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Zhao H, Karppi J, Nguyen TTM, Bellemare A, Tsang A, Master E, Tenkanen M. Characterization of a novel AA3_1 xylooligosaccharide dehydrogenase from Thermothelomyces myriococcoides CBS 398.93. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:135. [PMID: 36476312 PMCID: PMC9730589 DOI: 10.1186/s13068-022-02231-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND The Carbohydrate-Active enZymes (CAZy) auxiliary activity family 3 (AA3) comprises flavin adenine dinucleotide-dependent (FAD) oxidoreductases from the glucose-methanol-choline (GMC) family, which play auxiliary roles in lignocellulose conversion. The AA3 subfamily 1 predominantly consists of cellobiose dehydrogenases (CDHs) that typically comprise a dehydrogenase domain, a cytochrome domain, and a carbohydrate-binding module from family 1 (CBM1). RESULTS In this work, an AA3_1 gene from T. myriococcoides CBS 398.93 encoding only a GMC dehydrogenase domain was expressed in Aspergillus niger. Like previously characterized CDHs, this enzyme (TmXdhA) predominantly accepts linear saccharides with β-(1 → 4) linkage and targets the hydroxyl on the reducing anomeric carbon. TmXdhA was distinguished, however, by its preferential activity towards xylooligosaccharides over cellooligosaccharides. Amino acid sequence analysis showed that TmXdhA possesses a glutamine at the substrate-binding site rather than a threonine or serine that occupies this position in previously characterized CDHs, and structural models suggest the glutamine in TmXdhA could facilitate binding to pentose sugars. CONCLUSIONS The biochemical analysis of TmXdhA revealed a catalytic preference for xylooligosaccharide substrates. The modeled structure of TmXdhA provides a reference for the screening of oxidoreductases targeting xylooligosaccharides. We anticipate TmXdhA to be a good candidate for the conversion of xylooligosaccharides to added-value chemicals by its exceptional catalytic ability.
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Affiliation(s)
- Hongbo Zhao
- grid.7737.40000 0004 0410 2071Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Johanna Karppi
- grid.7737.40000 0004 0410 2071Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Thi Truc Minh Nguyen
- grid.410319.e0000 0004 1936 8630Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Annie Bellemare
- grid.410319.e0000 0004 1936 8630Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Adrian Tsang
- grid.410319.e0000 0004 1936 8630Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Emma Master
- grid.5373.20000000108389418Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland ,grid.17063.330000 0001 2157 2938Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON Canada
| | - Maija Tenkanen
- grid.7737.40000 0004 0410 2071Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
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Dilokpimol A, Verkerk B, Li X, Bellemare A, Lavallee M, Frommhagen M, Nørmølle Underlin E, Kabel MA, Powlowski J, Tsang A, de Vries RP. Screening of novel fungal Carbohydrate Esterase family 1 enzymes identifies three novel dual feruloyl/acetyl xylan esterases. FEBS Lett 2022; 596:1932-1943. [DOI: 10.1002/1873-3468.14322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Adiphol Dilokpimol
- Fungal Physiology Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology Utrecht University Uppsalalaan 8 3584 CT Utrecht The Netherlands
- Current address: Protein Production Team VTT Technical Research Center of Finland Ltd Tietotie 2 02150 Espoo Finland
| | - Bart Verkerk
- Fungal Physiology Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology Utrecht University Uppsalalaan 8 3584 CT Utrecht The Netherlands
| | - Xinxin Li
- Fungal Physiology Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology Utrecht University Uppsalalaan 8 3584 CT Utrecht The Netherlands
| | - Annie Bellemare
- Centre for Functional and Structural Genomics Concordia University Sherbrooke St. W. Montreal QC H4B 1R6 Canada
| | - Mathieu Lavallee
- Centre for Functional and Structural Genomics Concordia University Sherbrooke St. W. Montreal QC H4B 1R6 Canada
| | - Matthias Frommhagen
- Laboratory of Food Chemistry Wageningen University and Research Bornse Weilanden 9 6708 WG Wageningen The Netherlands
| | - Emilie Nørmølle Underlin
- Laboratory of Food Chemistry Wageningen University and Research Bornse Weilanden 9 6708 WG Wageningen The Netherlands
- Department of Chemistry Technical University of Denmark Building 207 Kemitorvet DK‐2800 Denmark
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry Wageningen University and Research Bornse Weilanden 9 6708 WG Wageningen The Netherlands
| | - Justin Powlowski
- Centre for Functional and Structural Genomics Concordia University Sherbrooke St. W. Montreal QC H4B 1R6 Canada
| | - Adrian Tsang
- Centre for Functional and Structural Genomics Concordia University Sherbrooke St. W. Montreal QC H4B 1R6 Canada
