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Singh V, Raheja Y, Basotra N, Sharma G, Tsang A, Chadha BS. CRISPR/Cas9 mediated gene editing of transcription factor ACE1 for enhanced cellulase production in thermophilic fungus Rasamsonia emersonii. Fungal Biol Biotechnol 2023; 10:18. [PMID: 37658430 PMCID: PMC10472679 DOI: 10.1186/s40694-023-00165-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/28/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND The filamentous fungus Rasamsonia emersonii has immense potential to produce biorefinery relevant thermostable cellulase and hemicellulase enzymes using lignocellulosic biomass. Previously in our lab, a hyper-cellulase producing strain of R. emersonii was developed through classical breeding and system biology approaches. ACE1, a pivotal transcription factor in fungi, plays a crucial role in negatively regulating the expression of cellulase genes. In order to identify the role of ACE1 in cellulase production and to further improve the lignocellulolytic enzyme production in R. emersonii, CRISPR/Cas9 mediated disruption of ACE1 gene was employed. RESULTS A gene-edited ∆ACE1 strain (GN11) was created, that showed 21.97, 20.70 and 24.63, 9.42, 18.12%, improved endoglucanase, cellobiohydrolase (CBHI), β-glucosidase, FPase, and xylanase, activities, respectively, as compared to parental strain M36. The transcriptional profiling showed that the expression of global regulator (XlnR) and different CAZymes genes including endoglucanases, cellobiohydrolase, β-xylosidase, xylanase, β-glucosidase and lytic polysaccharide mono-oxygenases (LPMOs) were significantly enhanced, suggesting critical roles of ACE1 in negatively regulating the expression of various key genes associated with cellulase production in R. emersonii. Whereas, the disruption of ACE1 significantly down-regulated the expression of CreA repressor gene as also evidenced by 2-deoxyglucose (2-DG) resistance phenotype exhibited by edited strain GN11 as well as appreciably higher constitutive production of cellulases in the presence of glucose and mixture of glucose and disaccharide (MGDs) both in batch and flask fed batch mode of culturing. Furthermore, ∆ACE1 strains were evaluated for the hydrolysis of biorefinery relevant steam/acid pretreated unwashed rice straw slurry (Praj Industries Ltd; 15% substrate loading rate) and were found to be significantly superior when compared to the benchmark enzymes produced by parent strain M36 and Cellic Ctec3. CONCLUSIONS Current work uncovers the crucial role of ACE1 in regulating the expression of the various cellulase genes and carbon catabolite repression mechanism in R. emersonii. This study represents the first successful report of utilizing CRISPR/Cas9 genome editing technology to disrupt the ACE1 gene in the thermophlic fungus R. emersonii. The improved methodologies presented in this work might be applied to other commercially important fungal strains for which genetic manipulation tools are limited.
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Affiliation(s)
- Varinder Singh
- Department of Microbiology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Yashika Raheja
- Department of Microbiology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Neha Basotra
- Department of Microbiology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Gaurav Sharma
- Department of Microbiology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Adrian Tsang
- Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC, H4B 1R6, Canada
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Filiatrault-Chastel C, Heiss-Blanquet S, Margeot A, Berrin JG. From fungal secretomes to enzymes cocktails: The path forward to bioeconomy. Biotechnol Adv 2021; 52:107833. [PMID: 34481893 DOI: 10.1016/j.biotechadv.2021.107833] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/17/2022]
Abstract
Bioeconomy is seen as a way to mitigate the carbon footprint of human activities by reducing at least part of the fossil resources-based economy. In this new paradigm of sustainable development, the use of enzymes as biocatalysts will play an increasing role to provide services and goods. In industry, most of multicomponent enzyme cocktails are of fungal origin. Filamentous fungi secrete complex enzyme sets called "secretomes" that can be utilized as enzyme cocktails to valorize different types of bioresources. In this review, we highlight recent advances in the study of fungal secretomes using improved computational and experimental secretomics methods, the progress in the understanding of industrially important fungi, and the discovery of new enzymatic mechanisms and interplays to degrade renewable resources rich in polysaccharides (e.g. cellulose). We review current biotechnological applications focusing on the benefits and challenges of fungal secretomes for industrial applications with some examples of commercial cocktails of fungal origin containing carbohydrate-active enzymes (CAZymes) and we discuss future trends.
