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Thieme N, Wu VW, Dietschmann A, Salamov AA, Wang M, Johnson J, Singan VR, Grigoriev IV, Glass NL, Somerville CR, Benz JP. The transcription factor PDR-1 is a multi-functional regulator and key component of pectin deconstruction and catabolism in Neurospora crassa. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:149. [PMID: 28616073 PMCID: PMC5469009 DOI: 10.1186/s13068-017-0807-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 04/29/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Pectin is an abundant component in many fruit and vegetable wastes and could therefore be an excellent resource for biorefinery, but is currently underutilized. Fungal pectinases already play a crucial role for industrial purposes, such as for foodstuff processing. However, the regulation of pectinase gene expression is still poorly understood. For an optimal utilization of plant biomass for biorefinery and biofuel production, a detailed analysis of the underlying regulatory mechanisms is warranted. In this study, we applied the genetic resources of the filamentous ascomycete species Neurospora crassa to screen for transcription factors that play a major role in pectinase induction. RESULTS The pectin degradation regulator-1 (PDR-1) was identified through a transcription factor mutant screen in N. crassa. The Δpdr-1 mutant exhibited a severe growth defect on pectin and all tested pectin-related poly- and monosaccharides. Biochemical as well as transcriptional analyses of WT and the Δpdr-1 mutant revealed that while PDR-1-mediated gene induction was dependent on the presence of l-rhamnose, it also strongly affected the degradation of the homogalacturonan backbone. The expression of the endo-polygalacturonase gh28-1 was greatly reduced in the Δpdr-1 mutant, while the expression levels of all pectate lyase genes increased. Moreover, a pdr-1 overexpression strain displayed substantially increased pectinase production. Promoter analysis of the PDR-1 regulon allowed refinement of the putative PDR-1 DNA-binding motif. CONCLUSIONS PDR-1 is highly conserved in filamentous ascomycete fungi and is present in many pathogenic and industrially important fungi. Our data demonstrate that the function of PDR-1 in N. crassa combines features of two recently described transcription factors in Aspergillus niger (RhaR) and Botrytis cinerea (GaaR). The results presented in this study contribute to a broader understanding of how pectin degradation is orchestrated in filamentous fungi and how it could be manipulated for optimized pectinase production.
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Affiliation(s)
- Nils Thieme
- HFM, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Vincent W. Wu
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA USA
- Energy Biosciences Institute, University of California, Berkeley, Berkeley, CA USA
| | - Axel Dietschmann
- HFM, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- Department of Infection Biology, Institute for Clinical Microbiology, Immunology and Hygiene, Universitätsklinikum Erlangen and Friedrich-Alexander Universität, Erlangen-Nuremberg, Germany
| | - Asaf A. Salamov
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA USA
| | - Mei Wang
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA USA
| | - Jenifer Johnson
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA USA
| | - Vasanth R. Singan
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA USA
| | - Igor V. Grigoriev
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA USA
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA USA
| | - N. Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA USA
- Energy Biosciences Institute, University of California, Berkeley, Berkeley, CA USA
- Environmental Genomics and System Biology, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Chris R. Somerville
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA USA
- Energy Biosciences Institute, University of California, Berkeley, Berkeley, CA USA
| | - J. Philipp Benz
- HFM, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
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53
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Alazi E, Niu J, Kowalczyk JE, Peng M, Aguilar Pontes MV, van Kan JAL, Visser J, de Vries RP, Ram AFJ. The transcriptional activator GaaR of Aspergillus niger is required for release and utilization of d-galacturonic acid from pectin. FEBS Lett 2016; 590:1804-15. [PMID: 27174630 PMCID: PMC5111758 DOI: 10.1002/1873-3468.12211] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/04/2016] [Accepted: 05/05/2016] [Indexed: 01/15/2023]
Abstract
We identified the d-galacturonic acid (GA)-responsive transcriptional activator GaaR of the saprotrophic fungus, Aspergillus niger, which was found to be essential for growth on GA and polygalacturonic acid (PGA). Growth of the ΔgaaR strain was reduced on complex pectins. Genome-wide expression analysis showed that GaaR is required for the expression of genes necessary to release GA from PGA and more complex pectins, to transport GA into the cell, and to induce the GA catabolic pathway. Residual growth of ΔgaaR on complex pectins is likely due to the expression of pectinases acting on rhamnogalacturonan and subsequent metabolism of the monosaccharides other than GA.
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Affiliation(s)
- Ebru Alazi
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Jing Niu
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Joanna E Kowalczyk
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Mao Peng
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Maria Victoria Aguilar Pontes
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Jan A L van Kan
- Laboratory of Phytopathology, Wageningen University, The Netherlands
| | - Jaap Visser
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands.,Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Arthur F J Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
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Raulo R, Kokolski M, Archer DB. The roles of the zinc finger transcription factors XlnR, ClrA and ClrB in the breakdown of lignocellulose by Aspergillus niger. AMB Express 2016; 6:5. [PMID: 26780227 PMCID: PMC4715039 DOI: 10.1186/s13568-016-0177-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 11/23/2022] Open
Abstract
Genes encoding the key transcription factors (TF) XlnR, ClrA and ClrB were deleted from Aspergillus niger and the resulting strains were assessed for growth on glucose and wheat straw, transcription of genes encoding glycosyl hydrolases and saccharification activity. Growth of all mutant strains, based in straw on measurement of pH and assay of glucosamine, was impaired in relation to the wild-type (WT) strain although deletion of clrA had less effect than deletion of xlnR or clrB. Release of sugars from wheat straw was also lowered when culture filtrates from TF deletion strains were compared with WT culture filtrates. Transcript levels of cbhA, eglC and xynA were measured in all strains in glucose and wheat straw media in batch culture with and without pH control. Transcript levels from cbhA and eglC were lowered in all mutant strains compared to WT although the impact of deleting clrA was not pronounced with expression of eglC and had no effect on xynA. The impact on transcription was not related to changes in pH. In addition to impaired growth on wheat straw, the ΔxlnR strain was sensitive to oxidative stress and displayed cell wall defects in the glucose condition suggesting additional roles for XlnR. The characterisation of TFs, such as ClrB, provides new areas of improvement for industrial processes for production of second generation biofuels.