| | - Ronald P. de Vries
- Fungal Physiology Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology Utrecht University Uppsalalaan 8 3584 CT Utrecht The Netherlands
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Four Aromatic Intradiol Ring Cleavage Dioxygenases from Aspergillus niger. Appl Environ Microbiol 2019; 85:AEM.01786-19. [PMID: 31540981 DOI: 10.1128/aem.01786-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/13/2019] [Indexed: 11/20/2022] Open
Abstract
Ring cleavage dioxygenases catalyze the critical ring-opening step in the catabolism of aromatic compounds. The archetypal filamentous fungus Aspergillus niger previously has been reported to be able to utilize a range of monocyclic aromatic compounds as sole sources of carbon and energy. The genome of A. niger has been sequenced, and deduced amino acid sequences from a large number of gene models show various levels of similarity to bacterial intradiol ring cleavage dioxygenases, but no corresponding enzyme has been purified and characterized. Here, the cloning, heterologous expression, purification, and biochemical characterization of four nonheme iron(III)-containing intradiol dioxygenases (NRRL3_02644, NRRL3_04787, NRRL3_05330, and NRRL3_01405) from A. niger are reported. Purified enzymes were tested for their ability to cleave model catecholate substrates, and their apparent kinetic parameters were determined. Comparisons of k cat /Km values show that NRRL3_02644 and NRRL3_05330 are specific for hydroxyquinol (1,2,4-trihydroxybenzene), and phylogenetic analysis shows that these two enzymes are related to bacterial hydroxyquinol 1,2-dioxygenases. A high-activity catechol 1,2-dioxygenase (NRRL3_04787), which is phylogenetically related to other characterized and putative fungal catechol 1,2-dioxygenases, was also identified. The fourth enzyme (NRRL3_01405) appears to be a novel homodimeric Fe(III)-containing protocatechuate 3,4-dioxygenase that is phylogenetically distantly related to heterodimeric bacterial protocatechuate 3,4-dioxygenases. These investigations provide experimental evidence for the molecular function of these proteins and open the way to further investigations of the physiological roles for these enzymes in fungal metabolism of aromatic compounds.IMPORTANCE Aromatic ring opening using molecular oxygen is one of the critical steps in the degradation of aromatic compounds by microorganisms. While enzymes catalyzing this step have been well-studied in bacteria, their counterparts from fungi are poorly characterized despite the abundance of genes annotated as ring cleavage dioxygenases in fungal genomes. Aspergillus niger degrades a variety of aromatic compounds, and its genome harbors 5 genes encoding putative intracellular intradiol dioxygenases. The ability to predict the substrate specificities of the encoded enzymes from sequence data are limited. Here, we report the characterization of four purified intradiol ring cleavage dioxygenases from A. niger, revealing two hydroxyquinol-specific dioxygenases, a catechol dioxygenase, and a unique homodimeric protocatechuate dioxygenase. Their characteristics, as well as their phylogenetic relationships to predicted ring cleavage dioxygenases from other fungal species, provide insights into their molecular functions in aromatic compound metabolism by this fungus and other fungi.
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McCluskey K, Baker SE. Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era. Mycology 2017; 8:67-83. [PMID: 30123633 PMCID: PMC6059044 DOI: 10.1080/21501203.2017.1281849] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/10/2017] [Indexed: 01/14/2023] Open
Abstract
Filamentous fungi have been important as model organisms since the beginning of modern biological inquiry and have benefitted from open data since the earliest genetic maps were shared. From early origins in simple Mendelian genetics of mating types, parasexual genetics of colony colour, and the foundational demonstration of the segregation of a nutritional requirement, the contribution of research systems utilising filamentous fungi has spanned the biochemical genetics era, through the molecular genetics era, and now are at the very foundation of diverse omics approaches to research and development. Fungal model organisms have come from most major taxonomic groups although Ascomycete filamentous fungi have seen the most major sustained effort. In addition to the published material about filamentous fungi, shared molecular tools have found application in every area of fungal biology. Similarly, shared data has contributed to the success of model systems. The scale of data supporting research with filamentous fungi has grown by 10 to 12 orders of magnitude. From genetic to molecular maps, expression databases, and finally genome resources, the open and collaborative nature of the research communities has assured that the rising tide of data has lifted all of the research systems together.
