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Carbohydrate esterase family 16 contains fungal hemicellulose acetyl esterases (HAEs) with varying specificity. N Biotechnol 2022; 70:28-38. [DOI: 10.1016/j.nbt.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 11/18/2022]
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Kun RS, Garrigues S, Di Falco M, Tsang A, de Vries RP. Blocking utilization of major plant biomass polysaccharides leads Aspergillus niger towards utilization of minor components. Microb Biotechnol 2021; 14:1683-1698. [PMID: 34114741 PMCID: PMC8313289 DOI: 10.1111/1751-7915.13835] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 11/28/2022] Open
Abstract
Fungi produce a wide range of enzymes that allow them to grow on diverse plant biomass. Wheat bran is a low-cost substrate with high potential for biotechnological applications. It mainly contains cellulose and (arabino)xylan, as well as starch, proteins, lipids and lignin to a lesser extent. In this study, we dissected the regulatory network governing wheat bran degradation in Aspergillus niger to assess the relative contribution of the regulators to the utilization of this plant biomass substrate. Deletion of genes encoding transcription factors involved in (hemi-)cellulose utilization (XlnR, AraR, ClrA and ClrB) individually and in combination significantly reduced production of polysaccharide-degrading enzymes, but retained substantial growth on wheat bran. Proteomic analysis suggested the ability of A. niger to grow on other carbon components, such as starch, which was confirmed by the additional deletion of the amylolytic regulator AmyR. Growth was further reduced but not impaired, indicating that other minor components provide sufficient energy for residual growth, displaying the flexibility of A. niger, and likely other fungi, in carbon utilization. Better understanding of the complexity and flexibility of fungal regulatory networks will facilitate the generation of more efficient fungal cell factories that use plant biomass as a substrate.
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Affiliation(s)
- Roland S. Kun
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
| | - Sandra Garrigues
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
| | - Marcos Di Falco
- Centre for Structural and Functional GenomicsConcordia University7141 Sherbrooke Street WestMontrealQCH4B 1R6Canada
| | - Adrian Tsang
- Centre for Structural and Functional GenomicsConcordia University7141 Sherbrooke Street WestMontrealQCH4B 1R6Canada
| | - Ronald P. de Vries
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
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Terebieniec A, Chroumpi T, Dilokpimol A, Aguilar-Pontes MV, Mäkelä MR, de Vries RP. Characterization of d-xylose reductase, XyrB, from Aspergillus niger. BIOTECHNOLOGY REPORTS 2021; 30:e00610. [PMID: 33842213 PMCID: PMC8020424 DOI: 10.1016/j.btre.2021.e00610] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/21/2021] [Accepted: 03/12/2021] [Indexed: 11/09/2022]
Abstract
XyrB is involved in conversion of d-xylose and l-arabinose in A. niger. The xyrB expression is induced both by d-xylose and l-arabinose. XyrB expression is controlled by xlnR and araR regulators.
d-xylose reductase is a member of the aldo-keto reductase family, and is involved in d-xylose and l-arabinose conversion through the Pentose Catabolic Pathway (PCP) in fungi. In this study, we biochemically characterized a newly identified second d-xylose reductase (XyrB) from Aspergillus niger. This NADPH-dependent reductase is able to efficiently convert d-xylose and l-arabinose, and it has the highest affinity for these sugars of all currently known fungal pentose reductases. A combination of biochemical data, transcriptomics and phylogenetic analysis further illustrated the role of XyrB in the PCP. Enzymes: D-xylose reductase (EC 1.1.1.307), L-arabinose reductase (EC 1.1.1.21).
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Chroumpi T, Peng M, Markillie LM, Mitchell HD, Nicora CD, Hutchinson CM, Paurus V, Tolic N, Clendinen CS, Orr G, Baker SE, Mäkelä MR, de Vries RP. Re-routing of Sugar Catabolism Provides a Better Insight Into Fungal Flexibility in Using Plant Biomass-Derived Monomers as Substrates. Front Bioeng Biotechnol 2021; 9:644216. [PMID: 33763411 PMCID: PMC7982397 DOI: 10.3389/fbioe.2021.644216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 02/16/2021] [Indexed: 11/13/2022] Open
Abstract
The filamentous ascomycete Aspergillus niger has received increasing interest as a cell factory, being able to efficiently degrade plant cell wall polysaccharides as well as having an extensive metabolism to convert the released monosaccharides into value added compounds. The pentoses D-xylose and L-arabinose are the most abundant monosaccharides in plant biomass after the hexose D-glucose, being major constituents of xylan, pectin and xyloglucan. In this study, the influence of selected pentose catabolic pathway (PCP) deletion strains on growth on plant biomass and re-routing of sugar catabolism was addressed to gain a better understanding of the flexibility of this fungus in using plant biomass-derived monomers. The transcriptome, metabolome and proteome response of three PCP mutant strains, ΔlarAΔxyrAΔxyrB, ΔladAΔxdhAΔsdhA and ΔxkiA, grown on wheat bran (WB) and sugar beet pulp (SBP), was evaluated. Our results showed that despite the absolute impact of these PCP mutations on pure pentose sugars, they are not as critical for growth of A. niger on more complex biomass substrates, such as WB and SBP. However, significant phenotypic variation was observed between the two biomass substrates, but also between the different PCP mutants. This shows that the high sugar heterogeneity of these substrates in combination with the high complexity and adaptability of the fungal sugar metabolism allow for activation of alternative strategies to support growth.