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Affiliation(s)
- Camille Filiatrault-Chastel
- INRAE, Aix Marseille Univ., Biodiversité et Biotechnologie Fongiques, UMR1163, Marseille, France; IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Senta Heiss-Blanquet
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Antoine Margeot
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ., Biodiversité et Biotechnologie Fongiques, UMR1163, Marseille, France.
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Agrawal R, Verma A, Singhania RR, Varjani S, Di Dong C, Kumar Patel A. Current understanding of the inhibition factors and their mechanism of action for the lignocellulosic biomass hydrolysis. BIORESOURCE TECHNOLOGY 2021; 332:125042. [PMID: 33813178 DOI: 10.1016/j.biortech.2021.125042] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Biorefining of lignocellulosic biomass is a relatively new concept but it has strong potential to develop and partially replace the fossil derived fuels and myriad of value products to subsequently reduce the greenhouse gas emissions. However, the energy and cost intensive process of releasing the entrapped fermentable sugars is a major challenge for its commercialization. Various factors playing a detrimental role during enzymatic hydrolysis of biomass are inherent recalcitrance of lignocellulosic biomass, expensive enzymes, sub-optimal enzyme composition, lack of synergistic activity and enzyme inhibition caused by various inhibitors. The current study investigated the mechanism of enzyme inhibition during lignocellulosic biomass saccharification especially at high solid loadings. These inhibition factors are categorized into physio-chemical factors, water-soluble and -insoluble enzyme inhibitors, oligomers and enzyme-lignin binding. Furthermore, different approaches are proposed to alleviate the challenges and improve the enzymatic hydrolysis efficiency such as supplementation with surfactants, synergistic catalytic/non-catalytic proteins, and bioprocess modifications.
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Affiliation(s)
- Ruchi Agrawal
- The Energy and Resources Institute, TERI Gram, Gwal Pahari, Gurugram, Haryana, India
| | - Amit Verma
- College of Basic Science and Humanities, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar - 385506 (Banaskantha), Gujarat, India
| | - Reeta Rani Singhania
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan
| | - Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar, Gujarat 382010, India
| | - Cheng Di Dong
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan
| | - Anil Kumar Patel
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan.
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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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Gérard D, Méline T, Muzard M, Deleu M, Plantier-Royon R, Rémond C. Enzymatically-synthesized xylo-oligosaccharides laurate esters as surfactants of interest. Carbohydr Res 2020; 495:108090. [PMID: 32807358 DOI: 10.1016/j.carres.2020.108090] [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] [Received: 03/13/2020] [Revised: 06/12/2020] [Accepted: 07/01/2020] [Indexed: 01/29/2023]
Abstract
Lipase-catalyzed synthesis of xylo-oligosaccharides esters from pure xylobiose, xylotriose and xylotetraose in the presence of vinyl laurate was investigated. The influence of different experimental parameters such as the loading of lipase, the reaction duration or the use of a co-solvent was studied and the reaction conditions were optimized with xylobiose. Under the best conditions, a regioselective esterification occurred to yield a monoester with the acyl chain at the OH-4 of the xylose unit at the non-reducing end. Surface-active properties of these pure xylo-oligosaccharides fatty esters have been evaluated. They display interesting surfactant activities that differ according to the degree of polymerization (DP) of the glycone moiety.
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Affiliation(s)
- D Gérard
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51686, Reims, France; Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, Université de Reims Champagne-Ardenne, 51687, Reims Cedex, France
| | - T Méline
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51686, Reims, France
| | - M Muzard
- Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, Université de Reims Champagne-Ardenne, 51687, Reims Cedex, France
| | - M Deleu
- Université de Liège, Gembloux Agro-Bio Tech, Laboratoire de Biophysique Moléculaire Aux Interfaces, 2 Passage des Déportés, B-5030, Gembloux, Belgium
| | - R Plantier-Royon
- Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, Université de Reims Champagne-Ardenne, 51687, Reims Cedex, France
| | - C Rémond
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51686, Reims, France.
