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3. Discovery and Functional Analysis of a Salicylic Acid Hydroxylase from Aspergillus niger

Author

Lubbers, Ronnie J M, Dilokpimol, Adiphol, Visser, Jaap, Hildén, Kristiina S, Mäkelä, Miia R, de Vries, Ronald P, Lubbers, Ronnie J M, Dilokpimol, Adiphol, Visser, Jaap, Hildén, Kristiina S, Mäkelä, Miia R, and de Vries, Ronald P

Abstract

Salicylic acid plays an important role in the plant immune response, and its degradation is therefore important for plant-pathogenic fungi. However, many nonpathogenic microorganisms can also degrade salicylic acid. In the filamentous fungus Aspergillus niger, two salicylic acid metabolic pathways have been suggested. The first pathway converts salicylic acid to catechol by a salicylate hydroxylase (ShyA). In the second pathway, salicylic acid is 3-hydroxylated to 2,3-dihydroxybenzoic acid, followed by decarboxylation to catechol by 2,3-dihydroxybenzoate decarboxylase (DhbA). A. niger cleaves the aromatic ring of catechol catalyzed by catechol 1,2-dioxygenase (CrcA) to form cis,cis-muconic acid. However, the identification and role of the genes and characterization of the enzymes involved in these pathways are lacking. In this study, we used transcriptome data of A. niger grown on salicylic acid to identify genes (shyA and crcA) involved in salicylic acid metabolism. Heterologous production in Escherichia coli followed by biochemical characterization confirmed the function of ShyA and CrcA. The combination of ShyA and CrcA demonstrated that cis,cis-muconic acid can be produced from salicylic acid. In addition, the in vivo roles of shyA, dhbA, and crcA were studied by creating A. niger deletion mutants which revealed the role of these genes in the fungal metabolism of salicylic acid.IMPORTANCE Nonrenewable petroleum sources are being depleted, and therefore, alternative sources are needed. Plant biomass is one of the most abundant renewable sources on Earth and is efficiently degraded by fungi. In order to utilize plant biomass efficiently, knowledge about the fungal metabolic pathways and the genes and enzymes involved is essential to create efficient strategies for producing valuable compounds such as cis,cis-muconic acid. cis,cis-Muconic acid is an important platform chemical that is used to synthesize nylon, polyethylene terephthalate (PET), polyurethane, resi

Published
2021

4. CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner

Author

Peng, Mao, Khosravi, Claire, Lubbers, Ronnie J M, Kun, Roland S, Aguilar Pontes, Maria Victoria, Battaglia, Evy, Chen, Cindy, Dalhuijsen, Sacha, Daly, Paul, Lipzen, Anna, Ng, Vivian, Yan, Juying, Wang, Mei, Visser, Jaap, Grigoriev, Igor V, Mäkelä, Miia R, de Vries, Ronald P, Peng, Mao, Khosravi, Claire, Lubbers, Ronnie J M, Kun, Roland S, Aguilar Pontes, Maria Victoria, Battaglia, Evy, Chen, Cindy, Dalhuijsen, Sacha, Daly, Paul, Lipzen, Anna, Ng, Vivian, Yan, Juying, Wang, Mei, Visser, Jaap, Grigoriev, Igor V, Mäkelä, Miia R, and de Vries, Ronald P

Abstract

Carbon catabolite repression enables fungi to utilize the most favourable carbon source in the environment, and is mediated by a key regulator, CreA, in most fungi. CreA-mediated regulation has mainly been studied at high monosaccharide concentrations, an uncommon situation in most natural biotopes. In nature, many fungi rely on plant biomass as their major carbon source by producing enzymes to degrade plant cell wall polysaccharides into metabolizable sugars. To determine the role of CreA when fungi grow in more natural conditions and in particular with respect to degradation and conversion of plant cell walls, we compared transcriptomes of a creA deletion and reference strain of the ascomycete Aspergillus niger during growth on sugar beet pulp and wheat bran. Transcriptomics, extracellular sugar concentrations and growth profiling of A. niger on a variety of carbon sources, revealed that also under conditions with low concentrations of free monosaccharides, CreA has a major effect on gene expression in a strong time and substrate composition dependent manner. In addition, we compared the CreA regulon from five fungi during their growth on crude plant biomass or cellulose. It showed that CreA commonly regulated genes related to carbon metabolism, sugar transport and plant cell wall degrading enzymes across different species. We therefore conclude that CreA has a crucial role for fungi also in adapting to low sugar concentrations as occurring in their natural biotopes, which is supported by the presence of CreA orthologs in nearly all fungi.

Published
2021

5. Vanillic acid and methoxyhydroquinone production from guaiacyl units and related aromatic compounds using Aspergillus niger cell factories

Author

Lubbers, Ronnie J.M., Dilokpimol, Adiphol, Nousiainen, Paula A., Cioc, Răzvan C., Visser, Jaap, Bruijnincx, Pieter C.A., de Vries, Ronald P., Lubbers, Ronnie J.M., Dilokpimol, Adiphol, Nousiainen, Paula A., Cioc, Răzvan C., Visser, Jaap, Bruijnincx, Pieter C.A., and de Vries, Ronald P.

Abstract

Background: The aromatic compounds vanillin and vanillic acid are important fragrances used in the food, beverage, cosmetic and pharmaceutical industries. Currently, most aromatic compounds used in products are chemically synthesized, while only a small percentage is extracted from natural sources. The metabolism of vanillin and vanillic acid has been studied for decades in microorganisms and many studies have been conducted that showed that both can be produced from ferulic acid using bacteria. In contrast, the degradation of vanillin and vanillic acid by fungi is poorly studied and no genes involved in this metabolic pathway have been identified. In this study, we aimed to clarify this metabolic pathway in Aspergillus niger and identify the genes involved. Results: Using whole-genome transcriptome data, four genes involved in vanillin and vanillic acid metabolism were identified. These include vanillin dehydrogenase (vdhA), vanillic acid hydroxylase (vhyA), and two genes encoding novel enzymes, which function as methoxyhydroquinone 1,2-dioxygenase (mhdA) and 4-oxo-monomethyl adipate esterase (omeA). Deletion of these genes in A. niger confirmed their role in aromatic metabolism and the enzymatic activities of these enzymes were verified. In addition, we demonstrated that mhdA and vhyA deletion mutants can be used as fungal cell factories for the accumulation of vanillic acid and methoxyhydroquinone from guaiacyl lignin units and related aromatic compounds. Conclusions: This study provides new insights into the fungal aromatic metabolic pathways involved in the degradation of guaiacyl units and related aromatic compounds. The identification of the involved genes unlocks new potential for engineering aromatic compound-producing fungal cell factories.