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Affiliation(s)
- Roxane Raulo
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Matthew Kokolski
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - David B. Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
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Klaubauf S, Zhou M, Lebrun MH, de Vries RP, Battaglia E. A novel L-arabinose-responsive regulator discovered in the rice-blast fungus Pyricularia oryzae (Magnaporthe oryzae). FEBS Lett 2016; 590:550-8. [PMID: 26790567 DOI: 10.1002/1873-3468.12070] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/19/2015] [Accepted: 01/04/2016] [Indexed: 11/12/2022]
Abstract
In this study we identified the L-arabinose-responsive regulator of Pyricularia oryzae that regulates L-arabinose release and catabolism. Previously we identified the Zn2Cys6 transcription factor (TF), AraR, that has this role in the Trichocomaceae family (Eurotiales), but is absent in other fungi. Candidate Zn2Cys6 TF genes were selected according to their transcript profiles on L-arabinose. Deletion mutants of these genes were screened for their growth phenotype on L-arabinose. One mutant, named Δara1, was further analyzed. Our analysis demonstrated that Ara1 from P. oryzae is the functional analog of AraR from A. niger, while there is no significant sequence similarity between them.
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Affiliation(s)
- Sylvia Klaubauf
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Miaomiao Zhou
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Marc-Henri Lebrun
- MPA, UMR 2847 CNRS-Bayer Crop science, Lyon, France.,UMR 1290 BIOGER-CPP, INRA, AgroParisTech, Campus AgroParisTech, Ave Louis Bretignières, F75850 Thiverval-Grignon, France
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Evy Battaglia
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
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Manzanares-Miralles L, Sarikaya-Bayram Ö, Smith EB, Dolan SK, Bayram Ö, Jones GW, Doyle S. Quantitative proteomics reveals the mechanism and consequence of gliotoxin-mediated dysregulation of the methionine cycle in Aspergillus niger. J Proteomics 2016; 131:149-162. [DOI: 10.1016/j.jprot.2015.10.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 10/14/2015] [Accepted: 10/18/2015] [Indexed: 12/25/2022]
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57
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Mardones W, Callegari E, Eyzaguirre J. Heterologous expression of a Penicillium purpurogenum exo-arabinanase in Pichia pastoris and its biochemical characterization. Fungal Biol 2015; 119:1267-1278. [DOI: 10.1016/j.funbio.2015.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 11/27/2022]
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Kowalczyk JE, Gruben BS, Battaglia E, Wiebenga A, Majoor E, de Vries RP. Genetic Interaction of Aspergillus nidulans galR, xlnR and araR in Regulating D-Galactose and L-Arabinose Release and Catabolism Gene Expression. PLoS One 2015; 10:e0143200. [PMID: 26580075 PMCID: PMC4651341 DOI: 10.1371/journal.pone.0143200] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/02/2015] [Indexed: 11/29/2022] Open
Abstract
In Aspergillus nidulans, the xylanolytic regulator XlnR and the arabinanolytic regulator AraR co-regulate pentose catabolism. In nature, the pentose sugars D-xylose and L-arabinose are both main building blocks of the polysaccharide arabinoxylan. In pectin and arabinogalactan, these two monosaccharides are found in combination with D-galactose. GalR, the regulator that responds to the presence of D-galactose, regulates the D-galactose catabolic pathway. In this study we investigated the possible interaction between XlnR, AraR and GalR in pentose and/or D-galactose catabolism in A. nidulans. Growth phenotypes and metabolic gene expression profiles were studied in single, double and triple disruptant A. nidulans strains of the genes encoding these paralogous transcription factors. Our results demonstrate that AraR and XlnR not only control pentose catabolic pathway genes, but also genes of the oxido-reductive D-galactose catabolic pathway. This suggests an interaction between three transcriptional regulators in D-galactose catabolism. Conversely, GalR is not involved in regulation of pentose catabolism, but controls only genes of the oxido-reductive D-galactose catabolic pathway.
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Affiliation(s)
- Joanna E. Kowalczyk
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Birgit S. Gruben
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
- Microbiology, Utrecht University, Utrecht, the Netherlands
| | - Evy Battaglia
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
- Microbiology, Utrecht University, Utrecht, the Netherlands
| | - Ad Wiebenga
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Eline Majoor
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Ronald P. de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
- * E-mail:
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59
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Enhancing saccharification of wheat straw by mixing enzymes from genetically-modified Trichoderma reesei and Aspergillus niger. Biotechnol Lett 2015; 38:65-70. [PMID: 26354856 PMCID: PMC4706842 DOI: 10.1007/s10529-015-1951-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/02/2015] [Indexed: 12/15/2022]
Abstract
Objectives To increase the efficiency of enzymatic hydrolysis for plant biomass conversion into renewable biofuel and chemicals. Results By overexpressing the point mutation A824 V transcriptional activator Xyr1 in Trichoderma reesei, carboxymethyl cellulase, cellobiosidase and β-d-glucosidase activities of the best mutant were increased from 1.8 IU/ml, 0.1 IU/ml and 0.05 IU/ml to 4.8 IU/ml, 0.4 IU/ml and 0.3 IU/ml, respectively. The sugar yield of wheat straw saccharification by combining enzymes from this mutant and the Aspergillus niger genetically modified strain ΔcreA/xlnRc/araRc was improved up to 7.5 mg/ml, a 229 % increase compared to the combination of wild type strains. Conclusions Mixing enzymes from T. reesei and A. niger combined with the genetic modification of transcription factors is a promising strategy to increase saccharification efficiency. Electronic supplementary material The online version of this article (doi:10.1007/s10529-015-1951-9) contains supplementary material, which is available to authorized users.
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Benoit I, Culleton H, Zhou M, DiFalco M, Aguilar-Osorio G, Battaglia E, Bouzid O, Brouwer CPJM, El-Bushari HBO, Coutinho PM, Gruben BS, Hildén KS, Houbraken J, Barboza LAJ, Levasseur A, Majoor E, Mäkelä MR, Narang HM, Trejo-Aguilar B, van den Brink J, vanKuyk PA, Wiebenga A, McKie V, McCleary B, Tsang A, Henrissat B, de Vries RP. Closely related fungi employ diverse enzymatic strategies to degrade plant biomass. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:107. [PMID: 26236396 PMCID: PMC4522099 DOI: 10.1186/s13068-015-0285-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/09/2015] [Indexed: 05/06/2023]
Abstract
BACKGROUND Plant biomass is the major substrate for the production of biofuels and biochemicals, as well as food, textiles and other products. It is also the major carbon source for many fungi and enzymes of these fungi are essential for the depolymerization of plant polysaccharides in industrial processes. This is a highly complex process that involves a large number of extracellular enzymes as well as non-hydrolytic proteins, whose production in fungi is controlled by a set of transcriptional regulators. Aspergillus species form one of the best studied fungal genera in this field, and several species are used for the production of commercial enzyme cocktails. RESULTS It is often assumed that related fungi use similar enzymatic approaches to degrade plant polysaccharides. In this study we have compared the genomic content and the enzymes produced by eight Aspergilli for the degradation of plant biomass. All tested Aspergilli have a similar genomic potential to degrade plant biomass, with the exception of A. clavatus that has a strongly reduced pectinolytic ability. Despite this similar genomic potential their approaches to degrade plant biomass differ markedly in the overall activities as well as the specific enzymes they employ. While many of the genes have orthologs in (nearly) all tested species, only very few of the corresponding enzymes are produced by all species during growth on wheat bran or sugar beet pulp. In addition, significant differences were observed between the enzyme sets produced on these feedstocks, largely correlating with their polysaccharide composition. CONCLUSIONS These data demonstrate that Aspergillus species and possibly also other related fungi employ significantly different approaches to degrade plant biomass. This makes sense from an ecological perspective where mixed populations of fungi together degrade plant biomass. The results of this study indicate that combining the approaches from different species could result in improved enzyme mixtures for industrial applications, in particular saccharification of plant biomass for biofuel production. Such an approach may result in a much better improvement of saccharification efficiency than adding specific enzymes to the mixture of a single fungus, which is currently the most common approach used in biotechnology.