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Affiliation(s)
- Tania Chroumpi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands
| | - Lye Meng Markillie
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Hugh D Mitchell
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Carrie D Nicora
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Chelsea M Hutchinson
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Vanessa Paurus
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Nikola Tolic
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Chaevien S Clendinen
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Galya Orr
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Scott E Baker
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Miia R Mäkelä
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands.,Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands
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Peng M, Khosravi C, Lubbers RJM, Kun RS, Aguilar Pontes MV, Battaglia E, Chen C, Dalhuijsen S, Daly P, Lipzen A, Ng V, Yan J, Wang M, Visser J, Grigoriev IV, Mäkelä MR, de Vries RP. CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner. ACTA ACUST UNITED AC 2021; 7:100050. [PMID: 33778219 PMCID: PMC7985698 DOI: 10.1016/j.tcsw.2021.100050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/28/2021] [Accepted: 02/28/2021] [Indexed: 12/15/2022]
Abstract
Carbon catabolite repression enables fungi to utilize the most favourable carbon source in the environment, and is mediated by a key regulator, CreA, in most fungi. CreA-mediated regulation has mainly been studied at high monosaccharide concentrations, an uncommon situation in most natural biotopes. In nature, many fungi rely on plant biomass as their major carbon source by producing enzymes to degrade plant cell wall polysaccharides into metabolizable sugars. To determine the role of CreA when fungi grow in more natural conditions and in particular with respect to degradation and conversion of plant cell walls, we compared transcriptomes of a creA deletion and reference strain of the ascomycete Aspergillus niger during growth on sugar beet pulp and wheat bran. Transcriptomics, extracellular sugar concentrations and growth profiling of A. niger on a variety of carbon sources, revealed that also under conditions with low concentrations of free monosaccharides, CreA has a major effect on gene expression in a strong time and substrate composition dependent manner. In addition, we compared the CreA regulon from five fungi during their growth on crude plant biomass or cellulose. It showed that CreA commonly regulated genes related to carbon metabolism, sugar transport and plant cell wall degrading enzymes across different species. We therefore conclude that CreA has a crucial role for fungi also in adapting to low sugar concentrations as occurring in their natural biotopes, which is supported by the presence of CreA orthologs in nearly all fungi.
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Affiliation(s)
- Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Claire Khosravi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Ronnie J M Lubbers
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Roland S Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Maria Victoria Aguilar Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Evy Battaglia
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Cindy Chen
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, United States
| | - Sacha Dalhuijsen
- Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Paul Daly
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Anna Lipzen
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, United States
| | - Vivian Ng
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, United States
| | - Juying Yan
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, United States
| | - Mei Wang
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, United States
| | - Jaap Visser
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Igor V Grigoriev
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, United States.,Department of Plant and Microbial Biology, University of California Berkeley, 111 Koshland Hall, Berkeley, CA 94720, USA
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - 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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Suhaimi H, Dailin DJ, Malek RA, Hanapi SZ, Ambehabati KK, Keat HC, Prakasham S, Elsayed EA, Misson M, El Enshasy H. Fungal Pectinases: Production and Applications in Food Industries. Fungal Biol 2021. [DOI: 10.1007/978-3-030-64406-2_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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7
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Effect of Oligosaccharide Degree of Polymerization on the Induction of Xylan-Degrading Enzymes by Fusarium oxysporum f. sp. Lycopersici. Molecules 2020; 25:molecules25245849. [PMID: 33322262 PMCID: PMC7764074 DOI: 10.3390/molecules25245849] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 01/15/2023] Open
Abstract
Xylan is one of the most abundant carbohydrates on Earth. Complete degradation of xylan is achieved by the collaborative action of endo-β-1,4-xylanases and β-d-xylosidases and a number of accessories enzymes. In filamentous fungi, the xylanolytic system is controlled through induction and repression. However, the exact mechanism remains unclear. Substrates containing xylan promote the induction of xylanases, which release xylooligosaccharides. These, in turn, induce expression of xylanase-encoding genes. Here, we aimed to determine which xylan degradation products acted as inducers, and whether the size of the released oligomer correlated with its induction strength. To this end, we compared xylanase production by different inducers, such as sophorose, lactose, cellooligosaccharides, and xylooligosaccharides in Fusarium oxysporum f. sp. lycopersici. Results indicate that xylooligosaccharides are more effective than other substrates at inducing endoxylanase and β-xylosidases. Moreover, we report a correlation between the degree of xylooligosaccharide polymerization and induction efficiency of each enzyme. Specifically, xylotetraose is the best inducer of endoxylanase, xylohexaose of extracellular β-xylosidase, and xylobiose of cell-bound β-xylosidase.
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Khosravi C, Kowalczyk JE, Chroumpi T, Battaglia E, Aguilar Pontes MV, Peng M, Wiebenga A, Ng V, Lipzen A, He G, Bauer D, Grigoriev IV, de Vries RP. Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network. BMC Genomics 2019; 20:853. [PMID: 31726994 PMCID: PMC6854810 DOI: 10.1186/s12864-019-6235-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/28/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Enzymatic plant biomass degradation by fungi is a highly complex process and one of the leading challenges in developing a biobased economy. Some industrial fungi (e.g. Aspergillus niger) have a long history of use with respect to plant biomass degradation and for that reason have become 'model' species for this topic. A. niger is a major industrial enzyme producer that has a broad ability to degrade plant based polysaccharides. A. niger wild-type, the (hemi-)cellulolytic regulator (xlnR) and xylulokinase (xkiA1) mutant strains were grown on a monocot (corn stover, CS) and dicot (soybean hulls, SBH) substrate. The xkiA1 mutant is unable to utilize the pentoses D-xylose and L-arabinose and the polysaccharide xylan, and was previously shown to accumulate inducers for the (hemi-)cellulolytic transcriptional activator XlnR and the arabinanolytic transcriptional activator AraR in the presence of pentoses, resulting in overexpression of their target genes. The xlnR mutant has reduced growth on xylan and down-regulation of its target genes. The mutants therefore have a similar phenotype on xylan, but an opposite transcriptional effect. D-xylose and L-arabinose are the most abundant monosaccharides after D-glucose in nearly all plant-derived biomass materials. In this study we evaluated the effect of the xlnR and xkiA1 mutation during growth on two pentose-rich substrates by transcriptome analysis. RESULTS Particular attention was given to CAZymes, metabolic pathways and transcription factors related to the plant biomass degradation. Genes coding for the main enzymes involved in plant biomass degradation were down-regulated at the beginning of the growth on CS and SBH. However, at a later time point, significant differences were found in the expression profiles of both mutants on CS compared to SBH. CONCLUSION This study demonstrates the high complexity of the plant biomass degradation process by fungi, by showing that mutant strains with fairly straightforward phenotypes on pure mono- and polysaccharides, have much less clear-cut phenotypes and transcriptomes on crude plant biomass.
