The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Ronald P. De Vries - One of the best experts on this subject based on the ideXlab platform.
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developments and opportunities in fungal strain engineering for the production of novel enzymes and enzyme cocktails for Plant Biomass degradation
Biotechnology Advances, 2019Co-Authors: Ana Carolina S Gomes, Miia R. Mäkelä, Kristiina Hildén, Sonia Salazar Cerezo, Ronald P. De VriesAbstract:Abstract Fungal strain engineering is commonly used in many areas of biotechnology, including the production of Plant Biomass degrading enzymes. Its aim varies from the production of specific enzymes to overall increased enzyme production levels and modification of the composition of the enzyme set that is produced by the fungus. Strain engineering involves a diverse range of methodologies, including classical mutagenesis, genetic engineering and genome editing. In this review, the main approaches for strain engineering of filamentous fungi in the field of Plant Biomass degradation will be discussed, including recent and not yet implemented methods, such as CRISPR/Cas9 genome editing and adaptive evolution.
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enzymatic adaptation of podospora anserina to different Plant Biomass provides leads to optimized commercial enzyme cocktails
Biotechnology Journal, 2019Co-Authors: Tiziano Benocci, Paul Daly, Maria Victoria Aguilarpontes, Kathleen Lail, Mei Wang, Anna Lipzen, Igor V Grigoriev, Ronald P. De VriesAbstract:As a late colonizer of herbivore dung, Podospora anserina has evolved an enzymatic machinery to degrade the more recalcitrant fraction of Plant Biomass, suggesting a great potential for biotechnology applications. The authors investigated its transcriptome during growth on two industrial feedstocks, soybean hulls (SBH) and corn stover (CS). Initially, CS and SBH results in the expression of hemicellulolytic and amylolytic genes, respectively, while at later time points a more diverse gene set is induced, especially for SBH. Substrate adaptation is also observed for carbon catabolism. Overall, SBH resulted in a larger diversity of expressed genes, confirming previous proteomics studies. The results not only provide an in depth view on the transcriptomic adaptation of P. anserina to substrate composition, but also point out strategies to improve saccharification of Plant Biomass at the industrial level.
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cultivation of podospora anserina on soybean hulls results in an efficient enzyme cocktail for Plant Biomass hydrolysis
New Biotechnology, 2017Co-Authors: Miia R. Mäkelä, Ourdia Bouzid, Diogo Robl, Harm Post, Mao Peng, Albert J R Heck, Maarten Altelaar, Ronald P. De VriesAbstract:The coprophilic ascomycete fungus Podospora anserina was cultivated on three different Plant Biomasses, i.e. cotton seed hulls (CSH), soybean hulls (SBH) and acid-pretreated wheat straw (WS) for four days, and the potential of the produced enzyme mixtures was compared in the enzymatic saccharification of the corresponding lignocellulose feedstocks. The enzyme cocktail P. anserina produced after three days of growth on SBH showed superior capacity to release reducing sugars from all tested Plant Biomass feedstocks compared to the enzyme mixtures from CSH and WS cultures. Detailed proteomics analysis of the culture supernatants revealed that SBH contained the most diverse set of enzymes targeted on Plant cell wall polymers and was particularly abundant in xylan, mannan and pectin acting enzymes. The importance of lytic polysaccharide monooxygenases (LPMOs) in Plant Biomass deconstruction was supported by identification of 20 out of 33 AA9 LPMOs in the SBH cultures. The results highlight the suitability of P. anserina as a source of Plant cell wall degrading enzymes for biotechnological applications and the importance of selecting the most optimal substrate for the production of enzyme mixtures.
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Regulators of Plant Biomass degradation in ascomycetous fungi
Biotechnology for Biofuels, 2017Co-Authors: Tiziano Benocci, Maria Victoria Aguilar-pontes, Miaomiao Zhou, Bernhard Seiboth, Ronald P. De VriesAbstract:Fungi play a major role in the global carbon cycle because of their ability to utilize Plant Biomass (polysaccharides, proteins, and lignin) as carbon source. Due to the complexity and heterogenic composition of Plant Biomass, fungi need to produce a broad range of degrading enzymes, matching the composition of (part of) the prevalent substrate. This process is dependent on a network of regulators that not only control the extracellular enzymes that degrade the Biomass, but also the metabolic pathways needed to metabolize the resulting monomers. This review will summarize the current knowledge on regulation of Plant Biomass utilization in fungi and compare the differences between fungal species, focusing in particular on the presence or absence of the regulators involved in this process.