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Affiliation(s)
- Isabelle Benoit
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- />Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Helena Culleton
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- />Megazyme International Ireland, IDA Business Park, Bray, Wicklow Ireland
| | - Miaomiao Zhou
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marcos DiFalco
- />Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Guillermo Aguilar-Osorio
- />Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- />Department of Food Science and Biotechnology, Faculty of Chemistry, National University of México, UNAM, Cd. Universitaria, C.P. 04510 Mexico, DF Mexico
| | - Evy Battaglia
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- />Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ourdia Bouzid
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- />Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Carlo P J M Brouwer
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Hala B O El-Bushari
- />Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Pedro M Coutinho
- />Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, 13288 Marseille, France
- />CNRS, UMR7257, Aix-Marseille University, 13288 Marseille, France
| | - Birgit S Gruben
- />Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Kristiina S Hildén
- />Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Jos Houbraken
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Luis Alexis Jiménez Barboza
- />Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Anthony Levasseur
- />INRA, UMR1163 de Biotechnologie des Champignons Filamenteux, ESIL, Marseille, France
| | - Eline Majoor
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Miia R Mäkelä
- />Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Hari-Mander Narang
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Blanca Trejo-Aguilar
- />Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Joost van den Brink
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Patricia A vanKuyk
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Ad Wiebenga
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Vincent McKie
- />Megazyme International Ireland, IDA Business Park, Bray, Wicklow Ireland
| | - Barry McCleary
- />Megazyme International Ireland, IDA Business Park, Bray, Wicklow Ireland
| | - Adrian Tsang
- />Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Bernard Henrissat
- />Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, 13288 Marseille, France
- />INRA, USC 1408 AFMB, 13288 Marseille, France
- />Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ronald P de Vries
- />Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- />Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Meyer V, Fiedler M, Nitsche B, King R. The Cell Factory Aspergillus Enters the Big Data Era: Opportunities and Challenges for Optimising Product Formation. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 149:91-132. [PMID: 25616499 DOI: 10.1007/10_2014_297] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Living with limits. Getting more from less. Producing commodities and high-value products from renewable resources including waste. What is the driving force and quintessence of bioeconomy outlines the lifestyle and product portfolio of Aspergillus, a saprophytic genus, to which some of the top-performing microbial cell factories belong: Aspergillus niger, Aspergillus oryzae and Aspergillus terreus. What makes them so interesting for exploitation in biotechnology and how can they help us to address key challenges of the twenty-first century? How can these strains become trimmed for better growth on second-generation feedstocks and how can we enlarge their product portfolio by genetic and metabolic engineering to get more from less? On the other hand, what makes it so challenging to deduce biological meaning from the wealth of Aspergillus -omics data? And which hurdles hinder us to model and engineer industrial strains for higher productivity and better rheological performance under industrial cultivation conditions? In this review, we will address these issues by highlighting most recent findings from the Aspergillus research with a focus on fungal growth, physiology, morphology and product formation. Indeed, the last years brought us many surprising insights into model and industrial strains. They clearly told us that similar is not the same: there are different ways to make a hypha, there are more protein secretion routes than anticipated and there are different molecular and physical mechanisms which control polar growth and the development of hyphal networks. We will discuss new conceptual frameworks derived from these insights and the future scientific advances necessary to create value from Aspergillus Big Data.
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Affiliation(s)
- Vera Meyer
- Department Applied and Molecular Microbiology, Institute of Biotechnology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355, Berlin, Germany,
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63
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FluG affects secretion in colonies of Aspergillus niger. Antonie van Leeuwenhoek 2014; 107:225-40. [DOI: 10.1007/s10482-014-0321-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 10/27/2014] [Indexed: 02/04/2023]
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64
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van Munster JM, Daly P, Delmas S, Pullan ST, Blythe MJ, Malla S, Kokolski M, Noltorp ECM, Wennberg K, Fetherston R, Beniston R, Yu X, Dupree P, Archer DB. The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger. Fungal Genet Biol 2014; 72:34-47. [PMID: 24792495 PMCID: PMC4217149 DOI: 10.1016/j.fgb.2014.04.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 03/21/2014] [Accepted: 04/18/2014] [Indexed: 11/06/2022]
Abstract
Fungi are an important source of enzymes for saccharification of plant polysaccharides and production of biofuels. Understanding of the regulation and induction of expression of genes encoding these enzymes is still incomplete. To explore the induction mechanism, we analysed the response of the industrially important fungus Aspergillus niger to wheat straw, with a focus on events occurring shortly after exposure to the substrate. RNA sequencing showed that the transcriptional response after 6h of exposure to wheat straw was very different from the response at 24h of exposure to the same substrate. For example, less than half of the genes encoding carbohydrate active enzymes that were induced after 24h of exposure to wheat straw, were also induced after 6h exposure. Importantly, over a third of the genes induced after 6h of exposure to wheat straw were also induced during 6h of carbon starvation, indicating that carbon starvation is probably an important factor in the early response to wheat straw. The up-regulation of the expression of a high number of genes encoding CAZymes that are active on plant-derived carbohydrates during early carbon starvation suggests that these enzymes could be involved in a scouting role during starvation, releasing inducing sugars from complex plant polysaccharides. We show, using proteomics, that carbon-starved cultures indeed release CAZymes with predicted activity on plant polysaccharides. Analysis of the enzymatic activity and the reaction products, indicates that these proteins are enzymes that can degrade various plant polysaccharides to generate both known, as well as potentially new, inducers of CAZymes.
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Affiliation(s)
- Jolanda M van Munster
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Paul Daly
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Stéphane Delmas
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Steven T Pullan
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Martin J Blythe
- Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Sunir Malla
- Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Matthew Kokolski
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Emelie C M Noltorp
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Kristin Wennberg
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Richard Fetherston
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Richard Beniston
- Biological Mass Spectrometry Facility biOMICS, University of Sheffield, Brook Hill Road, Sheffield S3 7HF, UK.
| | - Xiaolan Yu
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK.