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Affiliation(s)
- Claire Khosravi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Joanna E. Kowalczyk
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Tania Chroumpi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Evy Battaglia
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Maria-Victoria Aguilar Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Guifen He
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Diane Bauer
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
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Oka H, Kojima T, Ihara K, Kobayashi T, Nakano H. Comprehensive investigation of the gene expression system regulated by an Aspergillus oryzae transcription factor XlnR using integrated mining of gSELEX-Seq and microarray data. BMC Genomics 2019; 20:16. [PMID: 30621576 PMCID: PMC6323846 DOI: 10.1186/s12864-018-5375-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/16/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcription factors (TFs) specifically bind to DNA sequences and control the expression of target genes. AoXlnR is a key TF involved in the expression of xylanolytic and cellulolytic enzymes in the filamentous fungi, Aspergillus oryzae. Genomic SELEX-Seq (gSELEX-Seq) can reveal the in vitro binding sites of a TF in a genome. To date, the gene expression network controlled by AoXlnR in A. oryzae is not fully explored. In this study, the data from gSELEX-Seq analysis and data mining were applied toward a comprehensive investigation of the AoXlnR-regulated transcriptional network in A. oryzae. RESULTS Around 2000 promoters were selected as AoXlnR-binding DNAs using gSELEX-Seq, consequently identifying the genes downstream of them. On the other hand, 72 differentially expressed genes (DEGs) related to AoXlnR had been determined by microarray analysis. The intersecting set of genes, that were found using the gSELEX-Seq and the microarray analysis, had 51 genes. Further, the canonical AoXlnR-binding motifs, 5'-GGCT(A/G) A-3', were successfully identified in gSELEX-Seq. The motif numbers in each promoter of the DEGs and differential expression levels were correlated by in silico analysis. The analysis showed that the presence of both 5'-GGCTAA-3' and 5'-GGCTGA-3' motif has significantly high correlation with the differential expression levels of the genes. CONCLUSIONS Genes regulated directly by AoXlnR were identified by integrated mining of data obtained from gSELEX-Seq and microarray. The data mining of the promoters of differentially expressed genes revealed the close relation between the presence of the AoXlnR-binding motifs and the expression levels of the downstream genes. The knowledge obtained in this study can contribute greatly to the elucidation of AoXlnR-mediated cellulose and xylan metabolic network in A. oryzae. The pipeline, which is based on integrated mining of data consisting of both in vitro characterization of the DNA-binding sites and TF phenotype, can be a robust platform for comprehensive analysis of the gene expression network via the TFs.
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Affiliation(s)
- Hiroya Oka
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Takaaki Kojima
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Tetsuo Kobayashi
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Hideo Nakano
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
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Comparison of the paralogous transcription factors AraR and XlnR in Aspergillus oryzae. Curr Genet 2018; 64:1245-1260. [PMID: 29654355 DOI: 10.1007/s00294-018-0837-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/08/2018] [Accepted: 04/11/2018] [Indexed: 10/17/2022]
Abstract
The paralogous transcription factors AraR and XlnR in Aspergillus regulate genes that are involved in degradation of cellulose and hemicellulose and catabolism of pentose. AraR and XlnR target the same genes for pentose catabolism but target different genes encoding enzymes for polysaccharide degradation. To uncover the relationship between these paralogous transcription factors, we examined their contribution to regulation of the PCP genes and compared their preferred recognition sequences. Both AraR and XlnR are involved in induction of all the pentose catabolic genes in A. oryzae except larA encoding L-arabinose reductase, which was regulated by AraR but not by XlnR. DNA-binding studies revealed that the recognition sequences of AraR and XlnR also differ only slightly; AraR prefers CGGDTAAW, while XlnR prefers CGGNTAAW. All the pentose catabolic genes possess at least one recognition site to which both AraR and XlnR can bind. Cooperative binding by the factors was not observed. Instead, they competed to bind to the shared sites. XlnR bound to the recognition sites mentioned above as a monomer, but bound to the sequence TTAGSCTAA on the xylanase promoters as a dimer. Consequently, AraR and XlnR have significantly similar, but not the same, DNA-binding properties. Such a slight difference in these paralogous transcription factors may lead to complex outputs in enzyme production depending on the concentrations of coexisting inducer molecules in the natural environment.
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Adnan M, Zheng W, Islam W, Arif M, Abubakar YS, Wang Z, Lu G. Carbon Catabolite Repression in Filamentous Fungi. Int J Mol Sci 2017; 19:ijms19010048. [PMID: 29295552 PMCID: PMC5795998 DOI: 10.3390/ijms19010048] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 12/13/2017] [Accepted: 12/20/2017] [Indexed: 12/18/2022] Open
Abstract
Carbon Catabolite Repression (CCR) has fascinated scientists and researchers around the globe for the past few decades. This important mechanism allows preferential utilization of an energy-efficient and readily available carbon source over relatively less easily accessible carbon sources. This mechanism helps microorganisms to obtain maximum amount of glucose in order to keep pace with their metabolism. Microorganisms assimilate glucose and highly favorable sugars before switching to less-favored sources of carbon such as organic acids and alcohols. In CCR of filamentous fungi, CreA acts as a transcription factor, which is regulated to some extent by ubiquitination. CreD-HulA ubiquitination ligase complex helps in CreA ubiquitination, while CreB-CreC deubiquitination (DUB) complex removes ubiquitin from CreA, which causes its activation. CCR of fungi also involves some very crucial elements such as Hexokinases, cAMP, Protein Kinase (PKA), Ras proteins, G protein-coupled receptor (GPCR), Adenylate cyclase, RcoA and SnfA. Thorough study of molecular mechanism of CCR is important for understanding growth, conidiation, virulence and survival of filamentous fungi. This review is a comprehensive revision of the regulation of CCR in filamentous fungi as well as an updated summary of key regulators, regulation of different CCR-dependent mechanisms and its impact on various physical characteristics of filamentous fungi.
