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Pasari N, Gupta M, Sinha T, Ogunmolu FE, Yazdani SS. Systematic identification of CAZymes and transcription factors in the hypercellulolytic fungus Penicillium funiculosum NCIM1228 involved in lignocellulosic biomass degradation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:150. [PMID: 37794424 PMCID: PMC10552389 DOI: 10.1186/s13068-023-02399-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023]
Abstract
BACKGROUND Penicillium funiculosum NCIM1228 is a filamentous fungus that was identified in our laboratory to have high cellulolytic activity. Analysis of its secretome suggested that it responds to different carbon substrates by secreting specific enzymes capable of digesting those substrates. This phenomenon indicated the presence of a regulatory system guiding the expression of these hydrolyzing enzymes. Since transcription factors (TFs) are the key players in regulating the expression of enzymes, this study aimed first to identify the complete repertoire of Carbohydrate Active Enzymes (CAZymes) and TFs coded in its genome. The regulation of CAZymes was then analysed by studying the expression pattern of these CAZymes and TFs in different carbon substrates-Avicel (cellulosic substrate), wheat bran (WB; hemicellulosic substrate), Avicel + wheat bran, pre-treated wheat straw (a potential substrate for lignocellulosic ethanol), and glucose (control). RESULTS The P. funiculosum NCIM1228 genome was sequenced, and 10,739 genes were identified in its genome. These genes included a total of 298 CAZymes and 451 TF coding genes. A distinct expression pattern of the CAZymes was observed in different carbon substrates tested. Core cellulose hydrolyzing enzymes were highly expressed in the presence of Avicel, while pre-treated wheat straw and Avicel + wheat bran induced a mixture of CAZymes because of their heterogeneous nature. Wheat bran mainly induced hemicellulases, and the least number of CAZymes were expressed in glucose. TFs also exhibited distinct expression patterns in each of the carbon substrates. Though most of these TFs have not been functionally characterized before, homologs of NosA, Fcr1, and ATF21, which have been known to be involved in fruiting body development, protein secretion and stress response, were identified. CONCLUSIONS Overall, the P. funiculosum NCIM1228 genome was sequenced, and the CAZymes and TFs present in its genome were annotated. The expression of the CAZymes and TFs in response to various polymeric sugars present in the lignocellulosic biomass was identified. This work thus provides a comprehensive mapping of transcription factors (TFs) involved in regulating the production of biomass hydrolyzing enzymes.
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Affiliation(s)
- Nandita Pasari
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Mayank Gupta
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Tulika Sinha
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Funso Emmanuel Ogunmolu
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India.
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India.
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Liu D, Garrigues S, de Vries RP. Heterologous protein production in filamentous fungi. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12660-8. [PMID: 37405433 PMCID: PMC10386965 DOI: 10.1007/s00253-023-12660-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/06/2023]
Abstract
Filamentous fungi are able to produce a wide range of valuable proteins and enzymes for many industrial applications. Recent advances in fungal genomics and experimental technologies are rapidly changing the approaches for the development and use of filamentous fungi as hosts for the production of both homologous and heterologous proteins. In this review, we highlight the benefits and challenges of using filamentous fungi for the production of heterologous proteins. We review various techniques commonly employed to improve the heterologous protein production in filamentous fungi, such as strong and inducible promoters, codon optimization, more efficient signal peptides for secretion, carrier proteins, engineering of glycosylation sites, regulation of the unfolded protein response and endoplasmic reticulum associated protein degradation, optimization of the intracellular transport process, regulation of unconventional protein secretion, and construction of protease-deficient strains. KEY POINTS: • This review updates the knowledge on heterologous protein production in filamentous fungi. • Several fungal cell factories and potential candidates are discussed. • Insights into improving heterologous gene expression are given.
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Affiliation(s)
- Dujuan Liu
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Department of Food Biotechnology, Instituto de Agroquímica Y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.