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Cubas-Cano E, González-Fernández C, Ballesteros I, Tomás-Pejó E. Efficient utilization of hydrolysates from steam-exploded gardening residues for lactic acid production by optimization of enzyme addition and pH control. WASTE MANAGEMENT (NEW YORK, N.Y.) 2020; 107:235-243. [PMID: 32325410 DOI: 10.1016/j.wasman.2020.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/26/2020] [Accepted: 04/01/2020] [Indexed: 05/12/2023]
Abstract
The expansion of urban green areas has boosted the accumulation of gardening lignocellulosic residues that could be potentially used to produce platform chemicals like lactic acid. However, when using lignocelluloses, pretreatment step, such as steam explosion, is often needed to favour sugar release. Considering that the conversion of glucose from cellulose has been widely addressed, this work is focused on the valorisation of the steam-exploded gardening liquid fraction rich in hemicellulosic sugars. Since oligomeric sugars are usually solubilized during steam explosion, an enzymatic hydrolysis step was required in some cases to increase the monosaccharides content. Although the presence of inhibitors released during pretreatment (e.g. formic acid) hindered hydrolysis yields, the addition of hemicellulases and the enzyme dosage optimization resulted in 85%, 89% and 95% of glucose, xylose and arabinose release from soluble oligomers, respectively. Lactobacillus pentosus CECT4023T was used for lactic acid fermentation of C6 and C5 sugars from the hydrolysate with the highest sugars concentration, that did not require enzymatic hydrolysis. Xylose consumption was hampered due to the inhibitory effect of acids that produced pH drop. Different pH control systems were applied and automatic NaOH addition in bioreactor resulted in 21 g L-1 of lactic acid (95% of the maximum theoretical yield) that implied 44% increase in lactic acid production when compared with flask fermentation. These results provide new insights for the valorisation of emerging lignocellulosic materials like gardening residues into high added-value products.
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Affiliation(s)
- Enrique Cubas-Cano
- IMDEA Energy Institute, Biotechnological Processes Unit, 28935 Móstoles, Spain
| | | | | | - Elia Tomás-Pejó
- IMDEA Energy Institute, Biotechnological Processes Unit, 28935 Móstoles, Spain.
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Villena GK, Kitazono AA, Hernández-Macedo M L. Bioengineering Fungi and Yeast for the Production of Enzymes, Metabolites, and Value-Added Compounds. Fungal Biol 2020. [DOI: 10.1007/978-3-030-41870-0_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Cintra LC, da Costa IC, de Oliveira ICM, Fernandes AG, Faria SP, Jesuíno RSA, Ravanal MC, Eyzaguirre J, Ramos LP, de Faria FP, Ulhoa CJ. The boosting effect of recombinant hemicellulases on the enzymatic hydrolysis of steam-treated sugarcane bagasse. Enzyme Microb Technol 2019; 133:109447. [PMID: 31874680 DOI: 10.1016/j.enzmictec.2019.109447] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/17/2019] [Accepted: 10/10/2019] [Indexed: 10/25/2022]
Abstract
To increase the efficiency of enzyme cocktails in deconstructing cellulose and hemicelluloses present in the plant cell wall, a combination of enzymes with complementary activities is required. Xylan is the main hemicellulose component of energy crops and for its complete hydrolysis a system consisting of several enzymes acting cooperatively, including endoxylanases (XYN), β-xylosidases (XYL) and α-l-arabinofuranosidases (ABF) is necessary. The current work aimed at evaluating the effect of recombinant hemicellulolytic enzymes on the enzymatic hydrolysis of steam-exploded sugarcane bagasse (SEB). One recombinant endoxylanase (HXYN2) and one recombinant β-xylosidase (HXYLA) from Humicola grisea var thermoidea, together with an α-l-arabinofuranosidase (AFB3) from Penicillium pupurogenum, all produced in Pichia pastoris, were used to formulate an efficient enzyme mixture for SEB hydrolysis using a 23 Central Composite Rotatable Design (CCRD). The most potent enzyme for SEB hydrolysis was ABF3. Subsequently, the optimal enzyme mixture was used in combination with commercial cellulases (Accellerase 1500), either simultaneously or in sequential experiments. The supplementation of Accellerase 1500 with hemicellulases enhanced the glucose yield from SEB hydrolysis by 14.6%, but this effect could be raised to 50% when hemicellulases were added prior to hydrolysis with commercial cellulases. These results were supported by scanning electron microscopy, which revealed the effect of enzymatic hydrolysis on SEB fibers. Our results show the potential of complementary enzyme activities to improve enzymatic hydrolysis of SEB, thus improving the efficiency of the hydrolytic process.