Published
2021

6. CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner.

Author

Peng, Mao, Peng, Mao, Khosravi, Claire, Lubbers, Ronnie JM, Kun, Roland S, Aguilar Pontes, Maria Victoria, Battaglia, Evy, Chen, Cindy, Dalhuijsen, Sacha, Daly, Paul, Lipzen, Anna, Ng, Vivian, Yan, Juying, Wang, Mei, Visser, Jaap, Grigoriev, Igor V, Mäkelä, Miia R, de Vries, Ronald P, Peng, Mao, Peng, Mao, Khosravi, Claire, Lubbers, Ronnie JM, Kun, Roland S, Aguilar Pontes, Maria Victoria, Battaglia, Evy, Chen, Cindy, Dalhuijsen, Sacha, Daly, Paul, Lipzen, Anna, Ng, Vivian, Yan, Juying, Wang, Mei, Visser, Jaap, Grigoriev, Igor V, Mäkelä, Miia R, and de Vries, Ronald P

Abstract

Carbon catabolite repression enables fungi to utilize the most favourable carbon source in the environment, and is mediated by a key regulator, CreA, in most fungi. CreA-mediated regulation has mainly been studied at high monosaccharide concentrations, an uncommon situation in most natural biotopes. In nature, many fungi rely on plant biomass as their major carbon source by producing enzymes to degrade plant cell wall polysaccharides into metabolizable sugars. To determine the role of CreA when fungi grow in more natural conditions and in particular with respect to degradation and conversion of plant cell walls, we compared transcriptomes of a creA deletion and reference strain of the ascomycete Aspergillus niger during growth on sugar beet pulp and wheat bran. Transcriptomics, extracellular sugar concentrations and growth profiling of A. niger on a variety of carbon sources, revealed that also under conditions with low concentrations of free monosaccharides, CreA has a major effect on gene expression in a strong time and substrate composition dependent manner. In addition, we compared the CreA regulon from five fungi during their growth on crude plant biomass or cellulose. It showed that CreA commonly regulated genes related to carbon metabolism, sugar transport and plant cell wall degrading enzymes across different species. We therefore conclude that CreA has a crucial role for fungi also in adapting to low sugar concentrations as occurring in their natural biotopes, which is supported by the presence of CreA orthologs in nearly all fungi.

Published
2021

7. Vanillic acid and methoxyhydroquinone production from guaiacyl units and related aromatic compounds using Aspergillus niger cell factories

Author

Sub Organic Chemistry and Catalysis, Sub Molecular Plant Physiology, Organic Chemistry and Catalysis, Molecular Plant Physiology, Lubbers, Ronnie J.M., Dilokpimol, Adiphol, Nousiainen, Paula A., Cioc, Răzvan C., Visser, Jaap, Bruijnincx, Pieter C.A., de Vries, Ronald P., Sub Organic Chemistry and Catalysis, Sub Molecular Plant Physiology, Organic Chemistry and Catalysis, Molecular Plant Physiology, Lubbers, Ronnie J.M., Dilokpimol, Adiphol, Nousiainen, Paula A., Cioc, Răzvan C., Visser, Jaap, Bruijnincx, Pieter C.A., and de Vries, Ronald P.

Published
2021

9. CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner

Author

Peng, Mao, Khosravi, Claire, Lubbers, Ronnie J M, Kun, Roland S, Aguilar Pontes, Maria Victoria, Battaglia, Evy, Chen, Cindy, Dalhuijsen, Sacha, Daly, Paul, Lipzen, Anna, Ng, Vivian, Yan, Juying, Wang, Mei, Visser, Jaap, Grigoriev, Igor V, Mäkelä, Miia R, de Vries, Ronald P, Peng, Mao, Khosravi, Claire, Lubbers, Ronnie J M, Kun, Roland S, Aguilar Pontes, Maria Victoria, Battaglia, Evy, Chen, Cindy, Dalhuijsen, Sacha, Daly, Paul, Lipzen, Anna, Ng, Vivian, Yan, Juying, Wang, Mei, Visser, Jaap, Grigoriev, Igor V, Mäkelä, Miia R, and de Vries, Ronald P

Abstract

Carbon catabolite repression enables fungi to utilize the most favourable carbon source in the environment, and is mediated by a key regulator, CreA, in most fungi. CreA-mediated regulation has mainly been studied at high monosaccharide concentrations, an uncommon situation in most natural biotopes. In nature, many fungi rely on plant biomass as their major carbon source by producing enzymes to degrade plant cell wall polysaccharides into metabolizable sugars. To determine the role of CreA when fungi grow in more natural conditions and in particular with respect to degradation and conversion of plant cell walls, we compared transcriptomes of a creA deletion and reference strain of the ascomycete Aspergillus niger during growth on sugar beet pulp and wheat bran. Transcriptomics, extracellular sugar concentrations and growth profiling of A. niger on a variety of carbon sources, revealed that also under conditions with low concentrations of free monosaccharides, CreA has a major effect on gene expression in a strong time and substrate composition dependent manner. In addition, we compared the CreA regulon from five fungi during their growth on crude plant biomass or cellulose. It showed that CreA commonly regulated genes related to carbon metabolism, sugar transport and plant cell wall degrading enzymes across different species. We therefore conclude that CreA has a crucial role for fungi also in adapting to low sugar concentrations as occurring in their natural biotopes, which is supported by the presence of CreA orthologs in nearly all fungi.