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Taxeidis G, Nikolaivits E, Siaperas R, Gkountela C, Vouyiouka S, Pantelic B, Nikodinovic-Runic J, Topakas E. Triggering and identifying the polyurethane and polyethylene-degrading machinery of filamentous fungi secretomes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 325:121460. [PMID: 36940913 DOI: 10.1016/j.envpol.2023.121460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
The uncontrollable disposal of plastic waste has raised the concern of the scientific community, which tries to face this environmental burden by discovering and applying new techniques. Regarding the biotechnology field, several important microorganisms possessing the necessary enzymatic arsenal to utilize recalcitrant synthetic polymers as an energy source have been discovered. In the present study, we screened various fungi for their ability to degrade intact polymers, such as ether-based polyurethane (PU) and low-density polyethylene (LDPE). For this, ImpranIil® DLN-SD and a mixture of long-chain alkanes were used as sole carbon sources, indicating not only the most promising strains in agar plate screening but also inducing the secretion of depolymerizing enzymatic activities, useful for polymer degradation. The agar plate screening revealed three fungal strains belonging to Fusarium and Aspergillus genera, whose secretome was further studied for its ability to degrade the aforementioned non-treated polymers. Specifically for ether-based PU, the secretome of a Fusarium species reduced the sample mass and the average molecular weight of the polymer by 24.5 and 20.4%, respectively, while the secretome of an Aspergillus species caused changes in the molecular structure of LDPE, as evidenced by FTIR. The proteomics analysis revealed that the enzymatic activities induced in presence of Impranil® DLN-SD can be associated with urethane bond cleavage, a fact which was also supported by the observed degradation of the ether-based PU. Although, the mechanism of LDPE degradation was not completely elucidated, the presence of oxidative enzymes could be the main factor contributing to polymer modification.
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Affiliation(s)
- George Taxeidis
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Romanos Siaperas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Christina Gkountela
- Laboratory of Polymer Technology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Stamatina Vouyiouka
- Laboratory of Polymer Technology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Brana Pantelic
- Eco-Biotechnology & Drug Development Group, Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000, Belgrade, Serbia
| | - Jasmina Nikodinovic-Runic
- Eco-Biotechnology & Drug Development Group, Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000, Belgrade, Serbia
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece.
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Guo H, He T, Lee DJ. Contemporary proteomic research on lignocellulosic enzymes and enzymolysis: A review. BIORESOURCE TECHNOLOGY 2022; 344:126263. [PMID: 34728359 DOI: 10.1016/j.biortech.2021.126263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
This review overviewed the current researches on the isolation of novel strains, the development of novel identification protocols, the key enzymes and their synergistic interactions with other functional enzyme systems, and the strategies for enhancing enzymolysis efficiencies. The main obstacle for realizing biorefinery of lignocellulosic biomass to biofuels or biochemicals is the high cost of enzymolysis stage. Therefore, research prospects to reduce the costs for lignocellulose hydrolysis were outlined.
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Affiliation(s)
- Hongliang Guo
- College of Forestry, Northeast Forestry University, Harbin 150040, China; College of Food Engineering, Harbin University of Commerce, Harbin 150076, China
| | - Tongyuan He
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tang, Hong Kong.
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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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Randhawa A, Pasari N, Sinha T, Gupta M, Nair AM, Ogunyewo OA, Verma S, Verma PK, Yazdani SS. Blocking drug efflux mechanisms facilitate genome engineering process in hypercellulolytic fungus, Penicillium funiculosum NCIM1228. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:31. [PMID: 33494787 PMCID: PMC7836482 DOI: 10.1186/s13068-021-01883-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/09/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Penicillium funiculosum NCIM1228 is a non-model filamentous fungus that produces high-quality secretome for lignocellulosic biomass saccharification. Despite having desirable traits to be an industrial workhorse, P. funiculosum has been underestimated due to a lack of reliable genetic engineering tools. Tolerance towards common fungal antibiotics had been one of the major hindrances towards development of reliable transformation tools against the non-model fungi. In this study, we sought to understand the mechanism of drug tolerance of P. funiculosum and the provision to counter it. We then attempted to identify a robust method of transformation for genome engineering of this fungus. RESULTS Penicillium funiculosum showed a high degree of drug tolerance towards hygromycin, zeocin and nourseothricin, thereby hindering their use as selectable markers to obtain recombinant transformants. Transcriptome analysis suggested a high level expression of efflux pumps belonging to ABC and MFS family, especially when complex carbon was used in growth media. Antibiotic selection medium was optimized using a combination of efflux pump inhibitors and suitable carbon source to prevent drug tolerability. Protoplast-mediated and Agrobacterium-mediated transformation were attempted for identifying efficiencies of linear and circular DNA in performing genetic manipulation. After finding Ti-plasmid-based Agrobacterium-mediated transformation more suitable for P. funiculosum, we improvised the system to achieve random and homologous recombination-based gene integration and deletion, respectively. We found single-copy random integration of the T-DNA cassette and could achieve 60% efficiency in homologous recombination-based gene deletions. A faster, plasmid-free, and protoplast-based CRISPR/Cas9 gene-editing system was also developed for P. funiculosum. To show its utility in P. funiculosum, we deleted the gene coding for the most abundant cellulase Cellobiohydrolase I (CBH1) using a pair of sgRNA directed towards both ends of cbh1 open reading frame. Functional analysis of ∆cbh1 strain revealed its essentiality for the cellulolytic trait of P. funiculosum secretome. CONCLUSIONS In this study, we addressed drug tolerability of P. funiculosum and developed an optimized toolkit for its genome modification. Hence, we set the foundation for gene function analysis and further genetic improvements of P. funiculosum using both traditional and advanced methods.