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Affiliation(s)
- Muhammad Adnan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Wenhui Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Waqar Islam
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Muhammad Arif
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yakubu Saddeeq Abubakar
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Gruben BS, Mäkelä MR, Kowalczyk JE, Zhou M, Benoit-Gelber I, De Vries RP. Expression-based clustering of CAZyme-encoding genes of Aspergillus niger. BMC Genomics 2017; 18:900. [PMID: 29169319 PMCID: PMC5701360 DOI: 10.1186/s12864-017-4164-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 10/05/2017] [Indexed: 11/29/2022] Open
Abstract
Background The Aspergillus niger genome contains a large repertoire of genes encoding carbohydrate active enzymes (CAZymes) that are targeted to plant polysaccharide degradation enabling A. niger to grow on a wide range of plant biomass substrates. Which genes need to be activated in certain environmental conditions depends on the composition of the available substrate. Previous studies have demonstrated the involvement of a number of transcriptional regulators in plant biomass degradation and have identified sets of target genes for each regulator. In this study, a broad transcriptional analysis was performed of the A. niger genes encoding (putative) plant polysaccharide degrading enzymes. Microarray data focusing on the initial response of A. niger to the presence of plant biomass related carbon sources were analyzed of a wild-type strain N402 that was grown on a large range of carbon sources and of the regulatory mutant strains ΔxlnR, ΔaraR, ΔamyR, ΔrhaR and ΔgalX that were grown on their specific inducing compounds. Results The cluster analysis of the expression data revealed several groups of co-regulated genes, which goes beyond the traditionally described co-regulated gene sets. Additional putative target genes of the selected regulators were identified, based on their expression profile. Notably, in several cases the expression profile puts questions on the function assignment of uncharacterized genes that was based on homology searches, highlighting the need for more extensive biochemical studies into the substrate specificity of enzymes encoded by these non-characterized genes. The data also revealed sets of genes that were upregulated in the regulatory mutants, suggesting interaction between the regulatory systems and a therefore even more complex overall regulatory network than has been reported so far. Conclusions Expression profiling on a large number of substrates provides better insight in the complex regulatory systems that drive the conversion of plant biomass by fungi. In addition, the data provides additional evidence in favor of and against the similarity-based functions assigned to uncharacterized genes. Electronic supplementary material The online version of this article (10.1186/s12864-017-4164-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Birgit S Gruben
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Microbiology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Miia R Mäkelä
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Joanna E Kowalczyk
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
| | - Miaomiao Zhou
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Current affiliation: ATGM, Avans University of Applied Sciences, Lovensdijkstraat 61-63, 4818, AJ, Breda, The Netherlands
| | - Isabelle Benoit-Gelber
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Microbiology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Current affiliation: Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W, Montreal, QC, Canada
| | - Ronald P De Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. .,Microbiology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands. .,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.
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13
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Kowalczyk JE, Khosravi C, Purvine S, Dohnalkova A, Chrisler WB, Orr G, Robinson E, Zink E, Wiebenga A, Peng M, Battaglia E, Baker S, de Vries RP. High resolution visualization and exo-proteomics reveal the physiological role of XlnR and AraR in plant biomass colonization and degradation by Aspergillus niger. Environ Microbiol 2017; 19:4587-4598. [PMID: 29027734 DOI: 10.1111/1462-2920.13923] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/18/2017] [Accepted: 08/30/2017] [Indexed: 11/28/2022]
Abstract
In A. niger, two transcription factors, AraR and XlnR, regulate the production of enzymes involved in degradation of arabinoxylan and catabolism of the released l-arabinose and d-xylose. Deletion of both araR and xlnR in leads to reduced production of (hemi)cellulolytic enzymes and reduced growth on arabinan, arabinogalactan and xylan. In this study, we investigated the colonization and degradation of wheat bran by the A. niger reference strain CBS 137562 and araR/xlnR regulatory mutants using high-resolution microscopy and exo-proteomics. We discovered that wheat bran flakes have a 'rough' and 'smooth' surface with substantially different affinity towards fungal hyphae. While colonization of the rough side was possible for all strains, the xlnR mutants struggled to survive on the smooth side of the wheat bran particles after 20 and 40 h post inoculation. Impaired colonization ability of the smooth surface of wheat bran was linked to reduced potential of ΔxlnR to secrete arabinoxylan and cellulose-degrading enzymes and indicates that XlnR is the major regulator that drives colonization of wheat bran in A. niger.
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Affiliation(s)
- Joanna E Kowalczyk
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Claire Khosravi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Samuel Purvine
- Department of Energy, Environmental Molecular Sciences Laboratory, Richland, WA, USA
| | - Alice Dohnalkova
- Department of Energy, Environmental Molecular Sciences Laboratory, Richland, WA, USA
| | - William B Chrisler
- Department of Energy, Environmental Molecular Sciences Laboratory, Richland, WA, USA
| | - Galya Orr
- Department of Energy, Environmental Molecular Sciences Laboratory, Richland, WA, USA
| | - Errol Robinson
- Department of Energy, Environmental Molecular Sciences Laboratory, Richland, WA, USA
| | - Erika Zink
- Department of Energy, Environmental Molecular Sciences Laboratory, Richland, WA, USA
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Evy Battaglia
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Scott Baker
- Department of Energy, Environmental Molecular Sciences Laboratory, Richland, WA, USA
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
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14
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Daly P, van Munster JM, Blythe MJ, Ibbett R, Kokolski M, Gaddipati S, Lindquist E, Singan VR, Barry KW, Lipzen A, Ngan CY, Petzold CJ, Chan LJG, Pullan ST, Delmas S, Waldron PR, Grigoriev IV, Tucker GA, Simmons BA, Archer DB. Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:35. [PMID: 28184248 PMCID: PMC5294722 DOI: 10.1186/s13068-017-0700-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/05/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND The capacity of fungi, such as Aspergillus niger, to degrade lignocellulose is harnessed in biotechnology to generate biofuels and high-value compounds from renewable feedstocks. Most feedstocks are currently pretreated to increase enzymatic digestibility: improving our understanding of the transcriptomic responses of fungi to pretreated lignocellulosic substrates could help to improve the mix of activities and reduce the production costs of commercial lignocellulose saccharifying cocktails. RESULTS We investigated the responses of A. niger to untreated, ionic liquid and hydrothermally pretreated wheat straw over a 5-day time course using RNA-seq and targeted proteomics. The ionic liquid pretreatment altered the cellulose crystallinity while retaining more of the hemicellulosic sugars than the hydrothermal pretreatment. Ionic liquid pretreatment of straw led to a dynamic induction and repression of genes, which was correlated with the higher levels of pentose sugars saccharified from the ionic liquid-pretreated straw. Hydrothermal pretreatment of straw led to reduced levels of transcripts of genes encoding carbohydrate-active enzymes as well as the derived proteins and enzyme activities. Both pretreatments abolished the expression of a large set of genes encoding pectinolytic enzymes. These reduced levels could be explained by the removal of parts of the lignocellulose by the hydrothermal pretreatment. The time course also facilitated identification of temporally limited gene induction patterns. CONCLUSIONS The presented transcriptomic and biochemical datasets demonstrate that pretreatments caused modifications of the lignocellulose, to both specific structural features as well as the organisation of the overall lignocellulosic structure, that determined A. niger transcript levels. The experimental setup allowed reliable detection of substrate-specific gene expression patterns as well as hitherto non-expressed genes. Our data suggest beneficial effects of using untreated and IL-pretreated straw, but not HT-pretreated straw, as feedstock for CAZyme production.