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sugar catabolism in aspergillus and other fungi related to the utilization of Plant Biomass
Advances in Applied Microbiology, 2015Co-Authors: Claire Khosravi, Tiziano Benocci, Evy Battaglia, Isabelle Benoit, Ronald P. De VriesAbstract:Fungi are found in all natural and artificial biotopes and can use highly diverse carbon sources. They play a major role in the global carbon cycle by decomposing Plant Biomass and this Biomass is the main carbon source for many fungi. Plant Biomass is composed of cell wall polysaccharides (cellulose, hemicellulose, pectin) and lignin. To degrade cell wall polysaccharides to different monosaccharides, fungi produce a broad range of enzymes with a large variety in activities. Through a series of enzymatic reactions, sugar-specific and central metabolic pathways convert these monosaccharides into energy or metabolic precursors needed for the biosynthesis of biomolecules. This chapter describes the carbon catabolic pathways that are required to efficiently use Plant Biomass as a carbon source. It will give an overview of the known metabolic pathways in fungi, their interconnections, and the differences between fungal species.
Bernard Henrissat - One of the best experts on this subject based on the ideXlab platform.
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integrative visual omics of the white rot fungus polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw Plant Biomass
Biotechnology for Biofuels, 2018Co-Authors: Shingo Miyauchi, Sacha Grisel, Bernard Henrissat, Anaïs Rancon, Elodie Drula, Hayat Hage, Delphine Chaduli, Anne FavelAbstract:Plant Biomass conversion for green chemistry and bio-energy is a current challenge for a modern sustainable bioeconomy. The complex polyaromatic lignin polymers in raw Biomass feedstocks (i.e., agriculture and forestry by-products) are major obstacles for Biomass conversions. White-rot fungi are wood decayers able to degrade all polymers from lignocellulosic Biomass including cellulose, hemicelluloses, and lignin. The white-rot fungus Polyporus brumalis efficiently breaks down lignin and is regarded as having a high potential for the initial treatment of Plant Biomass in its conversion to bio-energy. Here, we describe the extraordinary ability of P. brumalis for lignin degradation using its enzymatic arsenal to break down wheat straw, a lignocellulosic substrate that is considered as a Biomass feedstock worldwide. We performed integrative multi-omics analyses by combining data from the fungal genome, transcriptomes, and secretomes. We found that the fungus possessed an unexpectedly large set of genes coding for Class II peroxidases involved in lignin degradation (19 genes) and GMC oxidoreductases/dehydrogenases involved in generating the hydrogen peroxide required for lignin peroxidase activity and promoting redox cycling of the fungal enzymes involved in oxidative cleavage of lignocellulose polymers (36 genes). The examination of interrelated multi-omics patterns revealed that eleven Class II Peroxidases were secreted by the fungus during fermentation and eight of them where tightly co-regulated with redox cycling enzymatic partners. As a peculiar feature of P. brumalis, we observed gene family extension, up-regulation and secretion of an abundant set of versatile peroxidases and manganese peroxidases, compared with other Polyporales species. The orchestrated secretion of an abundant set of these delignifying enzymes and redox cycling enzymatic partners could contribute to the delignification capabilities of the fungus. Our findings highlight the diversity of wood decay mechanisms present in Polyporales and the potentiality of further exploring this taxonomic order for enzymatic functions of biotechnological interest.