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Affiliation(s)
- Anmoldeep Randhawa
- 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
| | - Nandita Pasari
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
- National Institute of Plant Genome Research, New Delhi, 110067, India
| | - Tulika Sinha
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Mayank Gupta
- 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
| | - Anju M Nair
- 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
| | - Olusola A Ogunyewo
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Sandhya Verma
- National Institute of Plant Genome Research, New Delhi, 110067, India
| | | | - 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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Synergistic Action of a Lytic Polysaccharide Monooxygenase and a Cellobiohydrolase from Penicillium funiculosum in Cellulose Saccharification under High-Level Substrate Loading. Appl Environ Microbiol 2020; 86:AEM.01769-20. [PMID: 32978122 DOI: 10.1128/aem.01769-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/15/2020] [Indexed: 12/25/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are crucial industrial enzymes required in the biorefinery industry as well as in the natural carbon cycle. These enzymes, known to catalyze the oxidative cleavage of glycosidic bonds, are produced by numerous bacterial and fungal species to assist in the degradation of cellulosic biomass. In this study, we annotated and performed structural analysis of an uncharacterized LPMO from Penicillium funiculosum (PfLPMO9) based on computational methods in an attempt to understand the behavior of this enzyme in biomass degradation. PfLPMO9 exhibited 75% and 36% sequence identities with LPMOs from Thermoascus aurantiacus (TaLPMO9A) and Lentinus similis (LsLPMO9A), respectively. Furthermore, multiple fungal genetic manipulation tools were employed to simultaneously overexpress LPMO and cellobiohydrolase I (CBH1) in a catabolite-derepressed strain of Penicillium funiculosum, PfMig188 (an engineered variant of P. funiculosum), to improve its saccharification performance toward acid-pretreated wheat straw (PWS) at 20% substrate loading. The resulting transformants showed improved LPMO and CBH1 expression at both the transcriptional and translational levels, with ∼200% and ∼66% increases in ascorbate-induced LPMO and Avicelase activities, respectively. While the secretome of PfMig88 overexpressing LPMO or CBH1 increased the saccharification of PWS by 6% or 13%, respectively, over the secretome of PfMig188 at the same protein concentration, the simultaneous overexpression of these two genes led to a 20% increase in saccharification efficiency over that observed with PfMig188, which accounted for 82% saccharification of PWS under 20% substrate loading.IMPORTANCE The enzymatic hydrolysis of cellulosic biomass by cellulases continues to be a significant bottleneck in the development of second-generation biobased industries. While increasing efforts are being made to obtain indigenous cellulases for biomass hydrolysis, the high production cost of this enzyme remains a crucial challenge affecting its wide availability for the efficient utilization of cellulosic materials. This is because it is challenging to obtain an enzymatic cocktail with balanced activity from a single host. This report describes the annotation and structural analysis of an uncharacterized lytic polysaccharide monooxygenase (LPMO) gene in Penicillium funiculosum and its impact on biomass deconstruction upon overexpression in a catabolite-derepressed strain of P. funiculosum Cellobiohydrolase I (CBH1), which is the most important enzyme produced by many cellulolytic fungi for the saccharification of crystalline cellulose, was further overexpressed simultaneously with LPMO. The resulting secretome was analyzed for enhanced LPMO and exocellulase activities and the corresponding improvement in saccharification performance (by ∼20%) under high-level substrate loading using a minimal amount of protein.