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Affiliation(s)
- Paul Daly
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Jolanda M. van Munster
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Chemical Biology, Manchester Institute for Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Martin J. Blythe
- Deep Seq, Faculty of Medicine and Health Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Roger Ibbett
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Matt Kokolski
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Sanyasi Gaddipati
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Vasanth R. Singan
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Kerrie W. Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Chew Yee Ngan
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | | | | | - Steven T. Pullan
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- TB Programme, Microbiology Services, Public Health England, Salisbury, UK
| | - Stéphane Delmas
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- UPMC, Univ. Paris 06, CNRS UMR7238, Sorbonne Universités, 15 rue de l’Ecole de Médecine, 75270 Paris, France
| | - Paul R. Waldron
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Gregory A. Tucker
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | | | - David B. Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
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15
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Benocci T, Aguilar-Pontes MV, Zhou M, Seiboth B, de Vries RP. Regulators of plant biomass degradation in ascomycetous fungi. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:152. [PMID: 28616076 PMCID: PMC5468973 DOI: 10.1186/s13068-017-0841-x] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/06/2017] [Indexed: 05/05/2023]
Abstract
Fungi play a major role in the global carbon cycle because of their ability to utilize plant biomass (polysaccharides, proteins, and lignin) as carbon source. Due to the complexity and heterogenic composition of plant biomass, fungi need to produce a broad range of degrading enzymes, matching the composition of (part of) the prevalent substrate. This process is dependent on a network of regulators that not only control the extracellular enzymes that degrade the biomass, but also the metabolic pathways needed to metabolize the resulting monomers. This review will summarize the current knowledge on regulation of plant biomass utilization in fungi and compare the differences between fungal species, focusing in particular on the presence or absence of the regulators involved in this process.
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Affiliation(s)
- Tiziano Benocci
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Maria Victoria Aguilar-Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Miaomiao Zhou
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Bernhard Seiboth
- Research Area Biochemical Technology, Institute of Chemical and Biological Engineering, TU Wien, 1060 Vienna, Austria
| | - 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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16
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Sayer C, Szabo Z, Isupov MN, Ingham C, Littlechild JA. The Structure of a Novel Thermophilic Esterase from the Planctomycetes Species, Thermogutta terrifontis Reveals an Open Active Site Due to a Minimal 'Cap' Domain. Front Microbiol 2015; 6:1294. [PMID: 26635762 PMCID: PMC4655241 DOI: 10.3389/fmicb.2015.01294] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/06/2015] [Indexed: 11/29/2022] Open
Abstract
A carboxyl esterase (TtEst2) has been identified in a novel thermophilic bacterium, Thermogutta terrifontis from the phylum Planctomycetes and has been cloned and over-expressed in Escherichia coli. The enzyme has been characterized biochemically and shown to have activity toward small p-nitrophenyl (pNP) carboxylic esters with optimal activity for pNP-acetate. The enzyme shows moderate thermostability retaining 75% activity after incubation for 30 min at 70°C. The crystal structures have been determined for the native TtEst2 and its complexes with the carboxylic acid products propionate, butyrate, and valerate. TtEst2 differs from most enzymes of the α/β-hydrolase family 3 as it lacks the majority of the ‘cap’ domain and its active site cavity is exposed to the solvent. The bound ligands have allowed the identification of the carboxyl pocket in the enzyme active site. Comparison of TtEst2 with structurally related enzymes has given insight into how differences in their substrate preference can be rationalized based upon the properties of their active site pockets.
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Affiliation(s)
- Christopher Sayer
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
| | | | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
| | | | - Jennifer A Littlechild
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
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17
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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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18
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Tefsen B, Grijpstra J, Ordonez S, Lammers M, van Die I, de Cock H. Deletion of the CAP10 gene of Cryptococcus neoformans results in a pleiotropic phenotype with changes in expression of virulence factors. Res Microbiol 2014; 165:399-410. [PMID: 24751576 DOI: 10.1016/j.resmic.2014.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/31/2014] [Indexed: 12/18/2022]
Abstract
The human pathogen Cryptococcus neoformans causes meningo-encephalitis. The polysaccharide capsule is an important virulence factor for this yeast-like fungus. Previously, we had shown that disruption of the CAP10 gene, encoding a putative xylosyltransferase, results in mutant cells that lack most of the capsular polysaccharides on the cell surface, but do not show a typical acapsular phenotype. In contrast to the acapsular cap59 mutant, cap10 did not induce maturation of dendritic cells when exposed to components of the immune system. In order to gain further insight into the causes of this phenotype displayed by the cap10 mutant, we performed a more in-depth phenotypic analysis of the cell wall and surface structures of this mutant compared to the wild type strain and acapsular mutant cap59. Moreover, we analyzed the cap10 mutant and the wild type strain for differential gene expression of, amongst others, enzymes that are involved in biogenesis of cell wall and capsule components. We conclude that a mutation in the CAP10 gene results in a pleiotropic phenotype with effects on different cellular processes affecting, amongst others, cell size, expression of virulence factors and size of extracellular vesicles.
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Affiliation(s)
- Boris Tefsen
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands.
| | - Jan Grijpstra
- Microbiology, Institute of Biomembranes, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Soledad Ordonez
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands; Microbiology, Institute of Biomembranes, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Menno Lammers
- Microbiology, Institute of Biomembranes, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Irma van Die
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands.