Published
2021

11. Discovery and Functional Analysis of a Salicylic Acid Hydroxylase from Aspergillus niger

Author

Sub Molecular Plant Physiology, Molecular Plant Physiology, Lubbers, Ronnie J M, Dilokpimol, Adiphol, Visser, Jaap, Hildén, Kristiina S, Mäkelä, Miia R, de Vries, Ronald P, Sub Molecular Plant Physiology, Molecular Plant Physiology, Lubbers, Ronnie J M, Dilokpimol, Adiphol, Visser, Jaap, Hildén, Kristiina S, Mäkelä, Miia R, and de Vries, Ronald P

Published
2021

12. CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner

Author

Molecular Plant Physiology, Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Microbiology, Peng, Mao, Khosravi, Claire, Lubbers, Ronnie J M, Kun, Roland S, Aguilar Pontes, Maria Victoria, Battaglia, Evy, Chen, Cindy, Dalhuijsen, Sacha, Daly, Paul, Lipzen, Anna, Ng, Vivian, Yan, Juying, Wang, Mei, Visser, Jaap, Grigoriev, Igor V, Mäkelä, Miia R, de Vries, Ronald P, Molecular Plant Physiology, Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Microbiology, Peng, Mao, Khosravi, Claire, Lubbers, Ronnie J M, Kun, Roland S, Aguilar Pontes, Maria Victoria, Battaglia, Evy, Chen, Cindy, Dalhuijsen, Sacha, Daly, Paul, Lipzen, Anna, Ng, Vivian, Yan, Juying, Wang, Mei, Visser, Jaap, Grigoriev, Igor V, Mäkelä, Miia R, and de Vries, Ronald P

Published
2021

13. CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner.

Author

Peng, Mao, Peng, Mao, Khosravi, Claire, Lubbers, Ronnie JM, Kun, Roland S, Aguilar Pontes, Maria Victoria, Battaglia, Evy, Chen, Cindy, Dalhuijsen, Sacha, Daly, Paul, Lipzen, Anna, Ng, Vivian, Yan, Juying, Wang, Mei, Visser, Jaap, Grigoriev, Igor V, Mäkelä, Miia R, de Vries, Ronald P, Peng, Mao, Peng, Mao, Khosravi, Claire, Lubbers, Ronnie JM, Kun, Roland S, Aguilar Pontes, Maria Victoria, Battaglia, Evy, Chen, Cindy, Dalhuijsen, Sacha, Daly, Paul, Lipzen, Anna, Ng, Vivian, Yan, Juying, Wang, Mei, Visser, Jaap, Grigoriev, Igor V, Mäkelä, Miia R, and de Vries, Ronald P

Abstract

Carbon catabolite repression enables fungi to utilize the most favourable carbon source in the environment, and is mediated by a key regulator, CreA, in most fungi. CreA-mediated regulation has mainly been studied at high monosaccharide concentrations, an uncommon situation in most natural biotopes. In nature, many fungi rely on plant biomass as their major carbon source by producing enzymes to degrade plant cell wall polysaccharides into metabolizable sugars. To determine the role of CreA when fungi grow in more natural conditions and in particular with respect to degradation and conversion of plant cell walls, we compared transcriptomes of a creA deletion and reference strain of the ascomycete Aspergillus niger during growth on sugar beet pulp and wheat bran. Transcriptomics, extracellular sugar concentrations and growth profiling of A. niger on a variety of carbon sources, revealed that also under conditions with low concentrations of free monosaccharides, CreA has a major effect on gene expression in a strong time and substrate composition dependent manner. In addition, we compared the CreA regulon from five fungi during their growth on crude plant biomass or cellulose. It showed that CreA commonly regulated genes related to carbon metabolism, sugar transport and plant cell wall degrading enzymes across different species. We therefore conclude that CreA has a crucial role for fungi also in adapting to low sugar concentrations as occurring in their natural biotopes, which is supported by the presence of CreA orthologs in nearly all fungi.

Published
2021

14. CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner

Author

Molecular Plant Physiology, Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Microbiology, Peng, Mao, Khosravi, Claire, Lubbers, Ronnie J M, Kun, Roland S, Aguilar Pontes, Maria Victoria, Battaglia, Evy, Chen, Cindy, Dalhuijsen, Sacha, Daly, Paul, Lipzen, Anna, Ng, Vivian, Yan, Juying, Wang, Mei, Visser, Jaap, Grigoriev, Igor V, Mäkelä, Miia R, de Vries, Ronald P, Molecular Plant Physiology, Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Microbiology, Peng, Mao, Khosravi, Claire, Lubbers, Ronnie J M, Kun, Roland S, Aguilar Pontes, Maria Victoria, Battaglia, Evy, Chen, Cindy, Dalhuijsen, Sacha, Daly, Paul, Lipzen, Anna, Ng, Vivian, Yan, Juying, Wang, Mei, Visser, Jaap, Grigoriev, Igor V, Mäkelä, Miia R, and de Vries, Ronald P

Published
2021

15. Discovery and Functional Analysis of a Salicylic Acid Hydroxylase from Aspergillus niger

Author

Sub Molecular Plant Physiology, Molecular Plant Physiology, Lubbers, Ronnie J M, Dilokpimol, Adiphol, Visser, Jaap, Hildén, Kristiina S, Mäkelä, Miia R, de Vries, Ronald P, Sub Molecular Plant Physiology, Molecular Plant Physiology, Lubbers, Ronnie J M, Dilokpimol, Adiphol, Visser, Jaap, Hildén, Kristiina S, Mäkelä, Miia R, and de Vries, Ronald P

Published
2021

16. Vanillic acid and methoxyhydroquinone production from guaiacyl units and related aromatic compounds using Aspergillus niger cell factories

Author

Sub Organic Chemistry and Catalysis, Sub Molecular Plant Physiology, Organic Chemistry and Catalysis, Molecular Plant Physiology, Lubbers, Ronnie J.M., Dilokpimol, Adiphol, Nousiainen, Paula A., Cioc, Răzvan C., Visser, Jaap, Bruijnincx, Pieter C.A., de Vries, Ronald P., Sub Organic Chemistry and Catalysis, Sub Molecular Plant Physiology, Organic Chemistry and Catalysis, Molecular Plant Physiology, Lubbers, Ronnie J.M., Dilokpimol, Adiphol, Nousiainen, Paula A., Cioc, Răzvan C., Visser, Jaap, Bruijnincx, Pieter C.A., and de Vries, Ronald P.