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Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw Plant Biomass
Biotechnology for Biofuels, 2018Co-Authors: Shingo Miyauchi, Sacha Grisel, Bernard Henrissat, Anaïs Rancon, Elodie Drula, Hayat Hage, Delphine Chaduli, Anne Favel, Isabelle Herpoel-gimbert, Francisco J. Ruiz-duenasAbstract:Background: Plant Biomass conversion for green chemistry and bio-energy is a current challenge for a modern sustainable bioeconomy. The complex polyaromatic lignin polymers in raw Biomass feedstocks (i.e., agriculture and forestry by-products) are major obstacles for Biomass conversions. White-rot fungi are wood decayers able to degrade all polymers from lignocellulosic Biomass including cellulose, hemicelluloses, and lignin. The white-rot fungus Polyporus brumalis efficiently breaks down lignin and is regarded as having a high potential for the initial treatment of Plant Biomass in its conversion to bio-energy. Here, we describe the extraordinary ability of P. brumalis for lignin degradation using its enzymatic arsenal to break down wheat straw, a lignocellulosic substrate that is considered as a Biomass feedstock worldwide. Results: We performed integrative multi-omics analyses by combining data from the fungal genome, transcriptomes, and secretomes. We found that the fungus possessed an unexpectedly large set of genes coding for Class II peroxidases involved in lignin degradation (19 genes) and GMC oxidoreductases/dehydrogenases involved in generating the hydrogen peroxide required for lignin peroxidase activity and promoting redox cycling of the fungal enzymes involved in oxidative cleavage of lignocellulose polymers (36 genes). The examination of interrelated multiomics patterns revealed that eleven Class II Peroxidases were secreted by the fungus during fermentation and eight of them where tightly co-regulated with redox cycling enzymatic partners. Conclusion: As a peculiar feature of P. brumalis, we observed gene family extension, up-regulation and secretion of an abundant set of versatile peroxidases and manganese peroxidases, compared with other Polyporales species. The orchestrated secretion of an abundant set of these delignifying enzymes and redox cycling enzymatic partners could contribute to the delignification capabilities of the fungus. Our findings highlight the diversity of wood decay mechanisms present in Polyporales and the potentiality of further exploring this taxonomic order for enzymatic functions of biotechnological interest.
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Visual comparative omics of fungi for Plant Biomass deconstruction
Frontiers Media S.A., 2016Co-Authors: Shingo Miyauchi, Anna Lipzen, Igor V Grigoriev, David Navarro, Robert Riley, Didier Chevret, Sacha Grisel, Jean-guy Berrin, Bernard HenrissatAbstract:Wood-decay fungi are able to decompose Plant cell wall components such as cellulose, hemicelluloses and lignin. Such fungal capabilities may be exploited for the enhancement of directed enzymatic degradation of recalcitrant Plant Biomass. The comparative analysis of wood-decay fungi using a multi-omics approach gives not only new insights into the strategies for decomposing complex Plant materials but also basic knowledge for the design of combinations of enzymes for biotechnological applications. We have developed an analytical workflow, Applied Biomass Conversion Design for Efficient Fungal Green Technology (ABCDEFGT), to simplify the analysis and interpretation of transcriptomic and secretomic data. The ABCDEFGT workflow is primarily constructed of self-organizing maps for grouping genes with similar transcription patterns and an overlay with secreted proteins. The ABCDEFGT workflow produces simple graphic outputs of genome-wide transcriptomes and secretomes. It enables visual inspection without a priori of the omics data, facilitating discoveries of co-regulated genes and proteins. Genome-wide omics landscapes were built with the newly sequenced fungal species Pycnoporus coccineus, Pycnoporus sanguineus, and Pycnoporus cinnabarinus grown on various carbon sources. Integration of the post-genomic data showed a global overlap, confirming the pertinence of the genome-wide approach to study the fungal biological responses to the carbon sources. Our method was compared to a recently-developed clustering method in order to assess the biological relevance of the method and ease of interpretation. Our approach provided a better biological representation of fungal behaviors. The genome-wide multi-omics strategy allowed us to determine the potential synergy of enzymes participating in the decomposition of cellulose, hemicellulose and lignin such as Lytic Polysaccharide Monooxygenases (LPMO), modular enzymes associated with a cellulose binding module (CBM1), and Class II Peroxidase isoforms co-regulated with oxido-reductases. Since enzymes active on Plant Biomass polymers are often members of multi-copy gene families, the strategy was particularly effective to identify the individual gene copies regulated in response to specific growth conditions. Overall, our omics data-mining platform was capable of visualizing genome-wide transcriptional and secretomic profiles for intuitive interpretations and is suitable for exploration of newly-sequenced organisms