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Affiliation(s)
- Kevin McCluskey
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Scott E. Baker
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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Pawar PMA, Derba-Maceluch M, Chong SL, Gómez LD, Miedes E, Banasiak A, Ratke C, Gaertner C, Mouille G, McQueen-Mason SJ, Molina A, Sellstedt A, Tenkanen M, Mellerowicz EJ. Expression of fungal acetyl xylan esterase in Arabidopsis thaliana improves saccharification of stem lignocellulose. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:387-97. [PMID: 25960248 DOI: 10.1111/pbi.12393] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/20/2015] [Accepted: 03/28/2015] [Indexed: 05/08/2023]
Abstract
Cell wall hemicelluloses and pectins are O-acetylated at specific positions, but the significance of these substitutions is poorly understood. Using a transgenic approach, we investigated how reducing the extent of O-acetylation in xylan affects cell wall chemistry, plant performance and the recalcitrance of lignocellulose to saccharification. The Aspergillus niger acetyl xylan esterase AnAXE1 was expressed in Arabidopsis under the control of either the constitutively expressed 35S CAMV promoter or a woody-tissue-specific GT43B aspen promoter, and the protein was targeted to the apoplast by its native signal peptide, resulting in elevated acetyl esterase activity in soluble and wall-bound protein extracts and reduced xylan acetylation. No significant alterations in cell wall composition were observed in the transgenic lines, but their xylans were more easily digested by a β-1,4-endoxylanase, and more readily extracted by hot water, acids or alkali. Enzymatic saccharification of lignocellulose after hot water and alkali pretreatments produced up to 20% more reducing sugars in several lines. Fermentation by Trametes versicolor of tissue hydrolysates from the line with a 30% reduction in acetyl content yielded ~70% more ethanol compared with wild type. Plants expressing 35S:AnAXE1 and pGT43B:AnAXE1 developed normally and showed increased resistance to the biotrophic pathogen Hyaloperonospora arabidopsidis, probably due to constitutive activation of defence pathways. However, unintended changes in xyloglucan and pectin acetylation were only observed in 35S:AnAXE1-expressing plants. This study demonstrates that postsynthetic xylan deacetylation in woody tissues is a promising strategy for optimizing lignocellulosic biomass for biofuel production.
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Affiliation(s)
- Prashant Mohan-Anupama Pawar
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå Plant Science Centre, Umeå, Sweden
| | - Marta Derba-Maceluch
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå Plant Science Centre, Umeå, Sweden
| | - Sun-Li Chong
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Leonardo D Gómez
- Center for Novel Agricultural Products Department of Biology, University of York, York, UK
| | - Eva Miedes
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Alicja Banasiak
- Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland
| | - Christine Ratke
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå Plant Science Centre, Umeå, Sweden
| | - Cyril Gaertner
- Institut Jean-Pierre Bourgin UMR 1318 INRA/AgroParisTech, Saclay Plant Sciences, Centre de Versailles-Grignon, Versailles Cedex, France
| | - Grégory Mouille
- Institut Jean-Pierre Bourgin UMR 1318 INRA/AgroParisTech, Saclay Plant Sciences, Centre de Versailles-Grignon, Versailles Cedex, France
| | - Simon J McQueen-Mason
- Center for Novel Agricultural Products Department of Biology, University of York, York, UK
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Anita Sellstedt
- Department of Plant Physiology, Umea University, Umeå Plant Science Centre, Umeå, Sweden
| | - Maija Tenkanen
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Ewa J Mellerowicz
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå Plant Science Centre, Umeå, Sweden
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Genetics of mating in members of the Chaetomiaceae as revealed by experimental and genomic characterization of reproduction in Myceliophthora heterothallica. Fungal Genet Biol 2015; 86:9-19. [PMID: 26608618 DOI: 10.1016/j.fgb.2015.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 01/01/2023]
Abstract
Members of the Chaetomiaceae are among the most studied fungi in industry and among the most reported in investigations of biomass degradation in both natural and laboratory settings. The family is recognized for production of carbohydrate-active enzymes and antibiotics. Thermophilic species are of special interest for their abilities to produce thermally stable enzymes and to be grown under conditions that are unsuitable for potential contaminant microorganisms. Such interests led to the recent acquisition of genome sequences from several members of the family, including thermophilic species, several of which are reported here for the first time. To date, however, thermophilic fungi in industry have served primarily as parts reservoirs and there has been no good genetic model for species in the family Chaetomiaceae or for thermophiles in general. We report here on the reproductive biology of the thermophile Myceliophthora heterothallica, which is heterothallic, unlike most described species in the family. We confirmed heterothallism genetically by following the segregation of mating type idiomorphs and other markers. We have expanded the number of known sexually-compatible individuals from the original isolates from Indiana and Germany to include several isolates from New Mexico. An interesting aspect of development in M. heterothallica is that ascocarp formation is optimal at approximately 30 °C, whereas vegetative growth is optimal at 45 °C. Genome sequences obtained from several strains, including isolates of each mating type, revealed mating-type regions whose genes are organized similarly to those of other members of the Sordariales, except for the presence of a truncated version of the mat A-1 (MAT1-1-1) gene in mating-type a (MAT1-2) strains. In M. heterothallica and other Chaetomiaceae, mating-type A (MAT1-1) strains have the full-length version of mat A-1 that is typical of mating-type A strains of diverse Ascomycota, whereas a strains have only the truncated version. This truncated mat A-1 has an intact open reading frame and a derived start codon that is not present in mat A-1 from A strains. The predicted protein contains a region that is conserved across diverse mat A-1 genes, but it lacks the major alpha1 domain, which characterizes proteins in this family and is known to be required for fertility in A strains from other Ascomycota. Finally, we have used genes from M. heterothallica to probe for mating genes in other homothallic and heterothallic members of the Chaetomiaceae. The majority of homothallic species examined have a typical mat A-1,2,3 (MAT1-1-1,2,3) region in addition to an unlinked mat a-1 (MAT1-2-1) gene, reflecting one type of homothallism commonly observed in diverse Ascomycota.