Published
2021

17. Discovery and Functional Analysis of a Salicylic Acid Hydroxylase from Aspergillus niger

Author

Sub Molecular Plant Physiology, Molecular Plant Physiology, Lubbers, Ronnie J M, Dilokpimol, Adiphol, Visser, Jaap, Hildén, Kristiina S, Mäkelä, Miia R, de Vries, Ronald P, Sub Molecular Plant Physiology, Molecular Plant Physiology, Lubbers, Ronnie J M, Dilokpimol, Adiphol, Visser, Jaap, Hildén, Kristiina S, Mäkelä, Miia R, and de Vries, Ronald P

Published
2021

18. CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner

Author

Molecular Plant Physiology, Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Microbiology, Peng, Mao, Khosravi, Claire, Lubbers, Ronnie J M, Kun, Roland S, Aguilar Pontes, Maria Victoria, Battaglia, Evy, Chen, Cindy, Dalhuijsen, Sacha, Daly, Paul, Lipzen, Anna, Ng, Vivian, Yan, Juying, Wang, Mei, Visser, Jaap, Grigoriev, Igor V, Mäkelä, Miia R, de Vries, Ronald P, Molecular Plant Physiology, Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Microbiology, Peng, Mao, Khosravi, Claire, Lubbers, Ronnie J M, Kun, Roland S, Aguilar Pontes, Maria Victoria, Battaglia, Evy, Chen, Cindy, Dalhuijsen, Sacha, Daly, Paul, Lipzen, Anna, Ng, Vivian, Yan, Juying, Wang, Mei, Visser, Jaap, Grigoriev, Igor V, Mäkelä, Miia R, and de Vries, Ronald P

Published
2021

19. Vanillic acid and methoxyhydroquinone production from guaiacyl units and related aromatic compounds using Aspergillus niger cell factories

Author

Sub Organic Chemistry and Catalysis, Sub Molecular Plant Physiology, Organic Chemistry and Catalysis, Molecular Plant Physiology, Lubbers, Ronnie J.M., Dilokpimol, Adiphol, Nousiainen, Paula A., Cioc, Răzvan C., Visser, Jaap, Bruijnincx, Pieter C.A., de Vries, Ronald P., Sub Organic Chemistry and Catalysis, Sub Molecular Plant Physiology, Organic Chemistry and Catalysis, Molecular Plant Physiology, Lubbers, Ronnie J.M., Dilokpimol, Adiphol, Nousiainen, Paula A., Cioc, Răzvan C., Visser, Jaap, Bruijnincx, Pieter C.A., and de Vries, Ronald P.

Published
2021

20. CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner

Author

Peng, Mao, Khosravi, Claire, Lubbers, Ronnie J M, Kun, Roland S, Aguilar Pontes, Maria Victoria, Battaglia, Evy, Chen, Cindy, Dalhuijsen, Sacha, Daly, Paul, Lipzen, Anna, Ng, Vivian, Yan, Juying, Wang, Mei, Visser, Jaap, Grigoriev, Igor V, Mäkelä, Miia R, de Vries, Ronald P, Peng, Mao, Khosravi, Claire, Lubbers, Ronnie J M, Kun, Roland S, Aguilar Pontes, Maria Victoria, Battaglia, Evy, Chen, Cindy, Dalhuijsen, Sacha, Daly, Paul, Lipzen, Anna, Ng, Vivian, Yan, Juying, Wang, Mei, Visser, Jaap, Grigoriev, Igor V, Mäkelä, Miia R, and de Vries, Ronald P

Abstract

Carbon catabolite repression enables fungi to utilize the most favourable carbon source in the environment, and is mediated by a key regulator, CreA, in most fungi. CreA-mediated regulation has mainly been studied at high monosaccharide concentrations, an uncommon situation in most natural biotopes. In nature, many fungi rely on plant biomass as their major carbon source by producing enzymes to degrade plant cell wall polysaccharides into metabolizable sugars. To determine the role of CreA when fungi grow in more natural conditions and in particular with respect to degradation and conversion of plant cell walls, we compared transcriptomes of a creA deletion and reference strain of the ascomycete Aspergillus niger during growth on sugar beet pulp and wheat bran. Transcriptomics, extracellular sugar concentrations and growth profiling of A. niger on a variety of carbon sources, revealed that also under conditions with low concentrations of free monosaccharides, CreA has a major effect on gene expression in a strong time and substrate composition dependent manner. In addition, we compared the CreA regulon from five fungi during their growth on crude plant biomass or cellulose. It showed that CreA commonly regulated genes related to carbon metabolism, sugar transport and plant cell wall degrading enzymes across different species. We therefore conclude that CreA has a crucial role for fungi also in adapting to low sugar concentrations as occurring in their natural biotopes, which is supported by the presence of CreA orthologs in nearly all fungi.

Published
2021

23. Discovery of Novel p-Hydroxybenzoate-m-hydroxylase, Protocatechuate 3,4 Ring-Cleavage Dioxygenase, and Hydroxyquinol 1,2 Ring-Cleavage Dioxygenase from the Filamentous Fungus Aspergillus niger

Author

Lubbers, Ronnie J. M., Dilokpimol, Adiphol, Peng, Mao, Visser, Jaap, Mäkelä, Miia R., Hildén, Kristiina S., De Vries, Ronald P., Lubbers, Ronnie J. M., Dilokpimol, Adiphol, Peng, Mao, Visser, Jaap, Mäkelä, Miia R., Hildén, Kristiina S., and De Vries, Ronald P.

Abstract

The aromatic compound benzoic acid and its derivatives are frequently used preservatives in food and beverages due to their strong antimicrobial properties. Benzoic acid naturally occurs in plants and serves as a building block for primary and secondary metabolites. Several Aspergilli are able to degrade benzoic acid to p-hydroxybenzoic acid by p-hydroxylation followed by m-hydroxylation to protocatechuic acid. The aromatic ring of protocatechuic acid is then cleaved and further converted through the oxoadipate pathway where it is used as a carbon source. The benzoic acid pathway is well studied in the filamentous fungus Aspergillus niger; however, only one enzyme, benzoate-4-monooxygenase, has been characterized. In this study, three novel enzymes of the benzoic acid pathway were identified and characterized. Transcriptome analysis of A. niger on p-hydroxybenzoic acid, protocatechuic acid, and the related compounds p-coumaric acid and caffeic acid revealed two genes of unknown function, which were highly expressed on all four aromatic compounds. Analysis of A. niger deletion mutants of these genes revealed their essential role in the utilization of benzoic acid, p-hydroxybenzoic acid, and protocatechuic acid. Biochemical analysis confirmed that the corresponding enzymes function as the p-hydroxybenzoate-m-hydroxylase and protocatechuate 3,4 ring-cleavage dioxygenase in the benzoic acid pathway. In addition, a hydroxyquinol 1,2 ring-cleavage dioxygenase, involved in an alternative protocatechuic acid metabolic pathway, was identified.