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Affiliation(s)
- Lorena Cardoso Cintra
- Department of Cellular Biology, University of Brasília, Brasília, Brazil; School of Veterinary and Animal Sciences, Federal University of Goiás, Goiânia, GO, Brazil
| | | | - Izadora Cristina Moreira de Oliveira
- Department of Cellular Biology, University of Brasília, Brasília, Brazil; Department of Biochemistry and Molecular Biology, Federal University of Goiás, Goiânia, GO, Brazil
| | - Amanda Gregorim Fernandes
- Department of Cellular Biology, University of Brasília, Brasília, Brazil; Department of Biochemistry and Molecular Biology, Federal University of Goiás, Goiânia, GO, Brazil
| | - Syd Pereira Faria
- Department of Biochemistry and Molecular Biology, Federal University of Goiás, Goiânia, GO, Brazil
| | | | - Maria Cristina Ravanal
- Department of Biological Sciences, Andrés Bello University, Santiago, Chile; Instituto de Ciencia y Tecnología de los Alimentos (ICYTAL), Facultad de Ciencias Agrarias, Universidad Austral de Chile, Valdivia, Chile
| | - Jaime Eyzaguirre
- Department of Biological Sciences, Andrés Bello University, Santiago, Chile
| | - Luiz Pereira Ramos
- Department of Chemistry, Federal University of Paraná, Curitiba, PR, Brazil
| | - Fabrícia Paula de Faria
- Department of Biochemistry and Molecular Biology, Federal University of Goiás, Goiânia, GO, Brazil
| | - Cirano José Ulhoa
- Department of Cellular Biology, University of Brasília, Brasília, Brazil; Department of Biochemistry and Molecular Biology, Federal University of Goiás, Goiânia, GO, Brazil.
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Duckweed (Lemna minor) is a novel natural inducer of cellulase production in Trichoderma reesei. J Biosci Bioeng 2018; 127:486-491. [PMID: 30366719 DOI: 10.1016/j.jbiosc.2018.09.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 08/13/2018] [Accepted: 09/26/2018] [Indexed: 02/03/2023]
Abstract
An inducer is crucial for cellulase production. In this study, duckweed was used as an inducer of cellulase production by Trichoderma reesei RUT C30. In a reaction induced by 50 g/L duckweed in shake flasks, the filter-paper activity (FPA) reached 6.5 FPU/mL, a value comparable to that induced by avicel. The enzyme-hydrolysis rate induced by steam-exploded corn stalk was 54.2%, representing a 28% improvement over that induced by avicel. The duckweed starch was hydrolyzed to glucose, which was subsequently used for biomass accumulation during the fermentation process. Furthermore, to optimize the control of the fermentation process, a combined substrate of avicel and duckweed was used to induce cellulase production by T. reesei RUT C30. The cellulase production and hydrolysis rates of the combined substrate, compared with avicel alone, were 39.6% and 36.7% higher, respectively. The results of this study suggest that duckweed is a good inducer of cellulase production in T. reesei, and it might aid in decreasing the cost of lignocellulosic materials hydrolysis.
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Hooker CA, Hillman ET, Overton JC, Ortiz-Velez A, Schacht M, Hunnicutt A, Mosier NS, Solomon KV. Hydrolysis of untreated lignocellulosic feedstock is independent of S-lignin composition in newly classified anaerobic fungal isolate, Piromyces sp. UH3-1. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:293. [PMID: 30386430 PMCID: PMC6203967 DOI: 10.1186/s13068-018-1292-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/15/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Plant biomass is an abundant but underused feedstock for bioenergy production due to its complex and variable composition, which resists breakdown into fermentable sugars. These feedstocks, however, are routinely degraded by many uncommercialized microbes such as anaerobic gut fungi. These gut fungi express a broad range of carbohydrate active enzymes and are native to the digestive tracts of ruminants and hindgut fermenters. In this study, we examine gut fungal performance on these substrates as a function of composition, and the ability of this isolate to degrade inhibitory high syringyl lignin-containing forestry residues. RESULTS We isolated a novel fungal specimen from a donkey in Independence, Indiana, United States. Phylogenetic analysis of the Internal Transcribed Spacer 1 sequence classified the isolate as a member of the genus Piromyces within the phylum Neocallimastigomycota (Piromyces sp. UH3-1, strain UH3-1). The isolate penetrates the substrate with an extensive rhizomycelial network and secretes many cellulose-binding enzymes, which are active on various components of lignocellulose. These activities enable the fungus to hydrolyze at least 58% of the glucan and 28% of the available xylan in untreated corn stover within 168 h and support growth on crude agricultural residues, food waste, and energy crops. Importantly, UH3-1 hydrolyzes high syringyl lignin-containing poplar that is inhibitory to many fungi with efficiencies equal to that of low syringyl lignin-containing poplar with no reduction in fungal growth. This behavior is correlated with slight remodeling of the fungal secretome whose composition adapts with substrate to express an enzyme cocktail optimized to degrade the available biomass. CONCLUSIONS Piromyces sp. UH3-1, a newly isolated anaerobic gut fungus, grows on diverse untreated substrates through production of a broad range of carbohydrate active enzymes that are robust to variations in substrate composition. Additionally, UH3-1 and potentially other anaerobic fungi are resistant to inhibitory lignin composition possibly due to changes in enzyme secretion with substrate. Thus, anaerobic fungi are an attractive platform for the production of enzymes that efficiently use mixed feedstocks of variable composition for second generation biofuels. More importantly, our work suggests that the study of anaerobic fungi may reveal naturally evolved strategies to circumvent common hydrolytic inhibitors that hinder biomass usage.