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Kaur AP, Nocek BP, Xu X, Lowden MJ, Leyva JF, Stogios PJ, Cui H, Di Leo R, Powlowski J, Tsang A, Savchenko A. Functional and structural diversity in GH62 α-L-arabinofuranosidases from the thermophilic fungus Scytalidium thermophilum. Microb Biotechnol 2014; 8:419-33. [PMID: 25267315 PMCID: PMC4408175 DOI: 10.1111/1751-7915.12168] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/16/2014] [Indexed: 01/22/2023] Open
Abstract
The genome of the thermophilic fungus Scytalidium thermophilum (strain CBS 625.91) harbours a wide range of genes involved in carbohydrate degradation, including three genes, abf62A, abf62B and abf62C, predicted to encode glycoside hydrolase family 62 (GH62) enzymes. Transcriptome analysis showed that only abf62A and abf62C are actively expressed during growth on diverse substrates including straws from barley, alfalfa, triticale and canola. The abf62A and abf62C genes were expressed in Escherichia coli and the resulting recombinant proteins were characterized. Calcium-free crystal structures of Abf62C in apo and xylotriose bound forms were determined to 1.23 and 1.48 Å resolution respectively. Site-directed mutagenesis confirmed Asp55, Asp171 and Glu230 as catalytic triad residues, and revealed the critical role of non-catalytic residues Asp194, Trp229 and Tyr338 in positioning the scissile α-L-arabinofuranoside bond at the catalytic site. Further, the +2R substrate-binding site residues Tyr168 and Asn339, as well as the +2NR residue Tyr226, are involved in accommodating long-chain xylan polymers. Overall, our structural and functional analysis highlights characteristic differences between Abf62A and Abf62C, which represent divergent subgroups in the GH62 family.
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Affiliation(s)
- Amrit Pal Kaur
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, M5S 3E5, Canada
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Kolbusz MA, Di Falco M, Ishmael N, Marqueteau S, Moisan MC, Baptista CDS, Powlowski J, Tsang A. Transcriptome and exoproteome analysis of utilization of plant-derived biomass by Myceliophthora thermophila. Fungal Genet Biol 2014; 72:10-20. [PMID: 24881579 DOI: 10.1016/j.fgb.2014.05.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 05/16/2014] [Accepted: 05/17/2014] [Indexed: 11/29/2022]
Abstract
Myceliophthora thermophila is a thermophilic fungus whose genome encodes a wide range of carbohydrate-active enzymes (CAZymes) involved in plant biomass degradation. Such enzymes have potential applications in turning different kinds of lignocellulosic feedstock into sugar precursors for biofuels and chemicals. The present study examined and compared the transcriptomes and exoproteomes of M. thermophila during cultivation on different types of complex biomass to gain insight into how its secreted enzymatic machinery varies with different sources of lignocellulose. In the transcriptome analysis three monocot (barley, oat, triticale) and three dicot (alfalfa, canola, flax) plants were used whereas in the proteome analysis additional substrates, i.e. wood and corn stover pulps, were included. A core set of 59 genes encoding CAZymes was up-regulated in response to both monocot and dicot straws, including nine polysaccharide monooxygenases and GH10, but not GH11, xylanases. Genes encoding additional xylanolytic enzymes were up-regulated during growth on monocot straws, while genes encoding additional pectinolytic enzymes were up-regulated in response to dicot biomass. Exoproteome analysis was generally consistent with the conclusions drawn from transcriptome analysis, but additional CAZymes that accumulated to high levels were identified. Despite the wide variety of biomass sources tested some CAZy family members were not expressed under any condition. The results of this study provide a comprehensive view from both transcriptome and exoproteome levels, of how M. thermophila responds to a wide range of biomass sources using its genomic resources.