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Visual comparative omics of fungi for Plant Biomass deconstruction
Frontiers in Microbiology, 2016Co-Authors: Shingo Miyauchi, Anna Lipzen, Igor V Grigoriev, David Navarro, Robert Riley, Didier Chevret, Sacha Grisel, Jean-guy Berrin, Bernard Henrissat, Marie-noëlle RossoAbstract:Wood-decay fungi contain the cellular mechanisms to decompose such Plant cell wall components as cellulose, hemicellulose, and lignin. A multi-omics approach to the comparative analysis of wood-decay fungi gives not only new insights into their strategies for decomposing recalcitrant Plant Biomass, but also an understanding of how to exploit these mechanisms for biotechnological applications. We have developed an analytical workflow, Applied Biomass Conversion Design for Efficient Fungal Green Technology (ABCDEFGT), to simplify the analysis and interpretation of transcriptomic and secretomic data. ABCDEFGT utilizes self-organizing maps for grouping genes with similar transcription patterns, and an overlay with secreted proteins. The key feature of ABCDEFGT is simple graphic outputs of genome-wide transcriptomic and secretomic topographies, which enables visual inspection without a priori of the omics data and facilitates discoveries of co-regulated genes and proteins. Genome-wide omics landscapes were built with the newly sequenced fungal species Pycnoporus coccineus, Pycnoporus sanguineus, and Pycnoporus cinnabarinus grown on various carbon sources. Integration of the post-genomic data revealed a global overlap, confirming the pertinence of the genome-wide approach. ABCDEFGT was evaluated by comparison with the latest clustering method for ease of output interpretation, and ABCDEFGT gave a better biological representation of fungal behaviors. The genome-wide multi-omics strategy allowed us to determine the potential synergy of particular enzymes decomposing cellulose, hemicellulose, and lignin such as Lytic Polysaccharide Monooxygenases, modular enzymes associated with a cellulose binding module1, and Class II Peroxidase isoforms co-regulated with oxido-reductases. Overall, ABCDEFGT was capable of visualizing genome-wide transcriptional and secretomic profiles for intuitive interpretations and is suitable for exploration of newly-sequenced organisms.
Shingo Miyauchi - One of the best experts on this subject based on the ideXlab platform.
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integrative visual omics of the white rot fungus polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw Plant Biomass
Biotechnology for Biofuels, 2018Co-Authors: Shingo Miyauchi, Sacha Grisel, Bernard Henrissat, Anaïs Rancon, Elodie Drula, Hayat Hage, Delphine Chaduli, Anne FavelAbstract:Plant Biomass conversion for green chemistry and bio-energy is a current challenge for a modern sustainable bioeconomy. The complex polyaromatic lignin polymers in raw Biomass feedstocks (i.e., agriculture and forestry by-products) are major obstacles for Biomass conversions. White-rot fungi are wood decayers able to degrade all polymers from lignocellulosic Biomass including cellulose, hemicelluloses, and lignin. The white-rot fungus Polyporus brumalis efficiently breaks down lignin and is regarded as having a high potential for the initial treatment of Plant Biomass in its conversion to bio-energy. Here, we describe the extraordinary ability of P. brumalis for lignin degradation using its enzymatic arsenal to break down wheat straw, a lignocellulosic substrate that is considered as a Biomass feedstock worldwide. We performed integrative multi-omics analyses by combining data from the fungal genome, transcriptomes, and secretomes. We found that the fungus possessed an unexpectedly large set of genes coding for Class II peroxidases involved in lignin degradation (19 genes) and GMC oxidoreductases/dehydrogenases involved in generating the hydrogen peroxide required for lignin peroxidase activity and promoting redox cycling of the fungal enzymes involved in oxidative cleavage of lignocellulose polymers (36 genes). The examination of interrelated multi-omics patterns revealed that eleven Class II Peroxidases were secreted by the fungus during fermentation and eight of them where tightly co-regulated with redox cycling enzymatic partners. As a peculiar feature of P. brumalis, we observed gene family extension, up-regulation and secretion of an abundant set of versatile peroxidases and manganese peroxidases, compared with other Polyporales species. The orchestrated secretion of an abundant set of these delignifying enzymes and redox cycling enzymatic partners could contribute to the delignification capabilities of the fungus. Our findings highlight the diversity of wood decay mechanisms present in Polyporales and the potentiality of further exploring this taxonomic order for enzymatic functions of biotechnological interest.