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK.
| | - David B Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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65
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Mäkelä MR, Donofrio N, de Vries RP. Plant biomass degradation by fungi. Fungal Genet Biol 2014; 72:2-9. [PMID: 25192611 DOI: 10.1016/j.fgb.2014.08.010] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 08/19/2014] [Accepted: 08/25/2014] [Indexed: 12/27/2022]
Abstract
Plant biomass degradation by fungi has implications for several fields of science. The enzyme systems employed by fungi for this are broadly used in various industrial sectors such as food & feed, pulp & paper, detergents, textile, wine, and more recently biofuels and biochemicals. In addition, the topic is highly relevant in the field of plant pathogenic fungi as they degrade plant biomass to either gain access to the plant or as carbon source, resulting in significant crop losses. Finally, fungi are the main degraders of plant biomass in nature and as such have an essential role in the global carbon cycle and ecology in general. In this review we provide a global view on the development of this research topic in saprobic ascomycetes and basidiomycetes and in plant pathogenic fungi and link this to the other papers of this special issue on plant biomass degradation by fungi.
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Affiliation(s)
- Miia R Mäkelä
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Nicole Donofrio
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
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66
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Battaglia E, Zhou M, de Vries RP. The transcriptional activators AraR and XlnR from Aspergillus niger regulate expression of pentose catabolic and pentose phosphate pathway genes. Res Microbiol 2014; 165:531-40. [PMID: 25086261 DOI: 10.1016/j.resmic.2014.07.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 07/08/2014] [Accepted: 07/21/2014] [Indexed: 11/26/2022]
Abstract
The pentose catabolic pathway (PCP) and the pentose phosphate pathway (PPP) are required for the conversion of pentose sugars in fungi and are linked via d-xylulose-5-phosphate. Previously, it was shown that the PCP is regulated by the transcriptional activators XlnR and AraR in Aspergillus niger. Here we assessed whether XlnR and AraR also regulate the PPP. Expression of two genes, rpiA and talB, was reduced in the ΔaraR/ΔxlnR strain and increased in the xylulokinase negative strain (xkiA1) on d-xylose and/or l-arabinose. Bioinformatic analysis of the 1 kb promoter regions of rpiA and talB showed the presence of putative XlnR binding sites. Combining all results in this study, it strongly suggests that these two PPP genes are under regulation of XlnR in A. niger.
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Affiliation(s)
- Evy Battaglia
- Microbiology & Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands; CBS Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CY, Utrecht, The Netherlands.
| | - Miaomiao Zhou
- CBS Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CY, Utrecht, The Netherlands.
| | - Ronald P de Vries
- Microbiology & Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands; CBS Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CY, Utrecht, The Netherlands.
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67
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Kowalczyk JE, Benoit I, de Vries RP. Regulation of plant biomass utilization in Aspergillus. ADVANCES IN APPLIED MICROBIOLOGY 2014; 88:31-56. [PMID: 24767425 DOI: 10.1016/b978-0-12-800260-5.00002-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The ability of fungi to survive in every known biotope, both natural and man-made, relies in part on their ability to use a wide range of carbon sources. Fungi degrade polymeric carbon sources present in the environment (polysaccharides, proteins, and lignins) to use the monomeric components as nutrients. However, the available carbon sources vary strongly in nature, both between biotopes and in time. The degradation of polymeric carbon sources is mediated through the production of a broad range of enzymes, the production of which is tightly controlled by a network of regulators and linked to the activation of catabolic pathways to convert the released monomers. This review summarizes the knowledge of Aspergillus regulators involved in plant biomass utilization.
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Affiliation(s)
| | - Isabelle Benoit
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
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68
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Klaubauf S, Narang HM, Post H, Zhou M, Brunner K, Mach-Aigner AR, Mach RL, Heck AJR, Altelaar AFM, de Vries RP. Similar is not the same: differences in the function of the (hemi-)cellulolytic regulator XlnR (Xlr1/Xyr1) in filamentous fungi. Fungal Genet Biol 2014; 72:73-81. [PMID: 25064064 DOI: 10.1016/j.fgb.2014.07.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 07/12/2014] [Accepted: 07/15/2014] [Indexed: 11/13/2022]
Abstract
The transcriptional activator XlnR (Xlr1/Xyr1) is a major regulator in fungal xylan and cellulose degradation as well as in the utilization of d-xylose via the pentose catabolic pathway. XlnR homologs are commonly found in filamentous ascomycetes and often assumed to have the same function in different fungi. However, a comparison of the saprobe Aspergillus niger and the plant pathogen Magnaporthe oryzae showed different phenotypes for deletion strains of XlnR. In this study wild type and xlnR/xlr1/xyr1 mutants of five fungi were compared: Fusarium graminearum, M. oryzae, Trichoderma reesei, A. niger and Aspergillus nidulans. Growth profiling on relevant substrates and a detailed analysis of the secretome as well as extracellular enzyme activities demonstrated a common role of this regulator in activating genes encoding the main xylanolytic enzymes. However, large differences were found in the set of genes that is controlled by XlnR in the different species, resulting in the production of different extracellular enzyme spectra by these fungi. This comparison emphasizes the functional diversity of a fine-tuned (hemi-)cellulolytic regulatory system in filamentous fungi, which might be related to the adaptation of fungi to their specific biotopes. Data are available via ProteomeXchange with identifier PXD001190.
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Affiliation(s)
- Sylvia Klaubauf
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Hari Mander Narang
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Harm Post
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Miaomiao Zhou
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Kurt Brunner
- Institute of Chemical Engineering, Department for Biotechnology and Microbiology, Vienna University of Technology, Gumpendorferstr. 1a, 1060 Vienna, Austria
| | - Astrid R Mach-Aigner
- Institute of Chemical Engineering, Department for Biotechnology and Microbiology, Vienna University of Technology, Gumpendorferstr. 1a, 1060 Vienna, Austria
| | - Robert L Mach
- Institute of Chemical Engineering, Department for Biotechnology and Microbiology, Vienna University of Technology, Gumpendorferstr. 1a, 1060 Vienna, Austria
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - A F Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.
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69
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Brown NA, Ries LNA, Goldman GH. How nutritional status signalling coordinates metabolism and lignocellulolytic enzyme secretion. Fungal Genet Biol 2014; 72:48-63. [PMID: 25011009 DOI: 10.1016/j.fgb.2014.06.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 06/26/2014] [Accepted: 06/28/2014] [Indexed: 11/30/2022]
Abstract
The utilisation of lignocellulosic plant biomass as an abundant, renewable feedstock for green chemistries and biofuel production is inhibited by its recalcitrant nature. In the environment, lignocellulolytic fungi are naturally capable of breaking down plant biomass into utilisable saccharides. Nonetheless, within the industrial context, inefficiencies in the production of lignocellulolytic enzymes impede the implementation of green technologies. One of the primary causes of such inefficiencies is the tight transcriptional control of lignocellulolytic enzymes via carbon catabolite repression. Fungi coordinate metabolism, protein biosynthesis and secretion with cellular energetic status through the detection of intra- and extra-cellular nutritional signals. An enhanced understanding of the signals and signalling pathways involved in regulating the transcription, translation and secretion of lignocellulolytic enzymes is therefore of great biotechnological interest. This comparative review describes how nutrient sensing pathways regulate carbon catabolite repression, metabolism and the utilisation of alternative carbon sources in Saccharomyces cerevisiae and ascomycete fungi.