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Ogunyewo OA, Randhawa A, Joshi M, Jain KK, Wadekar P, Odaneth AA, Lali AM, Yazdani SS. Engineered Penicillium funiculosum produces potent lignocellulolytic enzymes for saccharification of various pretreated biomasses. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Champreda V, Mhuantong W, Lekakarn H, Bunterngsook B, Kanokratana P, Zhao XQ, Zhang F, Inoue H, Fujii T, Eurwilaichitr L. Designing cellulolytic enzyme systems for biorefinery: From nature to application. J Biosci Bioeng 2019; 128:637-654. [PMID: 31204199 DOI: 10.1016/j.jbiosc.2019.05.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/06/2019] [Accepted: 05/11/2019] [Indexed: 12/14/2022]
Abstract
Cellulolytic enzymes play a key role on conversion of lignocellulosic plant biomass to biofuels and biochemicals in sugar platform biorefineries. In this review, we survey composite carbohydrate-active enzymes (CAZymes) among groups of cellulolytic fungi and bacteria that exist under aerobic and anaerobic conditions. Recent advances in designing effective cellulase mixtures are described, starting from the most complex microbial consortium-based enzyme preparations, to single-origin enzymes derived from intensively studied cellulase producers such as Trichoderma reesei, Talaromyces cellulolyticus, and Penicellium funiculosum, and the simplest minimal enzyme systems comprising selected sets of mono-component enzymes tailor-made for specific lignocellulosic substrates. We provide a comprehensive update on studies in developing high-performance cellulases for biorefineries.
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Affiliation(s)
- Verawat Champreda
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand.
| | - Wuttichai Mhuantong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Hataikarn Lekakarn
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Benjarat Bunterngsook
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Pattanop Kanokratana
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hiroyuki Inoue
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Hiroshima 739-0046, Japan
| | - Tatsuya Fujii
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Hiroshima 739-0046, Japan
| | - Lily Eurwilaichitr
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
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Llanos A, Déjean S, Neugnot-Roux V, François JM, Parrou JL. Carbon sources and XlnR-dependent transcriptional landscape of CAZymes in the industrial fungus Talaromyces versatilis: when exception seems to be the rule. Microb Cell Fact 2019; 18:14. [PMID: 30691469 PMCID: PMC6348686 DOI: 10.1186/s12934-019-1062-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/13/2019] [Indexed: 11/19/2022] Open
Abstract
Background Research on filamentous fungi emphasized the remarkable redundancy in genes encoding hydrolytic enzymes, the similarities but also the large differences in their expression, especially through the role of the XlnR/XYR1 transcriptional activator. The purpose of this study was to evaluate the specificities of the industrial fungus Talaromyces versatilis, getting clues into the role of XlnR and the importance of glucose repression at the transcriptional level, to provide further levers for cocktail production. Results By studying a set of 62 redundant genes representative of several categories of enzymes, our results underlined the huge plasticity of transcriptional responses when changing nutritional status. As a general trend, the more heterogeneous the substrate, the more efficient to trigger activation. Genetic modifications of xlnR led to significant reorganisation of transcriptional patterns. Just a minimal set of genes actually fitted in a simplistic model of regulation by a transcriptional activator, and this under specific substrates. On the contrary, the diversity of xlnR+ versus ΔxlnR responses illustrated the existence of complex and unpredicted patterns of co-regulated genes that were highly dependent on the culture condition, even between genes that encode members of a functional category of enzymes. They notably revealed a dual, substrate-dependant repressor-activator role of XlnR, with counter-intuitive transcripts regulations that targeted specific genes. About glucose, it appeared as a formal repressive sugar as we observed a massive repression of most genes upon glucose addition to the mycelium grown on wheat straw. However, we also noticed a positive role of this sugar on the basal expression of a few genes, (notably those encoding cellulases), showing again the strong dependence of these regulatory mechanisms upon promoter and nutritional contexts. Conclusions The diversity of transcriptional patterns appeared to be the rule, while common and stable behaviour, both within gene families and with fungal literature, the exception. The setup of a new biotechnological process to reach optimized, if not customized expression patterns of enzymes, hence appeared tricky just relying on published data that can lead, in the best scenario, to approximate trends. We instead encourage preliminary experimental assays, carried out in the context of interest to reassess gene responses, as a mandatory step before thinking in (genetic) strategies for the improvement of enzyme production in fungi.![]() Electronic supplementary material The online version of this article (10.1186/s12934-019-1062-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Agustina Llanos