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Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw Plant Biomass
Biotechnology for Biofuels, 2018Co-Authors: Shingo Miyauchi, Sacha Grisel, Bernard Henrissat, Anaïs Rancon, Elodie Drula, Hayat Hage, Delphine Chaduli, Anne Favel, Isabelle Herpoel-gimbert, Francisco J. Ruiz-duenasAbstract:Background: Plant Biomass conversion for green chemistry and bio-energy is a current challenge for a modern sustainable bioeconomy. The complex polyaromatic lignin polymers in raw Biomass feedstocks (i.e., agriculture and forestry by-products) are major obstacles for Biomass conversions. White-rot fungi are wood decayers able to degrade all polymers from lignocellulosic Biomass including cellulose, hemicelluloses, and lignin. The white-rot fungus Polyporus brumalis efficiently breaks down lignin and is regarded as having a high potential for the initial treatment of Plant Biomass in its conversion to bio-energy. Here, we describe the extraordinary ability of P. brumalis for lignin degradation using its enzymatic arsenal to break down wheat straw, a lignocellulosic substrate that is considered as a Biomass feedstock worldwide. Results: We performed integrative multi-omics analyses by combining data from the fungal genome, transcriptomes, and secretomes. We found that the fungus possessed an unexpectedly large set of genes coding for Class II peroxidases involved in lignin degradation (19 genes) and GMC oxidoreductases/dehydrogenases involved in generating the hydrogen peroxide required for lignin peroxidase activity and promoting redox cycling of the fungal enzymes involved in oxidative cleavage of lignocellulose polymers (36 genes). The examination of interrelated multiomics patterns revealed that eleven Class II Peroxidases were secreted by the fungus during fermentation and eight of them where tightly co-regulated with redox cycling enzymatic partners. Conclusion: As a peculiar feature of P. brumalis, we observed gene family extension, up-regulation and secretion of an abundant set of versatile peroxidases and manganese peroxidases, compared with other Polyporales species. The orchestrated secretion of an abundant set of these delignifying enzymes and redox cycling enzymatic partners could contribute to the delignification capabilities of the fungus. Our findings highlight the diversity of wood decay mechanisms present in Polyporales and the potentiality of further exploring this taxonomic order for enzymatic functions of biotechnological interest.
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Visual comparative omics of fungi for Plant Biomass deconstruction
Frontiers Media S.A., 2016Co-Authors: Shingo Miyauchi, Anna Lipzen, Igor V Grigoriev, David Navarro, Robert Riley, Didier Chevret, Sacha Grisel, Jean-guy Berrin, Bernard HenrissatAbstract:Wood-decay fungi are able to decompose Plant cell wall components such as cellulose, hemicelluloses and lignin. Such fungal capabilities may be exploited for the enhancement of directed enzymatic degradation of recalcitrant Plant Biomass. The comparative analysis of wood-decay fungi using a multi-omics approach gives not only new insights into the strategies for decomposing complex Plant materials but also basic knowledge for the design of combinations of enzymes for biotechnological applications. We have developed an analytical workflow, Applied Biomass Conversion Design for Efficient Fungal Green Technology (ABCDEFGT), to simplify the analysis and interpretation of transcriptomic and secretomic data. The ABCDEFGT workflow is primarily constructed of self-organizing maps for grouping genes with similar transcription patterns and an overlay with secreted proteins. The ABCDEFGT workflow produces simple graphic outputs of genome-wide transcriptomes and secretomes. It enables visual inspection without a priori of the omics data, facilitating discoveries of co-regulated genes and proteins. Genome-wide omics landscapes were built with the newly sequenced fungal species Pycnoporus coccineus, Pycnoporus sanguineus, and Pycnoporus cinnabarinus grown on various carbon sources. Integration of the post-genomic data showed a global overlap, confirming the pertinence of the genome-wide approach to study the fungal biological responses to the carbon sources. Our method was compared to a recently-developed clustering method in order to assess the biological relevance of the method and ease of interpretation. Our approach provided a better biological representation of fungal behaviors. The genome-wide multi-omics strategy allowed us to determine the potential synergy of enzymes participating in the decomposition of cellulose, hemicellulose and lignin such as Lytic Polysaccharide Monooxygenases (LPMO), modular enzymes associated with a cellulose binding module (CBM1), and Class II Peroxidase isoforms co-regulated with oxido-reductases. Since enzymes active on Plant Biomass polymers are often members of multi-copy gene families, the strategy was particularly effective to identify the individual gene copies regulated in response to specific growth conditions. Overall, our omics data-mining platform was capable of visualizing genome-wide transcriptional and secretomic profiles for intuitive interpretations and is suitable for exploration of newly-sequenced organisms