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Affiliation(s)
- Neil Andrew Brown
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil.
| | | | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil; Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Campinas, Brazil.
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70
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Complex regulation of hydrolytic enzyme genes for cellulosic biomass degradation in filamentous fungi. Appl Microbiol Biotechnol 2014; 98:4829-37. [DOI: 10.1007/s00253-014-5707-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 03/17/2014] [Accepted: 03/17/2014] [Indexed: 12/17/2022]
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71
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Todd RB, Zhou M, Ohm RA, Leeggangers HACF, Visser L, de Vries RP. Prevalence of transcription factors in ascomycete and basidiomycete fungi. BMC Genomics 2014; 15:214. [PMID: 24650355 PMCID: PMC3998117 DOI: 10.1186/1471-2164-15-214] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Accepted: 03/11/2014] [Indexed: 12/18/2022] Open
Abstract
Background Gene regulation underlies fungal physiology and therefore is a major factor in fungal biodiversity. Analysis of genome sequences has revealed a large number of putative transcription factors in most fungal genomes. The presence of fungal orthologs for individual regulators has been analysed and appears to be highly variable with some regulators widely conserved and others showing narrow distribution. Although genome-scale transcription factor surveys have been performed before, no global study into the prevalence of specific regulators across the fungal kingdom has been presented. Results In this study we have analysed the number of members for 37 regulator classes in 77 ascomycete and 31 basidiomycete fungal genomes and revealed significant differences between ascomycetes and basidiomycetes. In addition, we determined the presence of 64 regulators characterised in ascomycetes across these 108 genomes. This demonstrated that overall the highest presence of orthologs is in the filamentous ascomycetes. A significant number of regulators lacked orthologs in the ascomycete yeasts and the basidiomycetes. Conversely, of seven basidiomycete regulators included in the study, only one had orthologs in ascomycetes. Conclusions This study demonstrates a significant difference in the regulatory repertoire of ascomycete and basidiomycete fungi, at the level of both regulator class and individual regulator. This suggests that the current regulatory systems of these fungi have been mainly developed after the two phyla diverged. Most regulators detected in both phyla are involved in central functions of fungal physiology and therefore were likely already present in the ancestor of the two phyla.
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Affiliation(s)
- Richard B Todd
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS 66506, USA.
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72
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Li J, Lin L, Li H, Tian C, Ma Y. Transcriptional comparison of the filamentous fungus Neurospora crassa growing on three major monosaccharides D-glucose, D-xylose and L-arabinose. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:31. [PMID: 24581151 PMCID: PMC4015282 DOI: 10.1186/1754-6834-7-31] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 02/14/2014] [Indexed: 05/09/2023]
Abstract
BACKGROUND D-glucose, D-xylose and L-arabinose are the three major monosaccharides in plant cell walls. Complete utilization of all three sugars is still a bottleneck for second-generation cellulolytic bioethanol production, especially for L-arabinose. However, little is known about gene expression profiles during L-arabinose utilization in fungi and a comparison of the genome-wide fungal response to these three major monosaccharides has not yet been reported. RESULTS Using next-generation sequencing technology, we have analyzed the transcriptome of N. crassa grown on L-arabinose versus D-xylose, with D-glucose as the reference. We found that the gene expression profiles on L-arabinose were dramatically different from those on D-xylose. It appears that L-arabinose can rewire the fungal cell metabolic pathway widely and provoke the expression of many kinds of sugar transporters, hemicellulase genes and transcription factors. In contrast, many fewer genes, mainly related to the pentose metabolic pathway, were upregulated on D-xylose. The rewired metabolic response to L-arabinose was significantly different and wider than that under no carbon conditions, although the carbon starvation response was initiated on L-arabinose. Three novel sugar transporters were identified and characterized for their substrates here, including one glucose transporter GLT-1 (NCU01633) and two novel pentose transporters, XAT-1 (NCU01132), XYT-1 (NCU05627). One transcription factor associated with the regulation of hemicellulase genes, HCR-1 (NCU05064) was also characterized in the present study. CONCLUSIONS We conducted the first transcriptome analysis of Neurospora crassa grown on L-arabinose and performed a comparative analysis with cells grown on D-xylose and D-glucose, which deepens the understanding of the utilization of L-arabinose and D-xylose in filamentous fungi. The dataset generated by this research will be useful for mining target genes for D-xylose and L-arabinose utilization engineering and the novel sugar transportes identified are good targets for pentose untilization and biofuels production. Moreover, hemicellulase production by fungi could be improved by modifying the hemicellulase regulator discovered here.
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Affiliation(s)
- Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangcai Lin
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Huiyan Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanhe Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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73
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Gruben BS, Zhou M, Wiebenga A, Ballering J, Overkamp KM, Punt PJ, de Vries RP. Aspergillus niger RhaR, a regulator involved in L-rhamnose release and catabolism. Appl Microbiol Biotechnol 2014; 98:5531-40. [PMID: 24682478 DOI: 10.1007/s00253-014-5607-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 02/07/2014] [Accepted: 02/10/2014] [Indexed: 10/25/2022]
Abstract
The genome of the filamentous fungus Aspergillus niger is rich in genes encoding pectinases, a broad class of enzymes that have been extensively studied due to their use in industrial applications. The sequencing of the A. niger genome provided more knowledge concerning the individual pectinolytic genes, but little is known about the regulatory genes involved in pectin degradation. Understanding regulation of the pectinolytic genes provides a tool to optimize the production of pectinases in this industrially important fungus. This study describes the identification and characterization of one of the activators of pectinase-encoding genes, RhaR. Inactivation of the gene encoding this regulator resulted in down-regulation of genes involved in the release of L-rhamnose from the pectin substructure rhamnogalacturonan I, as well as catabolism of this monosaccharide. The rhaR disruptant was unable to grow on L-rhamnose, but only a small reduction in growth on pectin was observed. This is likely caused by the presence of a second, so far unknown regulator that responds to the presence of D-galacturonic acid.