Published
2019

24. Myceliophthora thermophila Xyr1 is predominantly involved in xylan degradation and xylose catabolism

Author

Dos Santos Gomes, Ana Carolina, Falkoski, Daniel, Battaglia, Evy, Peng, Mao, Nicolau De Almeida, Maira, Coconi Linares, Nancy, Meijnen, Jean-paul, Visser, Jaap, De Vries, Ronald P., Dos Santos Gomes, Ana Carolina, Falkoski, Daniel, Battaglia, Evy, Peng, Mao, Nicolau De Almeida, Maira, Coconi Linares, Nancy, Meijnen, Jean-paul, Visser, Jaap, and De Vries, Ronald P.

Abstract

Background Myceliophthora thermophila is a thermophilic ascomycete fungus that is used as a producer of enzyme cocktails used in plant biomass saccharification. Further development of this species as an industrial enzyme factory requires a detailed understanding of its regulatory systems driving the production of plant biomass-degrading enzymes. In this study, we analyzed the function of MtXlr1, an ortholog of the (hemi-)cellulolytic regulator XlnR first identified in another industrially relevant fungus, Aspergillus niger. Results The Mtxlr1 gene was deleted and the resulting strain was compared to the wild type using growth profiling and transcriptomics. The deletion strain was unable to grow on xylan and D-xylose, but showed only a small growth reduction on L-arabinose, and grew similar to the wild type on Avicel and cellulose. These results were supported by the transcriptome analyses which revealed reduction of genes encoding xylan-degrading enzymes, enzymes of the pentose catabolic pathway and putative pentose transporters. In contrast, no or minimal effects were observed for the expression of cellulolytic genes. Conclusions Myceliophthora thermophila MtXlr1 controls the expression of xylanolytic genes and genes involved in pentose transport and catabolism, but has no significant effects on the production of cellulases. It therefore resembles more the role of its ortholog in Neurospora crassa, rather than the broader role described for this regulator in A. niger and Trichoderma reesei. By revealing the range of genes controlled by MtXlr1, our results provide the basic knowledge for targeted strain improvement by overproducing or constitutively activating this regulator, to further improve the biotechnological value of M. thermophila.

Published
2019

25. Myceliophthora thermophila Xyr1 is predominantly involved in xylan degradation and xylose catabolism

Author

Molecular Plant Physiology, Sub Molecular Plant Physiology, Dos Santos Gomes, Ana Carolina, Falkoski, Daniel, Battaglia, Evy, Peng, Mao, Nicolau De Almeida, Maira, Coconi Linares, Nancy, Meijnen, Jean-paul, Visser, Jaap, De Vries, Ronald P., Molecular Plant Physiology, Sub Molecular Plant Physiology, Dos Santos Gomes, Ana Carolina, Falkoski, Daniel, Battaglia, Evy, Peng, Mao, Nicolau De Almeida, Maira, Coconi Linares, Nancy, Meijnen, Jean-paul, Visser, Jaap, and De Vries, Ronald P.

Published
2019

26. Discovery of Novel p-Hydroxybenzoate-m-hydroxylase, Protocatechuate 3,4 Ring-Cleavage Dioxygenase, and Hydroxyquinol 1,2 Ring-Cleavage Dioxygenase from the Filamentous Fungus Aspergillus niger

Author

Molecular Plant Physiology, Sub Molecular Plant Physiology, Lubbers, Ronnie J. M., Dilokpimol, Adiphol, Peng, Mao, Visser, Jaap, Mäkelä, Miia R., Hildén, Kristiina S., De Vries, Ronald P., Molecular Plant Physiology, Sub Molecular Plant Physiology, Lubbers, Ronnie J. M., Dilokpimol, Adiphol, Peng, Mao, Visser, Jaap, Mäkelä, Miia R., Hildén, Kristiina S., and De Vries, Ronald P.

Published
2019

27. Cinnamic Acid and Sorbic acid Conversion Are Mediated by the Same Transcriptional Regulator in Aspergillus niger

Author

Molecular Plant Physiology, Sub Molecular Plant Physiology, Lubbers, Ronnie J. M., Dilokpimol, Adiphol, Navarro, Jorge, Peng, Mao, Wang, Mei, Lipzen, Anna, Ng, Vivian, Grigoriev, Igor V., Visser, Jaap, Hildén, Kristiina S., De Vries, Ronald P., Molecular Plant Physiology, Sub Molecular Plant Physiology, Lubbers, Ronnie J. M., Dilokpimol, Adiphol, Navarro, Jorge, Peng, Mao, Wang, Mei, Lipzen, Anna, Ng, Vivian, Grigoriev, Igor V., Visser, Jaap, Hildén, Kristiina S., and De Vries, Ronald P.

Published
2019

30. Myceliophthora thermophila Xyr1 is predominantly involved in xylan degradation and xylose catabolism

Author

Dos Santos Gomes, Ana Carolina, Falkoski, Daniel, Battaglia, Evy, Peng, Mao, Nicolau de Almeida, Maira, Coconi Linares, Nancy, Meijnen, Jean-Paul, Visser, Jaap, de Vries, Ronald P, Dos Santos Gomes, Ana Carolina, Falkoski, Daniel, Battaglia, Evy, Peng, Mao, Nicolau de Almeida, Maira, Coconi Linares, Nancy, Meijnen, Jean-Paul, Visser, Jaap, and de Vries, Ronald P

Abstract

Background: Myceliophthora thermophila is a thermophilic ascomycete fungus that is used as a producer of enzyme cocktails used in plant biomass saccharification. Further development of this species as an industrial enzyme factory requires a detailed understanding of its regulatory systems driving the production of plant biomass-degrading enzymes. In this study, we analyzed the function of MtXlr1, an ortholog of the (hemi-)cellulolytic regulator XlnR first identified in another industrially relevant fungus, Aspergillus niger.Results: The Mtxlr1 gene was deleted and the resulting strain was compared to the wild type using growth profiling and transcriptomics. The deletion strain was unable to grow on xylan and d-xylose, but showed only a small growth reduction on l-arabinose, and grew similar to the wild type on Avicel and cellulose. These results were supported by the transcriptome analyses which revealed reduction of genes encoding xylan-degrading enzymes, enzymes of the pentose catabolic pathway and putative pentose transporters. In contrast, no or minimal effects were observed for the expression of cellulolytic genes.Conclusions: Myceliophthora thermophila MtXlr1 controls the expression of xylanolytic genes and genes involved in pentose transport and catabolism, but has no significant effects on the production of cellulases. It therefore resembles more the role of its ortholog in Neurospora crassa, rather than the broader role described for this regulator in A. niger and Trichoderma reesei. By revealing the range of genes controlled by MtXlr1, our results provide the basic knowledge for targeted strain improvement by overproducing or constitutively activating this regulator, to further improve the biotechnological value of M. thermophila.