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Visual comparative omics of fungi for Plant Biomass deconstruction
Frontiers in Microbiology, 2016Co-Authors: Shingo Miyauchi, Anna Lipzen, Igor V Grigoriev, David Navarro, Robert Riley, Didier Chevret, Sacha Grisel, Jean-guy Berrin, Bernard Henrissat, Marie-noëlle RossoAbstract:Wood-decay fungi contain the cellular mechanisms to decompose such Plant cell wall components as cellulose, hemicellulose, and lignin. A multi-omics approach to the comparative analysis of wood-decay fungi gives not only new insights into their strategies for decomposing recalcitrant Plant Biomass, but also an understanding of how to exploit these mechanisms for biotechnological applications. We have developed an analytical workflow, Applied Biomass Conversion Design for Efficient Fungal Green Technology (ABCDEFGT), to simplify the analysis and interpretation of transcriptomic and secretomic data. ABCDEFGT utilizes self-organizing maps for grouping genes with similar transcription patterns, and an overlay with secreted proteins. The key feature of ABCDEFGT is simple graphic outputs of genome-wide transcriptomic and secretomic topographies, which enables visual inspection without a priori of the omics data and facilitates discoveries of co-regulated genes and proteins. Genome-wide omics landscapes were built with the newly sequenced fungal species Pycnoporus coccineus, Pycnoporus sanguineus, and Pycnoporus cinnabarinus grown on various carbon sources. Integration of the post-genomic data revealed a global overlap, confirming the pertinence of the genome-wide approach. ABCDEFGT was evaluated by comparison with the latest clustering method for ease of output interpretation, and ABCDEFGT gave a better biological representation of fungal behaviors. The genome-wide multi-omics strategy allowed us to determine the potential synergy of particular enzymes decomposing cellulose, hemicellulose, and lignin such as Lytic Polysaccharide Monooxygenases, modular enzymes associated with a cellulose binding module1, and Class II Peroxidase isoforms co-regulated with oxido-reductases. Overall, ABCDEFGT was capable of visualizing genome-wide transcriptional and secretomic profiles for intuitive interpretations and is suitable for exploration of newly-sequenced organisms.
Miia R. Mäkelä - One of the best experts on this subject based on the ideXlab platform.
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developments and opportunities in fungal strain engineering for the production of novel enzymes and enzyme cocktails for Plant Biomass degradation
Biotechnology Advances, 2019Co-Authors: Ana Carolina S Gomes, Miia R. Mäkelä, Kristiina Hildén, Sonia Salazar Cerezo, Ronald P. De VriesAbstract:Abstract Fungal strain engineering is commonly used in many areas of biotechnology, including the production of Plant Biomass degrading enzymes. Its aim varies from the production of specific enzymes to overall increased enzyme production levels and modification of the composition of the enzyme set that is produced by the fungus. Strain engineering involves a diverse range of methodologies, including classical mutagenesis, genetic engineering and genome editing. In this review, the main approaches for strain engineering of filamentous fungi in the field of Plant Biomass degradation will be discussed, including recent and not yet implemented methods, such as CRISPR/Cas9 genome editing and adaptive evolution.
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cultivation of podospora anserina on soybean hulls results in an efficient enzyme cocktail for Plant Biomass hydrolysis
New Biotechnology, 2017Co-Authors: Miia R. Mäkelä, Ourdia Bouzid, Diogo Robl, Harm Post, Mao Peng, Albert J R Heck, Maarten Altelaar, Ronald P. De VriesAbstract:The coprophilic ascomycete fungus Podospora anserina was cultivated on three different Plant Biomasses, i.e. cotton seed hulls (CSH), soybean hulls (SBH) and acid-pretreated wheat straw (WS) for four days, and the potential of the produced enzyme mixtures was compared in the enzymatic saccharification of the corresponding lignocellulose feedstocks. The enzyme cocktail P. anserina produced after three days of growth on SBH showed superior capacity to release reducing sugars from all tested Plant Biomass feedstocks compared to the enzyme mixtures from CSH and WS cultures. Detailed proteomics analysis of the culture supernatants revealed that SBH contained the most diverse set of enzymes targeted on Plant cell wall polymers and was particularly abundant in xylan, mannan and pectin acting enzymes. The importance of lytic polysaccharide monooxygenases (LPMOs) in Plant Biomass deconstruction was supported by identification of 20 out of 33 AA9 LPMOs in the SBH cultures. The results highlight the suitability of P. anserina as a source of Plant cell wall degrading enzymes for biotechnological applications and the importance of selecting the most optimal substrate for the production of enzyme mixtures.