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Affiliation(s)
- Magdalena Anna Kolbusz
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada; Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada; Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Marcos Di Falco
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Nadeeza Ishmael
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Sandrine Marqueteau
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Marie-Claude Moisan
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Cassio da Silva Baptista
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Justin Powlowski
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada; Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada; Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
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Cloning and enzymatic characterization of four thermostable fungal endo-1,4-β-xylanases. Appl Microbiol Biotechnol 2013; 98:3613-28. [DOI: 10.1007/s00253-013-5244-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 08/17/2013] [Accepted: 08/21/2013] [Indexed: 10/26/2022]
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Pereira EO, Tsang A, McAllister TA, Menassa R. The production and characterization of a new active lipase from Acremonium alcalophilum using a plant bioreactor. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:111. [PMID: 23915965 PMCID: PMC3750315 DOI: 10.1186/1754-6834-6-111] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/31/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Microorganisms are the most proficient decomposers in nature, using secreted enzymes in the hydrolysis of lignocellulose. As such, they present the most abundant source for discovery of new enzymes. Acremonium alcalophilum is the only known cellulolytic fungus that thrives in alkaline conditions and can be cultured readily in the laboratory. Its optimal conditions for growth are 30°C and pH 9.0-9.2. The genome sequence of Acremonium alcalophilum has revealed a large number of genes encoding biomass-degrading enzymes. Among these enzymes, lipases are interesting because of several industrial applications including biofuels, detergent, food processing and textile industries. RESULTS We identified a lipA gene in the genome sequence of Acremonium alcalophilum, encoding a protein with a predicted lipase domain with weak sequence identity to characterized enzymes. Unusually, the predicted lipase displays ≈ 30% amino acid sequence identity to both feruloyl esterase and lipase of Aspergillus niger. LipA, when transiently produced in Nicotiana benthamiana, accumulated to over 9% of total soluble protein. Plant-produced recombinant LipA is active towards p-nitrophenol esters of various carbon chain lengths with peak activity on medium-chain fatty acid (C8). The enzyme is also highly active on xylose tetra-acetate and oat spelt xylan. These results suggests that LipA is a novel lipolytic enzyme that possesses both lipase and acetylxylan esterase activity. We determined that LipA is a glycoprotein with pH and temperature optima at 8.0 and 40°C, respectively. CONCLUSION Besides being the first heterologous expression and characterization of a gene coding for a lipase from A. alcalophilum, this report shows that LipA is very versatile exhibiting both acetylxylan esterase and lipase activities potentially useful for diverse industry sectors, and that tobacco is a suitable bioreactor for producing fungal proteins.
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Affiliation(s)
- Eridan Orlando Pereira
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
- Department of Biology, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Tim A McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB T1J 4B1, Canada
| | - Rima Menassa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
- Department of Biology, The University of Western Ontario, London, ON N6A 5B7, Canada
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Arnaud MB, Cerqueira GC, Inglis DO, Skrzypek MS, Binkley J, Chibucos MC, Crabtree J, Howarth C, Orvis J, Shah P, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G, Wortman JR. The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources. Nucleic Acids Res 2011; 40:D653-9. [PMID: 22080559 PMCID: PMC3245136 DOI: 10.1093/nar/gkr875] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The Aspergillus Genome Database (AspGD; http://www.aspgd.org) is a freely available, web-based resource for researchers studying fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD curators have now completed comprehensive review of the entire published literature about Aspergillus nidulans and Aspergillus fumigatus, and this annotation is provided with streamlined, ortholog-based navigation of the multispecies information. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. AspGD also provides resources to foster interaction and dissemination of community information and resources. We welcome and encourage feedback at aspergillus-curator@lists.stanford.edu.
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Affiliation(s)
- Martha B Arnaud
- Department of Genetics, Stanford University Medical School, Stanford, CA 94305-5120, USA.
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Berka RM, Grigoriev IV, Otillar R, Salamov A, Grimwood J, Reid I, Ishmael N, John T, Darmond C, Moisan MC, Henrissat B, Coutinho PM, Lombard V, Natvig DO, Lindquist E, Schmutz J, Lucas S, Harris P, Powlowski J, Bellemare A, Taylor D, Butler G, de Vries RP, Allijn IE, van den Brink J, Ushinsky S, Storms R, Powell AJ, Paulsen IT, Elbourne LDH, Baker SE, Magnuson J, Laboissiere S, Clutterbuck AJ, Martinez D, Wogulis M, de Leon AL, Rey MW, Tsang A. Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. Nat Biotechnol 2011; 29:922-7. [PMID: 21964414 DOI: 10.1038/nbt.1976] [Citation(s) in RCA: 305] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 08/18/2011] [Indexed: 11/09/2022]
Abstract
Thermostable enzymes and thermophilic cell factories may afford economic advantages in the production of many chemicals and biomass-based fuels. Here we describe and compare the genomes of two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris. To our knowledge, these genomes are the first described for thermophilic eukaryotes and the first complete telomere-to-telomere genomes for filamentous fungi. Genome analyses and experimental data suggest that both thermophiles are capable of hydrolyzing all major polysaccharides found in biomass. Examination of transcriptome data and secreted proteins suggests that the two fungi use shared approaches in the hydrolysis of cellulose and xylan but distinct mechanisms in pectin degradation. Characterization of the biomass-hydrolyzing activity of recombinant enzymes suggests that these organisms are highly efficient in biomass decomposition at both moderate and high temperatures. Furthermore, we present evidence suggesting that aside from representing a potential reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using classical and molecular genetics.