Published
2019

31. Discovery of Novel p-Hydroxybenzoate-m-hydroxylase, Protocatechuate 3,4 Ring-Cleavage Dioxygenase, and Hydroxyquinol 1,2 Ring-Cleavage Dioxygenase from the Filamentous Fungus Aspergillus niger

Author

Molecular Plant Physiology, Sub Molecular Plant Physiology, Lubbers, Ronnie J. M., Dilokpimol, Adiphol, Peng, Mao, Visser, Jaap, Mäkelä, Miia R., Hildén, Kristiina S., De Vries, Ronald P., Molecular Plant Physiology, Sub Molecular Plant Physiology, Lubbers, Ronnie J. M., Dilokpimol, Adiphol, Peng, Mao, Visser, Jaap, Mäkelä, Miia R., Hildén, Kristiina S., and De Vries, Ronald P.

Published
2019

32. Cinnamic Acid and Sorbic acid Conversion Are Mediated by the Same Transcriptional Regulator in Aspergillus niger

Author

Molecular Plant Physiology, Sub Molecular Plant Physiology, Lubbers, Ronnie J. M., Dilokpimol, Adiphol, Navarro, Jorge, Peng, Mao, Wang, Mei, Lipzen, Anna, Ng, Vivian, Grigoriev, Igor V., Visser, Jaap, Hildén, Kristiina S., De Vries, Ronald P., Molecular Plant Physiology, Sub Molecular Plant Physiology, Lubbers, Ronnie J. M., Dilokpimol, Adiphol, Navarro, Jorge, Peng, Mao, Wang, Mei, Lipzen, Anna, Ng, Vivian, Grigoriev, Igor V., Visser, Jaap, Hildén, Kristiina S., and De Vries, Ronald P.

Published
2019

33. Myceliophthora thermophila Xyr1 is predominantly involved in xylan degradation and xylose catabolism

Author

Molecular Plant Physiology, Sub Molecular Plant Physiology, Dos Santos Gomes, Ana Carolina, Falkoski, Daniel, Battaglia, Evy, Peng, Mao, Nicolau De Almeida, Maira, Coconi Linares, Nancy, Meijnen, Jean-paul, Visser, Jaap, De Vries, Ronald P., Molecular Plant Physiology, Sub Molecular Plant Physiology, Dos Santos Gomes, Ana Carolina, Falkoski, Daniel, Battaglia, Evy, Peng, Mao, Nicolau De Almeida, Maira, Coconi Linares, Nancy, Meijnen, Jean-paul, Visser, Jaap, and De Vries, Ronald P.

Published
2019

34. Discovery of Novel p-Hydroxybenzoate-m-hydroxylase, Protocatechuate 3,4 Ring-Cleavage Dioxygenase, and Hydroxyquinol 1,2 Ring-Cleavage Dioxygenase from the Filamentous Fungus Aspergillus niger

Author

Molecular Plant Physiology, Sub Molecular Plant Physiology, Lubbers, Ronnie J. M., Dilokpimol, Adiphol, Peng, Mao, Visser, Jaap, Mäkelä, Miia R., Hildén, Kristiina S., De Vries, Ronald P., Molecular Plant Physiology, Sub Molecular Plant Physiology, Lubbers, Ronnie J. M., Dilokpimol, Adiphol, Peng, Mao, Visser, Jaap, Mäkelä, Miia R., Hildén, Kristiina S., and De Vries, Ronald P.

Published
2019

35. Myceliophthora thermophila Xyr1 is predominantly involved in xylan degradation and xylose catabolism

Author

Molecular Plant Physiology, Sub Molecular Plant Physiology, Dos Santos Gomes, Ana Carolina, Falkoski, Daniel, Battaglia, Evy, Peng, Mao, Nicolau De Almeida, Maira, Coconi Linares, Nancy, Meijnen, Jean-paul, Visser, Jaap, De Vries, Ronald P., Molecular Plant Physiology, Sub Molecular Plant Physiology, Dos Santos Gomes, Ana Carolina, Falkoski, Daniel, Battaglia, Evy, Peng, Mao, Nicolau De Almeida, Maira, Coconi Linares, Nancy, Meijnen, Jean-paul, Visser, Jaap, and De Vries, Ronald P.

Published
2019

36. Cinnamic Acid and Sorbic acid Conversion Are Mediated by the Same Transcriptional Regulator in Aspergillus niger

Author

Molecular Plant Physiology, Sub Molecular Plant Physiology, Lubbers, Ronnie J. M., Dilokpimol, Adiphol, Navarro, Jorge, Peng, Mao, Wang, Mei, Lipzen, Anna, Ng, Vivian, Grigoriev, Igor V., Visser, Jaap, Hildén, Kristiina S., De Vries, Ronald P., Molecular Plant Physiology, Sub Molecular Plant Physiology, Lubbers, Ronnie J. M., Dilokpimol, Adiphol, Navarro, Jorge, Peng, Mao, Wang, Mei, Lipzen, Anna, Ng, Vivian, Grigoriev, Igor V., Visser, Jaap, Hildén, Kristiina S., and De Vries, Ronald P.

Published
2019

39. Myceliophthora thermophila Xyr1 is predominantly involved in xylan degradation and xylose catabolism

Author

Dos Santos Gomes, Ana Carolina, Falkoski, Daniel, Battaglia, Evy, Peng, Mao, Nicolau de Almeida, Maira, Coconi Linares, Nancy, Meijnen, Jean-Paul, Visser, Jaap, de Vries, Ronald P, Dos Santos Gomes, Ana Carolina, Falkoski, Daniel, Battaglia, Evy, Peng, Mao, Nicolau de Almeida, Maira, Coconi Linares, Nancy, Meijnen, Jean-Paul, Visser, Jaap, and de Vries, Ronald P