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an improved and reproducible protocol for the extraction of high quality fungal rna from Plant Biomass substrates
Fungal Genetics and Biology, 2014Co-Authors: Aleksandrina Patyshakuliyeva, Outi-maaria Sietiö, Miia R. Mäkelä, Ronald P. De Vries, Kristiina HildénAbstract:Isolation of high quantity and quality RNA is a crucial step in the detection of meaningful gene expression data. Obtaining intact fungal RNA from complex lignocellulosic substrates is often difficult, producing low integrity RNA which perform poorly in downstream applications. In this study we developed an RNA extraction method using CsCl centrifugation procedure, modified from previous reports and adapted for isolation of RNA from Plant Biomass. This method provided high level of integrity and good quantity of RNA which were suitable for reliable analyses of gene expression and produced consistent and reproducible results.
De Vries, Ronald P. - One of the best experts on this subject based on the ideXlab platform.
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Glucose-Mediated Repression of Plant Biomass Utilization in the White-Rot Fungus Dichomitus squalens
'American Society for Microbiology', 2019Co-Authors: Daly Paul, Peng Mao, Di Falco Marcos, Lipzen Anna, Wang Mei, Ng Vivian, Grigoriev Igor, Tsang Adrian, Makela, Miia R., De Vries, Ronald P.Abstract:The extent of carbon catabolite repression (CCR) at a global level is unknown in wood-rotting fungi, which are critical to the carbon cycle and are a source of biotechnological enzymes. CCR occurs in the presence of sufficient concentrations of easily metabolizable carbon sources (e.g., glucose) and involves downregulation of the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. We investigated this phenomenon in the white-rot fungus Dichomitus squalens using transcriptomics and exoproteomics. In D. squalens cultures, approximately 7% of genes were repressed in the presence of glucose compared to Avicel or xylan alone. The glucose-repressed genes included the essential components for utilization of Plant Biomass-carbohydrate-active enzyme (CAZyme) and carbon catabolic genes. The majority of polysaccharide-degrading CAZyme genes were repressed and included activities toward all major carbohydrate polymers present in Plant cell walls, while repression of ligninolytic genes also occurred. The transcriptome-level repression of the CAZyme genes observed on the Avicel cultures was strongly supported by exoproteomics. Protease-encoding genes were generally not glucose repressed, indicating their likely dominant role in scavenging for nitrogen rather than carbon. The extent of CCR is surprising, given that D. squalens rarely experiences high free sugar concentrations in its woody environment, and it indicates that biotechnological use of D. squalens for modification of Plant Biomass would benefit from derepressed or constitutively CAZyme-expressing strains. IMPORTANCE White-rot fungi are critical to the carbon cycle because they can mineralize all wood components using enzymes that also have biotechnological potential. The occurrence of carbon catabolite repression (CCR) in white-rot fungi is poorly understood. Previously, CCR in wood-rotting fungi has only been demonstrated for a small number of genes. We demonstrated widespread glucose-mediated CCR of Plant Biomass utilization in the white-rot fungus Dichomitus squalens. This indicates that the CCR mechanism has been largely retained even though wood-rotting fungi rarely experience commonly considered CCR conditions in their woody environment. The general lack of repression of genes encoding proteases along with the reduction in secreted CAZymes during CCR suggested that the retention of CCR may be connected with the need to conserve nitrogen use during growth on nitrogen-scarce wood. The widespread repression indicates that derepressed strains could be beneficial for enzyme production.Peer reviewe
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Glucose-Mediated Repression of Plant Biomass Utilization in the White-Rot Fungus Dichomitus squalens.
