several microorganisms degrade lignocellulosic biomass through a set of enzymes that act synergistically. In this study, two fungal species, Aspergillus niger and Trichoderma reesei, were grown on sugarcane biomass with two levels of cell wall complexity, culm in natura and pretreated bagasse. The production of enzymes related to biomass degradation was monitored using secretome analyses after 6, 12 and 24 hours. Concurrently, we analyzed the sugars in the supernatant. RESULTS Analyzing the concentration of monosaccharides in the supernatant, we observed that both species are able to disassemble the polysaccharides of sugarcane cell walls since 6 hours post-inoculation. The sugars from the polysaccharides such as arabinoxylan and β-glucan (that compose the most external part of the cell wall in sugarcane) are likely the first to be released and assimilated by both species of fungi. At all time points tested, A. niger produced more enzymes (quantitatively and qualitatively) than T. reesei. However, the most important enzymes related to biomass degradation, including cellobiohydrolases, endoglucanases, β-glucosidases, β-xylosidases, endoxylanases, xyloglucanases, and α-arabinofuranosidases, were identified in both secretomes. We also noticed that the both fungi produce more enzymes when grown in culm as a single carbon source. CONCLUSION Our work provides a detailed qualitative and semi-quantitative secretome analysis of A. niger and T. reesei grown on sugarcane biomass. Our data indicate that a combination of enzymes from both fungi is an interesting option to increase saccharification efficiency. In other words, these two fungal species might be combined for their usage in industrial processes.
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Characterization of cellulase secretion and Cre1-mediated carbon source repression in the potential lignocellulose-degrading strain Trichoderma asperellum T-1. PLoS One 2015; 10:e0119237. [PMID: 25741694 PMCID: PMC4351060 DOI: 10.1371/journal.pone.0119237] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 01/11/2015] [Indexed: 12/15/2022] Open
Abstract
Trichoderma asperellum, a traditional bio-control species, was demonstrated to be an excellent candidate for lignocellulose degradation in this work. Comparing to the representatively industrial strain of Trichoderma reeseiQM6a, T. asperellum T-1 showed more robust growth, stronger spore production, faster secretion of lignocellulose-decomposing enzymes and better pH tolerance. The reducing sugar released by strain T-1 on the second day of fermentation was 87% higher than that of strain QM6a, although the maximum reducing sugar yield and the cellulase production persistence of the strain T-1 were lower. Our experiment found that the cellulase secretion was strongly inhibited by glucose, suggesting the existence of carbon source repression pathway in T. asperellum T-1. The inhibiting effect was enhanced with an increase in glucose concentration and was closely related to mycelium growth. SDS-PAGE and secondary mass-spectrum identification confirmed that the expression of endo-1,4-β-xylanase I in T. asperellum T-1 was down-regulated when glucose was added. The factor Cre1, which plays an important role in the down-regulation of the endo-1,4-β-xylanase I gene, was investigated by bioinformatics methods. The protein structure of Cre1, analyzed using multiple protein sequence alignment, indicates the existence of the Zn-fingers domain. Then, the binding sites of Cre1 on the endo-1,4-β-xylanase I gene promoter were further elucidated. This study is the first report about Cre1-mediated carbon repression in the bio-control strain T. asperellum T-1. All of the above results provided good references for better understanding T. asperellum T-1 and improving its application for lignocellulose degradation.
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Tian F, Xie ZL, Zhao LZ, Guo J, Han XB, Xie LF, Wang Y, Chang XY. Comparative secretome analysis of Fusarium sp. Q7-31T during liquid fermentation using oat straw as a carbon source. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1051-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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