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Tambor JH, Ren H, Ushinsky S, Zheng Y, Riemens A, St-Francois C, Tsang A, Powlowski J, Storms R. Recombinant expression, activity screening and functional characterization identifies three novel endo-1,4-β-glucanases that efficiently hydrolyse cellulosic substrates. Appl Microbiol Biotechnol 2011; 93:203-14. [DOI: 10.1007/s00253-011-3419-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 05/24/2011] [Accepted: 05/28/2011] [Indexed: 11/27/2022]
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Luo H, Sun C, Song J, Lan J, Li Y, Li X, Chen S. Generation and analysis of expressed sequence tags from a cDNA library of the fruiting body of Ganoderma lucidum. Chin Med 2010; 5:9. [PMID: 20230644 PMCID: PMC2848221 DOI: 10.1186/1749-8546-5-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 03/16/2010] [Indexed: 11/10/2022] Open
Abstract
Background Little genomic or trancriptomic information on Ganoderma lucidum (Lingzhi) is known. This study aims to discover the transcripts involved in secondary metabolite biosynthesis and developmental regulation of G. lucidum using an expressed sequence tag (EST) library. Methods A cDNA library was constructed from the G. lucidum fruiting body. Its high-quality ESTs were assembled into unique sequences with contigs and singletons. The unique sequences were annotated according to sequence similarities to genes or proteins available in public databases. The detection of simple sequence repeats (SSRs) was preformed by online analysis. Results A total of 1,023 clones were randomly selected from the G. lucidum library and sequenced, yielding 879 high-quality ESTs. These ESTs showed similarities to a diverse range of genes. The sequences encoding squalene epoxidase (SE) and farnesyl-diphosphate synthase (FPS) were identified in this EST collection. Several candidate genes, such as hydrophobin, MOB2, profilin and PHO84 were detected for the first time in G. lucidum. Thirteen (13) potential SSR-motif microsatellite loci were also identified. Conclusion The present study demonstrates a successful application of EST analysis in the discovery of transcripts involved in the secondary metabolite biosynthesis and the developmental regulation of G. lucidum.
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Affiliation(s)
- Hongmei Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haidian District, Beijing, PR China
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Chemical induction of silent biosynthetic pathway transcription in Aspergillus niger. J Ind Microbiol Biotechnol 2009; 36:1199-213. [DOI: 10.1007/s10295-009-0601-4] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 05/21/2009] [Indexed: 12/17/2022]
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Pecyna MJ, Ullrich R, Bittner B, Clemens A, Scheibner K, Schubert R, Hofrichter M. Molecular characterization of aromatic peroxygenase from Agrocybe aegerita. Appl Microbiol Biotechnol 2009; 84:885-97. [DOI: 10.1007/s00253-009-2000-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 03/31/2009] [Accepted: 04/01/2009] [Indexed: 02/08/2023]
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Wright JC, Sugden D, Francis-McIntyre S, Riba-Garcia I, Gaskell SJ, Grigoriev IV, Baker SE, Beynon RJ, Hubbard SJ. Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger. BMC Genomics 2009; 10:61. [PMID: 19193216 PMCID: PMC2644712 DOI: 10.1186/1471-2164-10-61] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Accepted: 02/04/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Proteomic data is a potentially rich, but arguably unexploited, data source for genome annotation. Peptide identifications from tandem mass spectrometry provide prima facie evidence for gene predictions and can discriminate over a set of candidate gene models. Here we apply this to the recently sequenced Aspergillus niger fungal genome from the Joint Genome Institutes (JGI) and another predicted protein set from another A.niger sequence. Tandem mass spectra (MS/MS) were acquired from 1d gel electrophoresis bands and searched against all available gene models using Average Peptide Scoring (APS) and reverse database searching to produce confident identifications at an acceptable false discovery rate (FDR). RESULTS 405 identified peptide sequences were mapped to 214 different A.niger genomic loci to which 4093 predicted gene models clustered, 2872 of which contained the mapped peptides. Interestingly, 13 (6%) of these loci either had no preferred predicted gene model or the genome annotators' chosen "best" model for that genomic locus was not found to be the most parsimonious match to the identified peptides. The peptides identified also boosted confidence in predicted gene structures spanning 54 introns from different gene models. CONCLUSION This work highlights the potential of integrating experimental proteomics data into genomic annotation pipelines much as expressed sequence tag (EST) data has been. A comparison of the published genome from another strain of A.niger sequenced by DSM showed that a number of the gene models or proteins with proteomics evidence did not occur in both genomes, further highlighting the utility of the method.
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Affiliation(s)
- James C Wright
- Dept Veterinary Preclinical Sciences, University of Liverpool, Liverpool, UK.