| | - Hans de Cock
- Microbiology, Institute of Biomembranes, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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Imoukhuede PI, Popel AS. Quantitative fluorescent profiling of VEGFRs reveals tumor cell and endothelial cell heterogeneity in breast cancer xenografts. Cancer Med 2014; 3:225-44. [PMID: 24449499 PMCID: PMC3987073 DOI: 10.1002/cam4.188] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 10/30/2013] [Accepted: 11/13/2013] [Indexed: 12/25/2022] Open
Abstract
Plasma membrane-localized vascular endothelial growth factor receptors (VEGFR) play a critical role in transducing VEGF signaling toward pro and antiangiogenic outcomes and quantitative characterization of these receptors is critical toward identifying biomarkers for antiangiogenic therapies, understanding mechanisms of action of antiangiogenic drugs, and advancing predictive computational models. While in vitro analysis of cell surface-VEGFRs has been performed, little is known about the levels of cell surface-VEGFR on tumor cells. Therefore, we inoculate nude mice with the human triple-negative breast cancer, MDA-MB-231, cell line; isolate human tumor cells and mouse tumor endothelial cells from xenografts; and quantitatively characterize the VEGFR localization on these cells. We observe 15,000 surface-VEGFR1/tumor endothelial cell versus 8200 surface-VEGFR1/tumor endothelial cell at 3 and 6 weeks of tumor growth, respectively; and we quantify 1200-1700 surface-VEGFR2/tumor endothelial cell. The tumor cell levels of VEGFR1 and VEGFR2 are relatively constant between 3 and 6 weeks: 2000-2200 surface-VEGFR1/tumor cell and ~1000 surface-VEGFR2/tumor cell. Cell-by-cell analysis provides additional insight into tumor heterogeneity by identifying four cellular subpopulations based on size and levels of cell membrane-localized VEGFR. Furthermore, when these ex vivo data are compared to in vitro data, we observe little to no VEGFRs on MDA-MB-231 cells, and the MDA-MB-231 VEGFR surface levels are not regulated by a saturating dose of VEGF. Overall, the quantification of these dissimilarities for the first time in tumor provides insight into the balance of modulatory (VEGFR1) and proangiogenic (VEGFR2) receptors.
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Affiliation(s)
- Princess I Imoukhuede
- Department of Bioengineering, University of Illinois at Urbana ChampaignUrbana, Illinois, 61801
| | - Aleksander S Popel
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins UniversityBaltimore, Maryland, 21205
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20
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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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21
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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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22
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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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23
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Rosa L, Ravanal MC, Mardones W, Eyzaguirre J. Characterization of a recombinant α-glucuronidase from Aspergillus fumigatus. Fungal Biol 2013; 117:380-7. [DOI: 10.1016/j.funbio.2013.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 03/05/2013] [Accepted: 04/07/2013] [Indexed: 11/16/2022]
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24
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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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Deciphering transcriptional regulatory mechanisms associated with hemicellulose degradation in Neurospora crassa. EUKARYOTIC CELL 2012; 11:482-93. [PMID: 22345350 DOI: 10.1128/ec.05327-11] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Hemicellulose, the second most abundant plant biomass fraction after cellulose, is widely viewed as a potential substrate for the production of liquid fuels and other value-added materials. Degradation of hemicellulose by filamentous fungi requires production of many different enzymes, which are induced by biopolymers or its derivatives and regulated mainly at the transcriptional level through transcription factors (TFs). Neurospora crassa, a model filamentous fungus, expresses and secretes enzymes required for plant cell wall deconstruction. To better understand genes specifically associated with degradation of hemicellulose, we applied secretome and transcriptome analysis to N. crassa grown on beechwood xylan. We identified 34 secreted proteins and 353 genes with elevated transcription on xylan. The xylanolytic phenotype of strains with deletions in genes identified from the secretome and transcriptome analysis of the wild type was assessed, revealing functions for known and unknown proteins associated with hemicellulose degradation. By evaluating phenotypes of strains containing deletions of predicted TF genes in N. crassa, we identified a TF (XLR-1; xylan degradation regulator 1) essential for hemicellulose degradation that is an ortholog to XlnR/XYR1 in Aspergillus and Trichoderma species, respectively, a major transcriptional regulator of genes encoding both cellulases and hemicellulases. Deletion of xlr-1 in N. crassa abolished growth on xylan and xylose, but growth on cellulose and cellulolytic activity were only slightly affected. To determine the regulatory mechanisms for hemicellulose degradation, we explored the transcriptional regulon of XLR-1 under xylose, xylanolytic, and cellulolytic conditions. XLR-1 regulated only some predicted hemicellulase genes in N. crassa and was required for a full induction of several cellulase genes. Hemicellulase gene expression was induced by a combination of release from carbon catabolite repression (CCR) and induction. This systematic analysis illustrates the similarities and differences in regulation of hemicellulose degradation among filamentous fungi.
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Battaglia E, Visser L, Nijssen A, van Veluw G, Wösten H, de Vries R. Analysis of regulation of pentose utilisation in Aspergillus niger reveals evolutionary adaptations in Eurotiales. Stud Mycol 2011; 69:31-8. [PMID: 21892241 PMCID: PMC3161754 DOI: 10.3114/sim.2011.69.03] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Aspergilli are commonly found in soil and on decaying plant material. D-xylose and L-arabinose are highly abundant components of plant biomass. They are released from polysaccharides by fungi using a set of extracellular enzymes and subsequently converted intracellularly through the pentose catabolic pathway (PCP). In this study, the L-arabinose responsive transcriptional activator (AraR) is identified in Aspergillus niger and was shown to control the L-arabinose catabolic pathway as well as expression of genes encoding extracellular L-arabinose releasing enzymes. AraR interacts with the D-xylose-responsive transcriptional activator XlnR in the regulation of the pentose catabolic pathway, but not with respect to release of L-arabinose and D-xylose. AraR was only identified in the Eurotiales, more specifically in the family Trichocomaceae and appears to have originated from a gene duplication event (from XlnR) after this order or family split from the other filamentous ascomycetes. XlnR is present in all filamentous ascomycetes with the exception of members of the Onygenales. Since the Onygenales and Eurotiales are both part of the subclass Eurotiomycetidae, this indicates that strong adaptation of the regulation of pentose utilisation has occurred at this evolutionary node. In Eurotiales a unique two-component regulatory system for pentose release and metabolism has evolved, while the regulatory system was lost in the Onygenales. The observed evolutionary changes (in Eurotiomycetidae) mainly affect the regulatory system as in contrast, homologues for most genes of the L-arabinose/D-xylose catabolic pathway are present in all the filamentous fungi, irrespective of the presence of XlnR and/or AraR.