Abstract

Background: Myceliophthora thermophila is a thermophilic ascomycete fungus that is used as a producer of enzyme cocktails used in plant biomass saccharification. Further development of this species as an industrial enzyme factory requires a detailed understanding of its regulatory systems driving the production of plant biomass-degrading enzymes. In this study, we analyzed the function of MtXlr1, an ortholog of the (hemi-)cellulolytic regulator XlnR first identified in another industrially relevant fungus, Aspergillus niger.Results: The Mtxlr1 gene was deleted and the resulting strain was compared to the wild type using growth profiling and transcriptomics. The deletion strain was unable to grow on xylan and d-xylose, but showed only a small growth reduction on l-arabinose, and grew similar to the wild type on Avicel and cellulose. These results were supported by the transcriptome analyses which revealed reduction of genes encoding xylan-degrading enzymes, enzymes of the pentose catabolic pathway and putative pentose transporters. In contrast, no or minimal effects were observed for the expression of cellulolytic genes.Conclusions: Myceliophthora thermophila MtXlr1 controls the expression of xylanolytic genes and genes involved in pentose transport and catabolism, but has no significant effects on the production of cellulases. It therefore resembles more the role of its ortholog in Neurospora crassa, rather than the broader role described for this regulator in A. niger and Trichoderma reesei. By revealing the range of genes controlled by MtXlr1, our results provide the basic knowledge for targeted strain improvement by overproducing or constitutively activating this regulator, to further improve the biotechnological value of M. thermophila.

Published
2019

40. Quantification of the catalytic performance of C1-cellulose-specific lytic polysaccharide monooxygenases

Author

Frommhagen, Matthias, Westphal, Adrie H., Hilgers, Roelant, Koetsier, Martijn J., Hinz, Sandra W.A., Visser, Jaap, Gruppen, Harry, Berkel, Willem J.H., van, Kabel, Mirjam A., Frommhagen, Matthias, Westphal, Adrie H., Hilgers, Roelant, Koetsier, Martijn J., Hinz, Sandra W.A., Visser, Jaap, Gruppen, Harry, Berkel, Willem J.H., van, and Kabel, Mirjam A.

Abstract

Lytic polysaccharide monooxygenases (LPMOs) have recently been shown to significantly enhance the degradation of recalcitrant polysaccharides and are of interest for the production of biochemicals and bioethanol from plant biomass. The copper-containing LPMOs utilize electrons, provided by reducing agents, to oxidatively cleave polysaccharides. Here, we report the development of a β-glucosidase-assisted method to quantify the release of C1-oxidized gluco-oligosaccharides from cellulose by two C1-oxidizing LPMOs from Myceliophthora thermophila C1. Based on this quantification method, we demonstrate that the catalytic performance of both MtLPMOs is strongly dependent on pH and temperature. The obtained results indicate that the catalytic performance of LPMOs depends on the interaction of multiple factors, which are affected by both pH and temperature.

Published
2018

41. Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans

Author

Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Plant Physiology, Khosravi, Claire, Battaglia, Evy, Kun, Roland S., Dalhuijsen, Sacha, Visser, Jaap, Aguilar-Pontes, María Victoria, Zhou, Miaomiao, Heyman, Heino M., Kim, Young Mo, Baker, Scott E., de Vries, Ronald P., Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Plant Physiology, Khosravi, Claire, Battaglia, Evy, Kun, Roland S., Dalhuijsen, Sacha, Visser, Jaap, Aguilar-Pontes, María Victoria, Zhou, Miaomiao, Heyman, Heino M., Kim, Young Mo, Baker, Scott E., and de Vries, Ronald P.

Published
2018

42. Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans

Author

Khosravi, Claire, Battaglia, Evy, Kun, Roland S., Dalhuijsen, Sacha, Visser, Jaap, Aguilar-Pontes, Maria Victoria, Zhou, Miaomiao, Heyman, Heino M., Kim, Young-Mo, Ronald, Scott E. Baker, de Vries, Ronald P., Khosravi, Claire, Battaglia, Evy, Kun, Roland S., Dalhuijsen, Sacha, Visser, Jaap, Aguilar-Pontes, Maria Victoria, Zhou, Miaomiao, Heyman, Heino M., Kim, Young-Mo, Ronald, Scott E. Baker, and de Vries, Ronald P.

Published
2018

43. Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans

Author

Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Plant Physiology, Khosravi, Claire, Battaglia, Evy, Kun, Roland S., Dalhuijsen, Sacha, Visser, Jaap, Aguilar-Pontes, María Victoria, Zhou, Miaomiao, Heyman, Heino M., Kim, Young Mo, Baker, Scott E., de Vries, Ronald P., Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Plant Physiology, Khosravi, Claire, Battaglia, Evy, Kun, Roland S., Dalhuijsen, Sacha, Visser, Jaap, Aguilar-Pontes, María Victoria, Zhou, Miaomiao, Heyman, Heino M., Kim, Young Mo, Baker, Scott E., and de Vries, Ronald P.

Published
2018

44. Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans

Author

Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Plant Physiology, Khosravi, Claire, Battaglia, Evy, Kun, Roland S., Dalhuijsen, Sacha, Visser, Jaap, Aguilar-Pontes, María Victoria, Zhou, Miaomiao, Heyman, Heino M., Kim, Young Mo, Baker, Scott E., de Vries, Ronald P., Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Plant Physiology, Khosravi, Claire, Battaglia, Evy, Kun, Roland S., Dalhuijsen, Sacha, Visser, Jaap, Aguilar-Pontes, María Victoria, Zhou, Miaomiao, Heyman, Heino M., Kim, Young Mo, Baker, Scott E., and de Vries, Ronald P.

Published
2018

45. Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans

Author

Khosravi, Claire, Battaglia, Evy, Kun, Roland S., Dalhuijsen, Sacha, Visser, Jaap, Aguilar-Pontes, Maria Victoria, Zhou, Miaomiao, Heyman, Heino M., Kim, Young-Mo, Ronald, Scott E. Baker, de Vries, Ronald P., Khosravi, Claire, Battaglia, Evy, Kun, Roland S., Dalhuijsen, Sacha, Visser, Jaap, Aguilar-Pontes, Maria Victoria, Zhou, Miaomiao, Heyman, Heino M., Kim, Young-Mo, Ronald, Scott E. Baker, and de Vries, Ronald P.

Published
2018

46. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.