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A Method for Construction, Cloning and Expression of Intron-Less Gene from Unannotated Genomic DNA. Mol Biotechnol 2008; 40:217-23. [DOI: 10.1007/s12033-008-9076-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Accepted: 05/23/2008] [Indexed: 10/22/2022]
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Analysis of expressed sequence tags (ESTs) from Lentinula edodes. Appl Microbiol Biotechnol 2008; 79:461-70. [DOI: 10.1007/s00253-008-1441-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Revised: 02/27/2008] [Accepted: 02/29/2008] [Indexed: 11/30/2022]
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A xyloglucan-specific family 12 glycosyl hydrolase from Aspergillus niger: recombinant expression, purification and characterization. Biochem J 2008; 411:161-70. [PMID: 18072936 DOI: 10.1042/bj20070819] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A new GH12 (glycosyl hydrolase 12) family XEG [xyloglucan-specific endo-β-1,4-glucanase (EC 3.2.1.151)] from Aspergillus niger, AnXEG12A, was overexpressed, purified and characterized. Whereas seven xyloglucanases from GH74 and two xyloglucanases from GH5 have been characterized previously, this is only the third characterized example of a GH12 family xyloglucanase. GH12 enzymes are structurally and mechanistically distinct from GH74 enzymes. Although over 100 GH12 sequences are now available, little is known about the structural and biochemical bases of xyloglucan binding and hydrolysis by GH12 enzymes. Comparison of the AnXEG12A cDNA sequence with the genome sequence of A. niger showed the presence of two introns, one in the coding region and the second one in the 333-nt-long 3′-untranslated region of the transcript. The enzyme was expressed recombinantly in A. niger and was readily purified from the culture supernatant. The isolated enzyme appeared to have been processed by a kexin-type protease, which removed a short prosequence. The substrate specificity was restricted to xyloglucan, with cleavage at unbranched glucose in the backbone. The apparent kinetic parameters were similar to those reported for other xyloglucan-degrading endoglucanases. The pH optimum (5.0) and temperature resulting in highest enzyme activity (50–60 °C) were higher than those reported for a GH12 family xyloglucanase from Aspergillus aculeatus, but similar to those of cellulose-specific endoglucanases from the GH12 family. Phylogenetic, sequence and structural comparisons of GH12 family endoglucanases helped to delineate features that appear to be correlated to xyloglucan specificity.
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Abstract
Filamentous fungi have been recognized as extraordinary producers of secreted proteins and are known to produce novel proteins and enzymes through dispensable metabolic pathways. Here, methods are described for the isolation and enrichment of samples of secreted proteins from cultures of filamentous fungi for analysis by gel electrophoresis and mass spectrometry techniques. These methods can be readily applied to the study of differential protein expression and secretion and metabolic pathways in filamentous fungi by proteomic approaches.
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Benech RO, Li X, Patton D, Powlowski J, Storms R, Bourbonnais R, Paice M, Tsang A. Recombinant expression, characterization, and pulp prebleaching property of a Phanerochaete chrysosporium endo-β-1,4-mannanase. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2007.06.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Abstract
Aspergillus niger is a filamentous ascomycete fungus that is ubiquitous in the environment and has been implicated in opportunistic infections of humans. In addition to its role as an opportunistic human pathogen, A. niger is economically important as a fermentation organism used for the production of citric acid. Industrial citric acid production by A. niger represents one of the most efficient, highest yield bioprocesses in use currently by industry. The genome size of A. niger is estimated to be between 35.5 and 38.5 megabases (Mb) divided among eight chromosomes/linkage groups that vary in size from 3.5-6.6 Mb. Currently, there are three independent A. niger genome projects, an indication of the economic importance of this organism. The rich amount of data resulting from these multiple A. niger genome sequences will be used for basic and applied research programs applicable to fermentation process development, morphology and pathogenicity.
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Affiliation(s)
- Scott E Baker
- Fungal Biotechnology Team, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
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Vizcaíno JA, Redondo J, Suárez MB, Cardoza RE, Hermosa R, González FJ, Rey M, Monte E. Generation, annotation, and analysis of ESTs from four different Trichoderma strains grown under conditions related to biocontrol. Appl Microbiol Biotechnol 2007; 75:853-62. [PMID: 17333173 DOI: 10.1007/s00253-007-0885-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Revised: 02/08/2007] [Accepted: 02/08/2007] [Indexed: 11/29/2022]
Abstract
The functional genomics project "TrichoEST" was developed focused on different taxonomic groups of Trichoderma with biocontrol potential. Four cDNA libraries were constructed, using similar growth conditions, from four different Trichoderma strains: Trichoderma longibrachiatum T52, Trichoderma asperellum T53, Trichoderma virens T59, and Trichoderma sp. T78. In this study, we present the analysis of the 8,160 expressed sequence tags (ESTs) generated. Each EST library was independently assembled and 1,000-1,300 unique sequences were identified in each strain. First, we queried our collection of ESTs against the NCBI nonredundant database using the BLASTX algorithm. Moreover, using the Gene Ontology hierarchy, we performed the annotation of 40.9% of the unique sequences. Later, based on the EST abundance, we examined the highly expressed genes in the four strains. A hydrophobin was found as the gene expressed at the highest level in two of the strains, but we also found that other unique sequences similar to the HEX1, QID3, and NMT1 proteins were highly represented in at least two of the Trichoderma strains.