- LISBP, Université de Toulouse, INSA, INRA, CNRS, Toulouse, France.,Adisseo France S.A.S, 135 Avenue de Rangueil, 31077, Toulouse, France
| | - Sébastien Déjean
- Institut de Mathématiques de Toulouse, UMR5219-Université de Toulouse; CNRS-UPS, 31062, Toulouse Cedex 9, France
| | | | - Jean M François
- LISBP, Université de Toulouse, INSA, INRA, CNRS, Toulouse, France
| | - Jean-Luc Parrou
- LISBP, Université de Toulouse, INSA, INRA, CNRS, Toulouse, France.
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Ren Z, You W, Wu S, Poetsch A, Xu C. Secretomic analyses of Ruminiclostridium papyrosolvens reveal its enzymatic basis for lignocellulose degradation. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:183. [PMID: 31338125 PMCID: PMC6628489 DOI: 10.1186/s13068-019-1522-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 07/05/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Efficient biotechnological conversion of lignocellulosic biomass to valuable products, such as transportation biofuels, is ecologically attractive, yet requires substantially improved mechanistic understanding and optimization to become economically feasible. Cellulolytic clostridia, such as Ruminiclostridium papyrosolvens (previously Clostridium papyrosolvens), produce a wide variety of carbohydrate-active enzymes (CAZymes) including extracellular multienzyme complexes-cellulosomes with different specificities for enhanced cellulosic biomass degradation. Identification of the secretory components, especially CAZymes, during bacterial growth on lignocellulose and their influence on bacterial catalytic capabilities provide insight into construction of potent cellulase systems of cell factories tuned or optimized for the targeted substrate by matching the type and abundance of enzymes and corresponding transporters. RESULTS In this study, we firstly predicted a total of 174 putative CAZymes from the genome of R. papyrosolvens, including 74 cellulosomal components. To explore profile of secreted proteins involved in lignocellulose degradation, we compared the secretomes of R. papyrosolvens grown on different substrates using label-free quantitative proteomics. CAZymes, extracellular solute-binding proteins (SBPs) of transport systems and proteins involved in spore formation were enriched in the secretome of corn stover for lignocellulose degradation. Furthermore, compared with free CAZymes, complex CAZymes (cellulosomal components) had larger fluctuations in variety and abundance of enzymes among four carbon sources. In particular, cellulosomal proteins encoded by the cip-cel operon and the xyl-doc gene cluster had the highest abundance with corn stover as substrate. Analysis of differential expression of CAZymes revealed a substrate-dependent secretion pattern of CAZymes, which was consistent with their catalytic activity from each secretome determined on different cellulosic substrates. The results suggest that the expression of CAZymes is regulated by the type of substrate in the growth medium. CONCLUSIONS In the present study, our results demonstrated the complexity of the lignocellulose degradation systems of R. papyrosolvens and showed the potency of its biomass degradation activity. Differential proteomic analyses and activity assays of CAZymes secreted by R. papyrosolvens suggested a distinct environment-sensing strategy for cellulose utilization in which R. papyrosolvens modulated the composition of the CAZymes, especially cellulosome, according to the degradation state of its natural substrate.
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Affiliation(s)
- Zhenxing Ren
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 Shanxi China
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006 Shanxi China
| | - Wuxin You
- Department of Plant Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Shasha Wu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 Shanxi China
| | - Ansgar Poetsch
- Department of Plant Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
- School of Biomedical and Healthcare Sciences, University of Plymouth, Plymouth, PL48AA UK
| | - Chenggang Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 Shanxi China
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