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Affiliation(s)
- Birgit S Gruben
- Microbiology & Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Utrecht, The Netherlands
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74
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Patyshakuliyeva A, Jurak E, Kohler A, Baker A, Battaglia E, de Bruijn W, Burton KS, Challen MP, Coutinho PM, Eastwood DC, Gruben BS, Mäkelä MR, Martin F, Nadal M, van den Brink J, Wiebenga A, Zhou M, Henrissat B, Kabel M, Gruppen H, de Vries RP. Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus. BMC Genomics 2013; 14:663. [PMID: 24074284 PMCID: PMC3852267 DOI: 10.1186/1471-2164-14-663] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 09/26/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Agaricus bisporus is commercially grown on compost, in which the available carbon sources consist mainly of plant-derived polysaccharides that are built out of various different constituent monosaccharides. The major constituent monosaccharides of these polysaccharides are glucose, xylose, and arabinose, while smaller amounts of galactose, glucuronic acid, rhamnose and mannose are also present. RESULTS In this study, genes encoding putative enzymes from carbon metabolism were identified and their expression was studied in different growth stages of A. bisporus. We correlated the expression of genes encoding plant and fungal polysaccharide modifying enzymes identified in the A. bisporus genome to the soluble carbohydrates and the composition of mycelium grown compost, casing layer and fruiting bodies. CONCLUSIONS The compost grown vegetative mycelium of A. bisporus consumes a wide variety of monosaccharides. However, in fruiting bodies only hexose catabolism occurs, and no accumulation of other sugars was observed. This suggests that only hexoses or their conversion products are transported from the vegetative mycelium to the fruiting body, while the other sugars likely provide energy for growth and maintenance of the vegetative mycelium. Clear correlations were found between expression of the genes and composition of carbohydrates. Genes encoding plant cell wall polysaccharide degrading enzymes were mainly expressed in compost-grown mycelium, and largely absent in fruiting bodies. In contrast, genes encoding fungal cell wall polysaccharide modifying enzymes were expressed in both fruiting bodies and vegetative mycelium, but different gene sets were expressed in these samples.
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Affiliation(s)
| | - Edita Jurak
- Wageningen University, Laboratory of Food Chemistry, Bomenweg 2, 6703 HD Wageningen, The Netherlands
| | - Annegret Kohler
- INRA, UMR1136 INRA/UHP, Interactions Arbres/ Micro-organismes, Centre de Nancy, Champenoux 54280, France
| | - Adam Baker
- University of Warwick, Warwick, CV35 9EF, Wellesbourne, UK
| | - Evy Battaglia
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Wouter de Bruijn
- Wageningen University, Laboratory of Food Chemistry, Bomenweg 2, 6703 HD Wageningen, The Netherlands
| | - Kerry S Burton
- East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK
| | - Michael P Challen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Pedro M Coutinho
- UMR 6098 CNRS–Universités Aix-Marseille I and II, Marseille Cedex 9 13288, France
| | - Daniel C Eastwood
- College of Science, University of Swansea, Singleton Park, Swansea SA2 8PP, UK
| | - Birgit S Gruben
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Miia R Mäkelä
- Department of Food and Environmental Sciences, University of Helsinki, P. O. Box 56, 00014 Helsinki, Finland
| | - Francis Martin
- INRA, UMR1136 INRA/UHP, Interactions Arbres/ Micro-organismes, Centre de Nancy, Champenoux 54280, France
| | - Marina Nadal
- Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Joost van den Brink
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Ad Wiebenga
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Miaomiao Zhou
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Bernard Henrissat
- UMR 6098 CNRS–Universités Aix-Marseille I and II, Marseille Cedex 9 13288, France
| | - Mirjam Kabel
- Wageningen University, Laboratory of Food Chemistry, Bomenweg 2, 6703 HD Wageningen, The Netherlands
| | - Harry Gruppen
- Wageningen University, Laboratory of Food Chemistry, Bomenweg 2, 6703 HD Wageningen, The Netherlands
| | - Ronald P de Vries
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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75
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The influence of Aspergillus niger transcription factors AraR and XlnR in the gene expression during growth in D-xylose, L-arabinose and steam-exploded sugarcane bagasse. Fungal Genet Biol 2013; 60:29-45. [PMID: 23892063 DOI: 10.1016/j.fgb.2013.07.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 07/03/2013] [Accepted: 07/17/2013] [Indexed: 12/29/2022]
Abstract
The interest in the conversion of plant biomass to renewable fuels such as bioethanol has led to an increased investigation into the processes regulating biomass saccharification. The filamentous fungus Aspergillus niger is an important microorganism capable of producing a wide variety of plant biomass degrading enzymes. In A. niger the transcriptional activator XlnR and its close homolog, AraR, controls the main (hemi-)cellulolytic system responsible for plant polysaccharide degradation. Sugarcane is used worldwide as a feedstock for sugar and ethanol production, while the lignocellulosic residual bagasse can be used in different industrial applications, including ethanol production. The use of pentose sugars from hemicelluloses represents an opportunity to further increase production efficiencies. In the present study, we describe a global gene expression analysis of A. niger XlnR- and AraR-deficient mutant strains, grown on a D-xylose/L-arabinose monosaccharide mixture and steam-exploded sugarcane bagasse. Different gene sets of CAZy enzymes and sugar transporters were shown to be individually or dually regulated by XlnR and AraR, with XlnR appearing to be the major regulator on complex polysaccharides. Our study contributes to understanding of the complex regulatory mechanisms responsible for plant polysaccharide-degrading gene expression, and opens new possibilities for the engineering of fungi able to produce more efficient enzymatic cocktails to be used in biofuel production.
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Battaglia E, Klaubauf S, Vallet J, Ribot C, Lebrun MH, de Vries RP. Xlr1 is involved in the transcriptional control of the pentose catabolic pathway, but not hemi-cellulolytic enzymes in Magnaporthe oryzae. Fungal Genet Biol 2013; 57:76-84. [PMID: 23810898 DOI: 10.1016/j.fgb.2013.06.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/14/2013] [Accepted: 06/15/2013] [Indexed: 10/26/2022]
Abstract
Magnaporthe oryzae is a fungal plant pathogen of many grasses including rice. Since arabinoxylan is one of the major components of the plant cell wall of grasses, M. oryzae is likely to degrade this polysaccharide for supporting its growth in infected leaves. D-Xylose is released from arabinoxylan by fungal depolymerising enzymes and catabolized through the pentose pathway. The expression of genes involved in these pathways is under control of the transcriptional activator XlnR/Xlr1, conserved among filamentous ascomycetes. In this study, we identified M. oryzae genes involved in the pentose catabolic pathway (PCP) and their function during infection, including the XlnR homolog, XLR1, through the phenotypic analysis of targeted null mutants. Growth of the Δxlr1 strain was reduced on D-xylose and xylan, but unaffected on L-arabinose and arabinan. A strong reduction of PCP gene expression was observed in the Δxlr1 strain on D-xylose and L-arabinose. However, there was no significant difference in xylanolytic and cellulolytic enzyme activities between the Δxlr1 mutant and the reference strain. These data demonstrate that XLR1 encodes the transcriptional activator of the PCP in M. oryzae, but does not appear to play a role in the regulation of the (hemi-) cellulolytic system in this fungus. This indicates only partial similarity in function between Xlr1 and A. niger XlnR. The deletion mutant of D-xylulose kinase encoding gene (XKI1) is clearly unable to grow on either D-xylose or L-arabinose and showed reduced growth on xylitol, L-arabitol and xylan. Δxki1 displayed an interesting molecular phenotype as it over-expressed other PCP genes as well as genes encoding (hemi-) cellulolytic enzymes. However, neither Δxlr1 nor Δxki1 showed significant differences in their pathogeny on rice and barley compared to the wild type, suggesting that D-xylose catabolism is not required for fungal growth in infected leaves.