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Affiliation(s)
- Juan Antonio Vizcaíno
- Centro de Investigaciones Científicas Isla de la Cartuja, Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC/University of Seville, 41092 Sevilla, Spain.
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Vizcaíno JA, González FJ, Suárez MB, Redondo J, Heinrich J, Delgado-Jarana J, Hermosa R, Gutiérrez S, Monte E, Llobell A, Rey M. Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413. BMC Genomics 2006; 7:193. [PMID: 16872539 PMCID: PMC1562415 DOI: 10.1186/1471-2164-7-193] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Accepted: 07/27/2006] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The filamentous fungus Trichoderma harzianum is used as biological control agent of several plant-pathogenic fungi. In order to study the genome of this fungus, a functional genomics project called "TrichoEST" was developed to give insights into genes involved in biological control activities using an approach based on the generation of expressed sequence tags (ESTs). RESULTS Eight different cDNA libraries from T. harzianum strain CECT 2413 were constructed. Different growth conditions involving mainly different nutrient conditions and/or stresses were used. We here present the analysis of the 8,710 ESTs generated. A total of 3,478 unique sequences were identified of which 81.4% had sequence similarity with GenBank entries, using the BLASTX algorithm. Using the Gene Ontology hierarchy, we performed the annotation of 51.1% of the unique sequences and compared its distribution among the gene libraries. Additionally, the InterProScan algorithm was used in order to further characterize the sequences. The identification of the putatively secreted proteins was also carried out. Later, based on the EST abundance, we examined the highly expressed genes and a hydrophobin was identified as the gene expressed at the highest level. We compared our collection of ESTs with the previous collections obtained from Trichoderma species and we also compared our sequence set with different complete eukaryotic genomes from several animals, plants and fungi. Accordingly, the presence of similar sequences in different kingdoms was also studied. CONCLUSION This EST collection and its annotation provide a significant resource for basic and applied research on T. harzianum, a fungus with a high biotechnological interest.
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Affiliation(s)
- Juan Antonio Vizcaíno
- IBVF-CIC Isla de la Cartuja, CSIC/Universidad de Sevilla. Avda. Américo Vespucio s/n. 41092, Sevilla, Spain
| | - Francisco Javier González
- Newbiotechnic, S. A. (NBT). Parque Industrial de Bollullos A-49 (PIBO). 41110, Bollullos de la Mitación. Sevilla, Spain
| | - M Belén Suárez
- IBVF-CIC Isla de la Cartuja, CSIC/Universidad de Sevilla. Avda. Américo Vespucio s/n. 41092, Sevilla, Spain
- Spanish-Portuguese Center of Agricultural Research (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, lab 208, Plaza Doctores de la Reina s/n, 37007, Salamanca, Spain
| | - José Redondo
- Newbiotechnic, S. A. (NBT). Parque Industrial de Bollullos A-49 (PIBO). 41110, Bollullos de la Mitación. Sevilla, Spain
| | - Julian Heinrich
- Newbiotechnic, S. A. (NBT). Parque Industrial de Bollullos A-49 (PIBO). 41110, Bollullos de la Mitación. Sevilla, Spain
| | - Jesús Delgado-Jarana
- IBVF-CIC Isla de la Cartuja, CSIC/Universidad de Sevilla. Avda. Américo Vespucio s/n. 41092, Sevilla, Spain
| | - Rosa Hermosa
- Spanish-Portuguese Center of Agricultural Research (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, lab 208, Plaza Doctores de la Reina s/n, 37007, Salamanca, Spain
| | - Santiago Gutiérrez
- Area of Microbiology. Escuela Superior y Técnica de Ingeniería Agraria. Universidad de León, Campus de Ponferrada. Avda. Astorga s/n. 24400, Ponferrada, Spain
| | - Enrique Monte
- Newbiotechnic, S. A. (NBT). Parque Industrial de Bollullos A-49 (PIBO). 41110, Bollullos de la Mitación. Sevilla, Spain
| | - Antonio Llobell
- IBVF-CIC Isla de la Cartuja, CSIC/Universidad de Sevilla. Avda. Américo Vespucio s/n. 41092, Sevilla, Spain
| | - Manuel Rey
- Newbiotechnic, S. A. (NBT). Parque Industrial de Bollullos A-49 (PIBO). 41110, Bollullos de la Mitación. Sevilla, Spain
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