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Affiliation(s)
- E. Battaglia
- Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - L. Visser
- Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - A. Nijssen
- Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - G.J. van Veluw
- Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - H.A.B. Wösten
- Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - R.P. de Vries
- Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- CBS-KNAW, Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Correspondence: Ronald P. de Vries,
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de Souza WR, de Gouvea PF, Savoldi M, Malavazi I, de Souza Bernardes LA, Goldman MHS, de Vries RP, de Castro Oliveira JV, Goldman GH. Transcriptome analysis of Aspergillus niger grown on sugarcane bagasse. BIOTECHNOLOGY FOR BIOFUELS 2011; 4:40. [PMID: 22008461 PMCID: PMC3219568 DOI: 10.1186/1754-6834-4-40] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 10/18/2011] [Indexed: 05/07/2023]
Abstract
BACKGROUND Considering that the costs of cellulases and hemicellulases contribute substantially to the price of bioethanol, new studies aimed at understanding and improving cellulase efficiency and productivity are of paramount importance. Aspergillus niger has been shown to produce a wide spectrum of polysaccharide hydrolytic enzymes. To understand how to improve enzymatic cocktails that can hydrolyze pretreated sugarcane bagasse, we used a genomics approach to investigate which genes and pathways are transcriptionally modulated during growth of A. niger on steam-exploded sugarcane bagasse (SEB). RESULTS Herein we report the main cellulase- and hemicellulase-encoding genes with increased expression during growth on SEB. We also sought to determine whether the mRNA accumulation of several SEB-induced genes encoding putative transporters is induced by xylose and dependent on glucose. We identified 18 (58% of A. niger predicted cellulases) and 21 (58% of A. niger predicted hemicellulases) cellulase- and hemicellulase-encoding genes, respectively, that were highly expressed during growth on SEB. CONCLUSIONS Degradation of sugarcane bagasse requires production of many different enzymes which are regulated by the type and complexity of the available substrate. Our presently reported work opens new possibilities for understanding sugarcane biomass saccharification by A. niger hydrolases and for the construction of more efficient enzymatic cocktails for second-generation bioethanol.
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Affiliation(s)
- Wagner R de Souza
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Paula F de Gouvea
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Marcela Savoldi
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos, Brazil
| | - Luciano A de Souza Bernardes
- Departamento de Ciências Exatas e Tecnológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, CEP 45662-000, Ilhéus, Bahia, Brazil
| | - Maria Helena S Goldman
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida dos Bandeirantes, 3900, CEP 14040-901, Ribeirão Preto, São Paulo, Brazil
| | - Ronald P de Vries
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Juliana V de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Caixa Postal 6170, 13083-970 Campinas, São Paulo, Brazil
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Caixa Postal 6170, 13083-970 Campinas, São Paulo, Brazil
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Sun J, Glass NL. Identification of the CRE-1 cellulolytic regulon in Neurospora crassa. PLoS One 2011; 6:e25654. [PMID: 21980519 PMCID: PMC3183063 DOI: 10.1371/journal.pone.0025654] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 09/09/2011] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In filamentous ascomycete fungi, the utilization of alternate carbon sources is influenced by the zinc finger transcription factor CreA/CRE-1, which encodes a carbon catabolite repressor protein homologous to Mig1 from Saccharomyces cerevisiae. In Neurospora crassa, deletion of cre-1 results in increased secretion of amylase and β-galactosidase. METHODOLOGY/PRINCIPAL FINDINGS Here we show that a strain carrying a deletion of cre-1 has increased cellulolytic activity and increased expression of cellulolytic genes during growth on crystalline cellulose (Avicel). Constitutive expression of cre-1 complements the phenotype of a N. crassa Δcre-1 strain grown on Avicel, and also results in stronger repression of cellulolytic protein secretion and enzyme activity. We determined the CRE-1 regulon by investigating the secretome and transcriptome of a Δcre-1 strain as compared to wild type when grown on Avicel versus minimal medium. Chromatin immunoprecipitation-PCR of putative target genes showed that CRE-1 binds to only some adjacent 5'-SYGGRG-3' motifs, consistent with previous findings in other fungi, and suggests that unidentified additional regulatory factors affect CRE-1 binding to promoter regions. Characterization of 30 mutants containing deletions in genes whose expression level increased in a Δcre-1 strain under cellulolytic conditions identified novel genes that affect cellulase activity and protein secretion. CONCLUSIONS/SIGNIFICANCE Our data provide comprehensive information on the CRE-1 regulon in N. crassa and contribute to deciphering the global role of carbon catabolite repression in filamentous ascomycete fungi during plant cell wall deconstruction.
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Affiliation(s)
- Jianping Sun
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - N. Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- * E-mail:
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vanKuyk PA, Benen JAE, Wösten HAB, Visser J, de Vries RP. A broader role for AmyR in Aspergillus niger: regulation of the utilisation of D-glucose or D-galactose containing oligo- and polysaccharides. Appl Microbiol Biotechnol 2011; 93:285-93. [PMID: 21874276 PMCID: PMC3251782 DOI: 10.1007/s00253-011-3550-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 08/06/2011] [Accepted: 08/13/2011] [Indexed: 11/23/2022]
Abstract
AmyR is commonly considered a regulator of starch degradation whose activity is induced by the presence of maltose, the disaccharide building block of starch. In this study, we demonstrate that the role of AmyR extends beyond starch degradation. Enzyme activity assays, genes expression analysis and growth profiling on d-glucose- and d-galactose-containing oligo- and polysaccharides showed that AmyR regulates the expression of some of the Aspergillus niger genes encoding α- and β-glucosidases, α- and β- galactosidases, as well as genes encoding α-amlyases and glucoamylases. In addition, we provide evidence that d-glucose or a metabolic product thereof may be the inducer of the AmyR system in A. niger and not maltose, as is commonly assumed.
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Affiliation(s)
- Patricia A vanKuyk
- Molecular Genetics of Industrial Microorganisms, Wageningen University, Wageningen, The Netherlands
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de Bekker C, Bruning O, Jonker MJ, Breit TM, Wösten HAB. Single cell transcriptomics of neighboring hyphae of Aspergillus niger. Genome Biol 2011; 12:R71. [PMID: 21816052 PMCID: PMC3245611 DOI: 10.1186/gb-2011-12-8-r71] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 08/04/2011] [Indexed: 11/10/2022] Open
Abstract
Single cell profiling was performed to assess differences in RNA accumulation in neighboring hyphae of the fungus Aspergillus niger. A protocol was developed to isolate and amplify RNA from single hyphae or parts thereof. Microarray analysis resulted in a present call for 4 to 7% of the A. niger genes, of which 12% showed heterogeneous RNA levels. These genes belonged to a wide range of gene categories.