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Affiliation(s)
- Casey A. Hooker
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN 47907-2022 USA
| | - Ethan T. Hillman
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, 155 South Grant Street, West Lafayette, IN 47907-2114 USA
| | - Jonathan C. Overton
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN 47907-2022 USA
| | - Adrian Ortiz-Velez
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
| | - Makayla Schacht
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 USA
| | - Abigail Hunnicutt
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
| | - Nathan S. Mosier
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN 47907-2022 USA
| | - Kevin V. Solomon
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN 47907-2022 USA
- Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, 155 South Grant Street, West Lafayette, IN 47907-2114 USA
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Lopes A, Ferreira Filho E, Moreira L. An update on enzymatic cocktails for lignocellulose breakdown. J Appl Microbiol 2018; 125:632-645. [DOI: 10.1111/jam.13923] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 03/20/2018] [Accepted: 05/14/2018] [Indexed: 12/01/2022]
Affiliation(s)
- A.M. Lopes
- Laboratory of Enzymology; Department of Cellular Biology; University of Brasília; Brasilia DF Brazil
| | - E.X. Ferreira Filho
- Laboratory of Enzymology; Department of Cellular Biology; University of Brasília; Brasilia DF Brazil
| | - L.R.S. Moreira
- Laboratory of Enzymology; Department of Cellular Biology; University of Brasília; Brasilia DF Brazil
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Pisa JH, Manfredi AP, Perotti NI, Romero HG, Breccia JD, Martínez MA. Agrowastes as Feedstock for the Production of Endo-β-Xylanase from Cohnella sp. Strain AR92. J Mol Microbiol Biotechnol 2017; 27:277-288. [DOI: 10.1159/000480541] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 08/17/2017] [Indexed: 11/19/2022] Open
Abstract
Members of <i>Cohnella </i>sp. isolated from a variety of environments have been shown to be glycoside hydrolase producers. Nevertheless, most evaluations of members of this genus are limited to their taxonomic description. The strain AR92, previously identified as belonging to the genus <i>Cohnella</i>, formed a well-supported cluster with <i>C. thailandensis</i> and <i>C. formosensis</i> (>80% bootstrap confidence). Its growth and xylanase production were approached by using a mineral-based medium containing alkali-pretreated sugarcane bagasse as the main carbon source, which was assayed as a convenient source to produce biocatalysts potentially fitting its degradation. By means of a two-step statistical approach, the production of endoxylanase was moderately improved (20%). However, a far more significant improvement was observed (145%), by increasing the inoculum size and lowering the fermentation temperature to 25°C, which is below the optimal growth temperature of the strain AR92 (37°C). The xylanolytic preparation produced by <i>Cohnella</i> sp. AR92 contained mild temperature-active endoxylanase (identified as redundant GH10 family) for the main activity which resulted in xylobiose and xylo-oligosaccharides as the main products from birchwood xylan.