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Affiliation(s)
- Evy Battaglia
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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77
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Nikolaev I, Farmer Hansen S, Madrid S, de Vries RP. Disruption of theL-arabitol dehydrogenase encoding gene inAspergillus tubingensisresults in increased xylanase production. Biotechnol J 2013; 8:905-11. [DOI: 10.1002/biot.201200256] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 03/29/2013] [Accepted: 05/20/2013] [Indexed: 11/08/2022]
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78
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Amore A, Giacobbe S, Faraco V. Regulation of cellulase and hemicellulase gene expression in fungi. Curr Genomics 2013; 14:230-49. [PMID: 24294104 PMCID: PMC3731814 DOI: 10.2174/1389202911314040002] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 04/22/2013] [Accepted: 04/23/2013] [Indexed: 11/22/2022] Open
Abstract
Research on regulation of cellulases and hemicellulases gene expression may be very useful for increasing the production of these enzymes in their native producers. Mechanisms of gene regulation of cellulase and hemicellulase expression in filamentous fungi have been studied, mainly in Aspergillus and Trichoderma. The production of these extracellular enzymes is an energy-consuming process, so the enzymes are produced only under conditions in which the fungus needs to use plant polymers as an energy and carbon source. Moreover, production of many of these enzymes is coordinately regulated, and induced in the presence of the substrate polymers. In addition to induction by mono- and oligo-saccharides, genes encoding hydrolytic enzymes involved in plant cell wall deconstruction in filamentous fungi can be repressed during growth in the presence of easily metabolizable carbon sources, such as glucose. Carbon catabolite repression is an important mechanism to repress the production of plant cell wall degrading enzymes during growth on preferred carbon sources. This manuscript reviews the recent advancements in elucidation of molecular mechanisms responsible for regulation of expression of cellulase and hemicellulase genes in fungi.
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Affiliation(s)
- Antonella Amore
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, via Cintia, 4 80126 Naples, Italy
| | - Simona Giacobbe
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, via Cintia, 4 80126 Naples, Italy
| | - Vincenza Faraco
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, via Cintia, 4 80126 Naples, Italy
- School of Biotechnological Sciences, University of Naples “Federico II” Italy
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79
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Culleton H, McKie V, de Vries RP. Physiological and molecular aspects of degradation of plant polysaccharides by fungi: What have we learned fromAspergillus? Biotechnol J 2013; 8:884-94. [DOI: 10.1002/biot.201200382] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 02/12/2013] [Accepted: 04/03/2013] [Indexed: 11/09/2022]
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80
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Caspeta L, Nielsen J. Toward systems metabolic engineering ofAspergillusandPichiaspecies for the production of chemicals and biofuels. Biotechnol J 2013; 8:534-44. [DOI: 10.1002/biot.201200345] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 02/19/2013] [Accepted: 03/14/2013] [Indexed: 12/11/2022]
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81
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Klaubauf S, Ribot C, Melayah D, Lagorce A, Lebrun MH, de Vries RP. The pentose catabolic pathway of the rice-blast fungus Magnaporthe oryzae
involves a novel pentose reductase restricted to few fungal species. FEBS Lett 2013; 587:1346-52. [DOI: 10.1016/j.febslet.2013.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 03/02/2013] [Indexed: 11/26/2022]
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82
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ManR, a novel Zn(II)2Cys6 transcriptional activator, controls the β-mannan utilization system in Aspergillus oryzae. Fungal Genet Biol 2012; 49:987-95. [DOI: 10.1016/j.fgb.2012.09.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 09/08/2012] [Accepted: 09/10/2012] [Indexed: 11/19/2022]
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83
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Gruben BS, Zhou M, de Vries RP. GalX regulates the D-galactose oxido-reductive pathway in Aspergillus niger. FEBS Lett 2012; 586:3980-5. [PMID: 23063944 DOI: 10.1016/j.febslet.2012.09.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/13/2012] [Accepted: 09/19/2012] [Indexed: 11/30/2022]
Abstract
Galactose catabolism in Aspergillus nidulans is regulated by at least two regulators, GalR and GalX. In Aspergillus niger only GalX is present, and its role in d-galactose catabolism in this fungus was investigated. Phenotypic and gene expression analysis of a wild type and a galX disruptant revealed that GalX regulates the d-galactose oxido-reductive pathway, but not the Leloir pathway in A. niger.
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Affiliation(s)
- Birgit S Gruben
- Microbiology & Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Utrecht, The Netherlands
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84
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Kunitake E, Tani S, Sumitani JI, Kawaguchi T. A novel transcriptional regulator, ClbR, controls the cellobiose- and cellulose-responsive induction of cellulase and xylanase genes regulated by two distinct signaling pathways in Aspergillus aculeatus. Appl Microbiol Biotechnol 2012; 97:2017-28. [DOI: 10.1007/s00253-012-4305-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 07/13/2012] [Accepted: 07/13/2012] [Indexed: 10/28/2022]
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85
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Benoit I, Coutinho PM, Schols HA, Gerlach JP, Henrissat B, de Vries RP. Degradation of different pectins by fungi: correlations and contrasts between the pectinolytic enzyme sets identified in genomes and the growth on pectins of different origin. BMC Genomics 2012; 13:321. [PMID: 22812459 PMCID: PMC3460790 DOI: 10.1186/1471-2164-13-321] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 07/07/2012] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Pectins are diverse and very complex biomolecules and their structure depends on the plant species and tissue. It was previously shown that derivatives of pectic polymers and oligosaccharides from pectins have positive effects on human health. To obtain specific pectic oligosaccharides, highly defined enzymatic mixes are required. Filamentous fungi are specialized in plant cell wall degradation and some produce a broad range of pectinases. They may therefore shed light on the enzyme mixes needed for partial hydrolysis. RESULTS The growth profiles of 12 fungi on four pectins and four structural elements of pectins show that the presence/absence of pectinolytic genes in the fungal genome clearly correlates with their ability to degrade pectins. However, this correlation is less clear when we zoom in to the pectic structural elements. CONCLUSIONS This study highlights the complexity of the mechanisms involved in fungal degradation of complex carbon sources such as pectins. Mining genomes and comparative genomics are promising first steps towards the production of specific pectinolytic fractions.