Author

de Vries, Ronald P, de Vries, Ronald P, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Uchima, Cristiane Akemi, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna A, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo C, Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Dos Santos, Renato Augusto Corrêa, Damásio, André Ricardo de Lima, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María Laura, Henrissat, Bernard, Hildén, Kristiina S, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen L, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio F, MacCabe, Andrew, Mäkelä, Miia R, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos P, Mulé, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean Paul, Overkamp, Karin M, Park, Hee-Soo, Perrone, Giancarlo, Piumi, Francois, Punt, Peter J, Ram, Arthur FJ, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego Mauricio, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S, Samson, Rob A, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio M, Sun, Hui, Susca, Antonia, Todd, Richard B, Tsang, Adrian, Unkles, Shiela E, van de Wiele, Nathalie, van Rossen-Uffink, Diana, Oliveira, Juliana Velasco de Castro, Vesth, Tammi C, Visser, Jaap, Yu, Jae-Hyuk, Zhou, Miaomiao, Andersen, Mikael R, de Vries, Ronald P, de Vries, Ronald P, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Uchima, Cristiane Akemi, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna A, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo C, Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Dos Santos, Renato Augusto Corrêa, Damásio, André Ricardo de Lima, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María Laura, Henrissat, Bernard, Hildén, Kristiina S, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen L, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio F, MacCabe, Andrew, Mäkelä, Miia R, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos P, Mulé, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean Paul, Overkamp, Karin M, Park, Hee-Soo, Perrone, Giancarlo, Piumi, Francois, Punt, Peter J, Ram, Arthur FJ, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego Mauricio, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S, Samson, Rob A, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio M, Sun, Hui, Susca, Antonia, Todd, Richard B, Tsang, Adrian, Unkles, Shiela E, van de Wiele, Nathalie, van Rossen-Uffink, Diana, Oliveira, Juliana Velasco de Castro, Vesth, Tammi C, Visser, Jaap, Yu, Jae-Hyuk, Zhou, Miaomiao, and Andersen, Mikael R

Abstract

BackgroundThe fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus.ResultsWe have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli.ConclusionsMany aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.

Published
2017

49. The pathway intermediate 2-keto-3-deoxy-L-galactonate mediates the induction of genes involved in D-galacturonic acid utilization in Aspergillus niger

Author

Alazi, Ebru, Khosravi, Claire, Homan, Tim G., du Pre, Saskia, Arentshorst, Mark, Di Falco, Marcos, Pham, Thi T. M., Peng, Mao, Aguilar-Pontes, Maria Victoria, Visser, Jaap, Tsang, Adrian, de Vries, Ronald P., Ram, Arthur F J, Alazi, Ebru, Khosravi, Claire, Homan, Tim G., du Pre, Saskia, Arentshorst, Mark, Di Falco, Marcos, Pham, Thi T. M., Peng, Mao, Aguilar-Pontes, Maria Victoria, Visser, Jaap, Tsang, Adrian, de Vries, Ronald P., and Ram, Arthur F J

Published
2017

50. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

de Vries, Ronald P., Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Uchima, Cristiane Akemi, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie W, Battaglia, Evy, Bayram, Ozgur, Benocci, Tiziano, Braus-Stromeyer, Susanna A., Caldana, Camila, Canovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Correa dos Santos, Renato Augusto, de Lima Damasio, Andre Ricardo, Diallinas, George, Emri, Tamas, Fekete, Erzsebet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Laura Harispe, Maria, Henrissat, Bernard, Hilden, Kristiina S., Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karanyi, Zsolt, Krasevec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt M, Lagendijk, Ellen L., Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika A, Lipzen, Anna M, Logrieco, Antonio F., Maccabe, Andrew, Makela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Marton, Molnar, Akos P., Mule, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsebet, Ouedraogo, Jean Paul, Overkamp, Karin M, Park, Hee-Soo, Perrone, Giancarlo, Piumi, Francois, Punt, Peter J, Ram, Arthur F J, Ramon, Ana, Rauscher, Stefan, Record, Eric, Riano-Pachon, Diego Mauricio, Robert, Vincent, Roehrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sandor, Erzsebet, Sanguinetti, Manuel, Schutze, Tabea, Sepcic, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, FabioM., Sun, Hui, Susca, Antonia, Todd, Richard B, Tsang, Adrian, Unkles, Shiela E., van de Wiele, Nathalie, van Rossen-Uffink, Diana, de Castro Oliveira, Juliana Velasco, Vesth, Tammi C., Visser, Jaap, Yu, Jae-Hyuk, Zhou, Miaomiao, Andersen, Mikael R, Archer, David B., Baker, Scott E, Benoit, Isabelle, Brakhage, Axel A, Braus, Gerhard H., Fischer, Reinhard, Frisvad, Jens C., Goldman, Gustavo H., Houbraken, Jos, Oakley, Berl R, Pocsi, Istvan, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A, Wortman, Jennifer Russo, Dyer, Paul S, Grigoriev, Igor V, de Vries, Ronald P., Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Uchima, Cristiane Akemi, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie W, Battaglia, Evy, Bayram, Ozgur, Benocci, Tiziano, Braus-Stromeyer, Susanna A., Caldana, Camila, Canovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Correa dos Santos, Renato Augusto, de Lima Damasio, Andre Ricardo, Diallinas, George, Emri, Tamas, Fekete, Erzsebet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Laura Harispe, Maria, Henrissat, Bernard, Hilden, Kristiina S., Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karanyi, Zsolt, Krasevec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt M, Lagendijk, Ellen L., Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika A, Lipzen, Anna M, Logrieco, Antonio F., Maccabe, Andrew, Makela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Marton, Molnar, Akos P., Mule, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsebet, Ouedraogo, Jean Paul, Overkamp, Karin M, Park, Hee-Soo, Perrone, Giancarlo, Piumi, Francois, Punt, Peter J, Ram, Arthur F J, Ramon, Ana, Rauscher, Stefan, Record, Eric, Riano-Pachon, Diego Mauricio, Robert, Vincent, Roehrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sandor, Erzsebet, Sanguinetti, Manuel, Schutze, Tabea, Sepcic, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, FabioM., Sun, Hui, Susca, Antonia, Todd, Richard B, Tsang, Adrian, Unkles, Shiela E., van de Wiele, Nathalie, van Rossen-Uffink, Diana, de Castro Oliveira, Juliana Velasco, Vesth, Tammi C., Visser, Jaap, Yu, Jae-Hyuk, Zhou, Miaomiao, Andersen, Mikael R, Archer, David B., Baker, Scott E, Benoit, Isabelle, Brakhage, Axel A, Braus, Gerhard H., Fischer, Reinhard, Frisvad, Jens C., Goldman, Gustavo H., Houbraken, Jos, Oakley, Berl R, Pocsi, Istvan, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A, Wortman, Jennifer Russo, Dyer, Paul S, and Grigoriev, Igor V

Published
2017

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