eScholarship University of California, 2019Co-Authors: Daly Paul, Peng Mao, Di Falco Marcos, Lipzen Anna, Wang Mei, Ng Vivian, Grigoriev Igor, Tsang Adrian, Makela, Miia R., De Vries, Ronald P.Abstract:The extent of carbon catabolite repression (CCR) at a global level is unknown in wood-rotting fungi, which are critical to the carbon cycle and are a source of biotechnological enzymes. CCR occurs in the presence of sufficient concentrations of easily metabolizable carbon sources (e.g., glucose) and involves downregulation of the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. We investigated this phenomenon in the white-rot fungus Dichomitus squalens using transcriptomics and exoproteomics. In D. squalens cultures, approximately 7% of genes were repressed in the presence of glucose compared to Avicel or xylan alone. The glucose-repressed genes included the essential components for utilization of Plant Biomass-carbohydrate-active enzyme (CAZyme) and carbon catabolic genes. The majority of polysaccharide-degrading CAZyme genes were repressed and included activities toward all major carbohydrate polymers present in Plant cell walls, while repression of ligninolytic genes also occurred. The transcriptome-level repression of the CAZyme genes observed on the Avicel cultures was strongly supported by exoproteomics. Protease-encoding genes were generally not glucose repressed, indicating their likely dominant role in scavenging for nitrogen rather than carbon. The extent of CCR is surprising, given that D. squalens rarely experiences high free sugar concentrations in its woody environment, and it indicates that biotechnological use of D. squalens for modification of Plant Biomass would benefit from derepressed or constitutively CAZyme-expressing strains.IMPORTANCE White-rot fungi are critical to the carbon cycle because they can mineralize all wood components using enzymes that also have biotechnological potential. The occurrence of carbon catabolite repression (CCR) in white-rot fungi is poorly understood. Previously, CCR in wood-rotting fungi has only been demonstrated for a small number of genes. We demonstrated widespread glucose-mediated CCR of Plant Biomass utilization in the white-rot fungus Dichomitus squalens This indicates that the CCR mechanism has been largely retained even though wood-rotting fungi rarely experience commonly considered CCR conditions in their woody environment. The general lack of repression of genes encoding proteases along with the reduction in secreted CAZymes during CCR suggested that the retention of CCR may be connected with the need to conserve nitrogen use during growth on nitrogen-scarce wood. The widespread repression indicates that derepressed strains could be beneficial for enzyme production
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Glucose-Mediated Repression of Plant Biomass Utilization in the White-Rot Fungus Dichomitus squalens
2019Co-Authors: Daly Paul, Peng Mao, Di Falco Marcos, Lipzen Anna, Wang Mei, Ng Vivian, Grigoriev Igor, Tsang Adrian, Makela, Miia R., De Vries, Ronald P.Abstract:The extent of carbon catabolite repression (CCR) at a global level is unknown in wood-rotting fungi, which are critical to the carbon cycle and are a source of biotechnological enzymes. CCR occurs in the presence of sufficient concentrations of easily metabolizable carbon sources (e.g., glucose) and involves downregulation of the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. We investigated this phenomenon in the white-rot fungus Dichomitus squalens using transcriptomics and exoproteomics. In D. squalens cultures, approximately 7% of genes were repressed in the presence of glucose compared to Avicel or xylan alone. The glucose-repressed genes included the essential components for utilization of Plant Biomass—carbohydrate-active enzyme (CAZyme) and carbon catabolic genes. The majority of polysaccharide-degrading CAZyme genes were repressed and included activities toward all major carbohydrate polymers present in Plant cell walls, while repression of ligninolytic genes also occurred. The transcriptome-level repression of the CAZyme genes observed on the Avicel cultures was strongly supported by exoproteomics. Protease-encoding genes were generally not glucose repressed, indicating their likely dominant role in scavenging for nitrogen rather than carbon. The extent of CCR is surprising, given that D. squalens rarely experiences high free sugar concentrations in its woody environment, and it indicates that biotechnological use of D. squalens for modification of Plant Biomass would benefit from derepressed or constitutively CAZyme-expressing strains
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Cultivation of Podospora anserina on soybean hulls results in an efficient enzyme cocktail for Plant Biomass hydrolysis
'Elsevier BV', 2017Co-Authors: Makela, Miia R., Peng Mao, Bouzid Ourdia, Robl Diogo, Post Harm, Heck Albert, Altelaar Maarten, De Vries, Ronald P.Abstract:The coprophilic ascomycete fungus Podospora anserina was cultivated on three different Plant Biomasses, i.e. cotton seed hulls (CSH), soybean hulls (SBH) and acid-pretreated wheat straw (WS) for four days, and the potential of the produced enzyme mixtures was compared in the enzymatic saccharification of the corresponding lignocellulose feedstocks. The enzyme cocktail P. anserina produced after three days of growth on SBH showed superior capacity to release reducing sugars from all tested Plant Biomass feedstocks compared to the enzyme mixtures from CSH and WS cultures. Detailed proteomics analysis of the culture supernatants revealed that SBH contained the most diverse set of enzymes targeted on Plant cell wall polymers and was particularly abundant in xylan, mannan and pectin acting enzymes. The importance of lytic polysaccharide monooxygenases (LPMOs) in Plant Biomass deconstruction was supported by identification of 20 out of 33 AA9 LPMOs in the SBH cultures. The results highlight the suitability of P. anserina as a source of Plant cell wall degrading enzymes for biotechnological applications and the importance of selecting the most optimal substrate for the production of enzyme mixtures. (C) 2017 Elsevier B.V. All rights reserved.Peer reviewe