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Affiliation(s)
- Isabelle Benoit
- Microbiology & Kluyver Centre for Genomics of Industrial Fermentations, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Pedro M Coutinho
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, CNRS UMR 7257, Case 932, 163 Av de Luminy, Marseille cedex 9, 13288, France
| | - Henk A Schols
- Laboratory of Food Chemistry, Wageningen University, Bomenweg 2, Wageningen, 6703HD, The Netherlands
| | - Jan P Gerlach
- Microbiology & Kluyver Centre for Genomics of Industrial Fermentations, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, CNRS UMR 7257, Case 932, 163 Av de Luminy, Marseille cedex 9, 13288, France
| | - Ronald P de Vries
- Microbiology & Kluyver Centre for Genomics of Industrial Fermentations, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
- Fungal Physiology, CBS-KNAW, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
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86
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Andersen MR, Giese M, de Vries RP, Nielsen J. Mapping the polysaccharide degradation potential of Aspergillus niger. BMC Genomics 2012; 13:313. [PMID: 22799883 PMCID: PMC3542576 DOI: 10.1186/1471-2164-13-313] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 06/08/2012] [Indexed: 11/10/2022] Open
Abstract
Background The degradation of plant materials by enzymes is an industry of increasing importance. For sustainable production of second generation biofuels and other products of industrial biotechnology, efficient degradation of non-edible plant polysaccharides such as hemicellulose is required. For each type of hemicellulose, a complex mixture of enzymes is required for complete conversion to fermentable monosaccharides. In plant-biomass degrading fungi, these enzymes are regulated and released by complex regulatory structures. In this study, we present a methodology for evaluating the potential of a given fungus for polysaccharide degradation. Results Through the compilation of information from 203 articles, we have systematized knowledge on the structure and degradation of 16 major types of plant polysaccharides to form a graphical overview. As a case example, we have combined this with a list of 188 genes coding for carbohydrate-active enzymes from Aspergillus niger, thus forming an analysis framework, which can be queried. Combination of this information network with gene expression analysis on mono- and polysaccharide substrates has allowed elucidation of concerted gene expression from this organism. One such example is the identification of a full set of extracellular polysaccharide-acting genes for the degradation of oat spelt xylan. Conclusions The mapping of plant polysaccharide structures along with the corresponding enzymatic activities is a powerful framework for expression analysis of carbohydrate-active enzymes. Applying this network-based approach, we provide the first genome-scale characterization of all genes coding for carbohydrate-active enzymes identified in A. niger.
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Affiliation(s)
- Mikael R Andersen
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
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87
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Unique regulatory mechanism for D-galactose utilization in Aspergillus nidulans. Appl Environ Microbiol 2011; 77:7084-7. [PMID: 21821745 DOI: 10.1128/aem.05290-11] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study describes two novel regulators, GalX and GalR, that control d-galactose utilization in Aspergillus nidulans. This system is unique for A. nidulans since no GalR homologs were found in other ascomycetes. GalR shares significant sequence identity with the arabinanolytic and xylanolytic regulators AraR and XlnR, but GalX is more distantly related.
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88
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Battaglia E, Hansen SF, Leendertse A, Madrid S, Mulder H, Nikolaev I, de Vries RP. Regulation of pentose utilisation by AraR, but not XlnR, differs in Aspergillus nidulans and Aspergillus niger. Appl Microbiol Biotechnol 2011; 91:387-97. [PMID: 21484208 PMCID: PMC3125510 DOI: 10.1007/s00253-011-3242-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 03/15/2011] [Accepted: 03/15/2011] [Indexed: 12/01/2022]
Abstract
Filamentous fungi are important producers of plant polysaccharide degrading enzymes that are used in many industrial applications. These enzymes are produced by the fungus to liberate monomeric sugars that are used as carbon source. Two of the main components of plant polysaccharides are l-arabinose and d-xylose, which are metabolized through the pentose catabolic pathway (PCP) in these fungi. In Aspergillus niger, the regulation of pentose release from polysaccharides and the PCP involves the transcriptional activators AraR and XlnR, which are also present in other Aspergilli such as Aspergillus nidulans. The comparative analysis revealed that the regulation of the PCP by AraR differs in A. nidulans and A. niger, whereas the regulation of the PCP by XlnR was similar in both species. This was demonstrated by the growth differences on l-arabinose between disruptant strains for araR and xlnR in A. nidulans and A. niger. In addition, the expression profiles of genes encoding l-arabinose reductase (larA), l-arabitol dehydrogenase (ladA) and xylitol dehydrogenase (xdhA) differed in these strains. This data suggests evolutionary changes in these two species that affect pentose utilisation. This study also implies that manipulating regulatory systems to improve the production of polysaccharide degrading enzymes, may give different results in different industrial fungi.
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Affiliation(s)
- Evy Battaglia
- Department of Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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89
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Seiboth B, Metz B. Fungal arabinan and L-arabinose metabolism. Appl Microbiol Biotechnol 2011; 89:1665-73. [PMID: 21212945 PMCID: PMC3044236 DOI: 10.1007/s00253-010-3071-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Revised: 12/08/2010] [Accepted: 12/08/2010] [Indexed: 12/04/2022]
Abstract
l-Arabinose is the second most abundant pentose beside d-xylose and is found in the plant polysaccharides, hemicellulose and pectin. The need to find renewable carbon and energy sources has accelerated research to investigate the potential of l-arabinose for the development and production of biofuels and other bioproducts. Fungi produce a number of extracellular arabinanases, including α-l-arabinofuranosidases and endo-arabinanases, to specifically release l-arabinose from the plant polymers. Following uptake of l-arabinose, its intracellular catabolism follows a four-step alternating reduction and oxidation path, which is concluded by a phosphorylation, resulting in d-xylulose 5-phosphate, an intermediate of the pentose phosphate pathway. The genes and encoding enzymes l-arabinose reductase, l-arabinitol dehydrogenase, l-xylulose reductase, xylitol dehydrogenase, and xylulokinase of this pathway were mainly characterized in the two biotechnological important fungi Aspergillus niger and Trichoderma reesei. Analysis of the components of the l-arabinose pathway revealed a number of specific adaptations in the enzymatic and regulatory machinery towards the utilization of l-arabinose. Further genetic and biochemical analysis provided evidence that l-arabinose and the interconnected d-xylose pathway are also involved in the oxidoreductive degradation of the hexose d-galactose.
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Affiliation(s)
- Bernhard Seiboth
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, Wien, Austria.
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