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Kansou K, Rémond C, Paës G, Bonnin E, Tayeb J, Bredeweg B. Testing scientific models using Qualitative Reasoning: Application to cellulose hydrolysis. Sci Rep 2017; 7:14122. [PMID: 29074872 PMCID: PMC5658447 DOI: 10.1038/s41598-017-14281-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/06/2017] [Indexed: 12/17/2022] Open
Abstract
With the accumulation of scientific information in natural science, even experts can find difficult to keep integrating new piece of information. It is critical to explore modelling solutions able to capture information scattered in publications as a computable representation form. Traditional modelling techniques are important in that regard, but relying on numerical information comes with limitations for integrating results from distinct studies, high-level representations can be more suited. We present an approach to stepwise construct mechanistic explanation from selected scientific papers using the Qualitative Reasoning framework. As a proof of concept, we apply the approach to modelling papers about cellulose hydrolysis mechanism, focusing on the causal explanations for the decreasing of hydrolytic rate. Two explanatory QR models are built to capture classical explanations for the phenomenon. Our results show that none of them provides sufficient explanation for a set of basic experimental observations described in the literature. Combining the two explanations into a third one allowed to get a new and sufficient explanation for the experimental results. In domains where numerical data are scarce and strongly related to the experimental conditions, this approach can aid assessing the conceptual validity of an explanation and support integration of knowledge from different sources.
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Affiliation(s)
- Kamal Kansou
- INRA, Biopolymères Interactions Assemblages, BP 71267, 44316, Nantes, France.
| | - Caroline Rémond
- FARE laboratory, INRA, University of Reims Champagne-Ardenne, 51100, Reims, France
| | - Gabriel Paës
- FARE laboratory, INRA, University of Reims Champagne-Ardenne, 51100, Reims, France
| | - Estelle Bonnin
- INRA, Biopolymères Interactions Assemblages, BP 71267, 44316, Nantes, France
| | - Jean Tayeb
- FARE laboratory, INRA, University of Reims Champagne-Ardenne, 51100, Reims, France
| | - Bert Bredeweg
- Informatics Institute, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
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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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Schuerg T, Prahl JP, Gabriel R, Harth S, Tachea F, Chen CS, Miller M, Masson F, He Q, Brown S, Mirshiaghi M, Liang L, Tom LM, Tanjore D, Sun N, Pray TR, Singer SW. Xylose induces cellulase production in Thermoascus aurantiacus. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:271. [PMID: 29167701 PMCID: PMC5688616 DOI: 10.1186/s13068-017-0965-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/07/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Lignocellulosic biomass is an important resource for renewable production of biofuels and bioproducts. Enzymes that deconstruct this biomass are critical for the viability of biomass-based biofuel production processes. Current commercial enzyme mixtures have limited thermotolerance. Thermophilic fungi may provide enzyme mixtures with greater thermal stability leading to more robust processes. Understanding the induction of biomass-deconstructing enzymes in thermophilic fungi will provide the foundation for strategies to construct hyper-production strains. RESULTS Induction of cellulases using xylan was demonstrated during cultivation of the thermophilic fungus Thermoascus aurantiacus. Simulated fed-batch conditions with xylose induced comparable levels of cellulases. These fed-batch conditions were adapted to produce enzymes in 2 and 19 L bioreactors using xylose and xylose-rich hydrolysate from dilute acid pretreatment of corn stover. Enzymes from T. aurantiacus that were produced in the xylose-fed bioreactor demonstrated comparable performance in the saccharification of deacetylated, dilute acid-pretreated corn stover when compared to a commercial enzyme mixture at 50 °C. The T. aurantiacus enzymes retained this activity at of 60 °C while the commercial enzyme mixture was largely inactivated. CONCLUSIONS Xylose induces both cellulase and xylanase production in T. aurantiacus and was used to produce enzymes at up to the 19 L bioreactor scale. The demonstration of induction by xylose-rich hydrolysate and saccharification of deacetylated, dilute acid-pretreated corn stover suggests a scenario to couple biomass pretreatment with onsite enzyme production in a biorefinery. This work further demonstrates the potential for T. aurantiacus as a thermophilic platform for cellulase development.
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Affiliation(s)
- Timo Schuerg
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Raphael Gabriel
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Simon Harth
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Firehiwot Tachea
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Chyi-Shin Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Matthew Miller
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Fabrice Masson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Qian He
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Sarah Brown
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Mona Mirshiaghi
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Ling Liang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Lauren M. Tom
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Ning Sun
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Todd R. Pray
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Steven W. Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
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