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Affiliation(s)
- Charissa de Bekker
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Fungal enzyme sets for plant polysaccharide degradation. Appl Microbiol Biotechnol 2011; 91:1477-92. [PMID: 21785931 PMCID: PMC3160556 DOI: 10.1007/s00253-011-3473-2] [Citation(s) in RCA: 347] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 06/27/2011] [Accepted: 07/10/2011] [Indexed: 02/01/2023]
Abstract
Enzymatic degradation of plant polysaccharides has many industrial applications, such as within the paper, food, and feed industry and for sustainable production of fuels and chemicals. Cellulose, hemicelluloses, and pectins are the main components of plant cell wall polysaccharides. These polysaccharides are often tightly packed, contain many different sugar residues, and are branched with a diversity of structures. To enable efficient degradation of these polysaccharides, fungi produce an extensive set of carbohydrate-active enzymes. The variety of the enzyme set differs between fungi and often corresponds to the requirements of its habitat. Carbohydrate-active enzymes can be organized in different families based on the amino acid sequence of the structurally related catalytic modules. Fungal enzymes involved in plant polysaccharide degradation are assigned to at least 35 glycoside hydrolase families, three carbohydrate esterase families and six polysaccharide lyase families. This mini-review will discuss the enzymes needed for complete degradation of plant polysaccharides and will give an overview of the latest developments concerning fungal carbohydrate-active enzymes and their corresponding families.
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32
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Xylose triggers reversible phosphorylation of XlnR, the fungal transcriptional activator of xylanolytic and cellulolytic genes in Aspergillus oryzae. Biosci Biotechnol Biochem 2011; 75:953-9. [PMID: 21597200 DOI: 10.1271/bbb.100923] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
XlnR is a transcription factor that mediates D-xylose-triggered induction of xylanolytic and cellulolytic genes in Aspergillus. In order to clarify the molecular mechanisms underlying XlnR-mediated induction, Aspergillus oryzae XlnR was fused with the c-myc tag and examined by Western blotting. Phosphate-affinity SDS-PAGE revealed that XlnR was present as a mixture of variously phosphorylated forms in the absence of D-xylose, and that D-xylose triggered additional phosphorylation of the protein. D-Xylose-triggered phosphorylation was a rapid process occurring within 5 min prior to the accumulation of xynG2 mRNA, and removal of D-xylose caused slow dephosphorylation, leading to less-phosphorylated forms. At 30 min after removal, the phosphorylation status was almost identical to that in the absence of D-xylose, and the level of xynG2 mRNA started to decrease. These results indicate that XlnR is highly phosphorylated when it is active in transactivation, implying that D-xylose-triggered reversible phosphorylation controls XlnR activity.
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Chong SL, Battaglia E, Coutinho PM, Henrissat B, Tenkanen M, de Vries RP. The α-glucuronidase Agu1 from Schizophyllum commune is a member of a novel glycoside hydrolase family (GH115). Appl Microbiol Biotechnol 2011; 90:1323-32. [DOI: 10.1007/s00253-011-3157-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 01/28/2011] [Accepted: 01/29/2011] [Indexed: 10/18/2022]
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Vinck A, de Bekker C, Ossin A, Ohm RA, de Vries RP, Wösten HAB. Heterogenic expression of genes encoding secreted proteins at the periphery of Aspergillus niger colonies. Environ Microbiol 2010; 13:216-225. [PMID: 20722697 DOI: 10.1111/j.1462-2920.2010.02322.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Colonization of a substrate by fungi starts with the invasion of exploring hyphae. These hyphae secrete enzymes that degrade the organic material into small molecules that can be taken up by the fungus to serve as nutrients. We previously showed that only part of the exploring hyphae of Aspergillus niger highly express the glucoamylase gene glaA. This was an unexpected finding since all exploring hyphae are exposed to the same environmental conditions. Using GFP as a reporter, we here demonstrate that the acid amylase gene aamA, the α-glucuronidase gene aguA, and the feruloyl esterase gene faeA of A. niger are also subject to heterogenic expression within the exploring mycelium. Coexpression studies using GFP and dTomato as reporters showed that hyphae that highly express one of these genes also highly express the other genes encoding secreted proteins. Moreover, these hyphae also highly express the amylolytic regulatory gene amyR, and the glyceraldehyde-3-phosphate dehydrogenase gene gpdA. In situ hybridization demonstrated that the high expressers are characterized by a high 18S rRNA content. Taken together, it is concluded that two subpopulations of hyphae can be distinguished within the exploring mycelium of A. niger. The experimental data indicate that these subpopulations differ in their transcriptional and translational activity.
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Affiliation(s)
- Arman Vinck
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Charissa de Bekker
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Adam Ossin
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Robin A Ohm
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ronald P de Vries
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Han A B Wösten
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Spatial and developmental differentiation of mannitol dehydrogenase and mannitol-1-phosphate dehydrogenase in Aspergillus niger. EUKARYOTIC CELL 2010; 9:1398-402. [PMID: 20305000 DOI: 10.1128/ec.00363-09] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The presence of a mannitol cycle in fungi has been subject to discussion for many years. Recent studies have found no evidence for the presence of this cycle and its putative role in regenerating NADPH. However, all enzymes of the cycle could be measured in cultures of Aspergillus niger. In this study we have analyzed the localization of two enzymes from the pathway, mannitol dehydrogenase and mannitol-1-phosphate dehydrogenase, and the expression of their encoding genes in nonsporulating and sporulating cultures of A. niger. Northern analysis demonstrated that mpdA was expressed in both sporulating and nonsporulating mycelia, while expression of mtdA was expressed only in sporulating mycelium. More detailed studies using green fluorescent protein and dTomato fused to the promoters of mtdA and mpdA, respectively, demonstrated that expression of mpdA occurs in vegetative hyphae while mtdA expression occurs in conidiospores. Activity assays for MtdA and MpdA confirmed the expression data, indicating that streaming of these proteins is not likely to occur. These results confirm the absence of the putative mannitol cycle in A. niger as two of the enzymes of the cycle are not present in the same part of A. niger colonies. The results also demonstrate the existence of spore-specific genes and enzymes in A. niger.
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Genes regulated by AoXlnR, the xylanolytic and cellulolytic transcriptional regulator, in Aspergillus oryzae. Appl Microbiol Biotechnol 2009; 85:141-54. [DOI: 10.1007/s00253-009-2236-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2009] [Revised: 08/24/2009] [Accepted: 08/31/2009] [Indexed: 10/20/2022]
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Furukawa T, Shida Y, Kitagami N, Mori K, Kato M, Kobayashi T, Okada H, Ogasawara W, Morikawa Y. Identification of specific binding sites for XYR1, a transcriptional activator of cellulolytic and xylanolytic genes in Trichoderma reesei. Fungal Genet Biol 2009; 46:564-74. [PMID: 19393758 DOI: 10.1016/j.fgb.2009.04.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2008] [Revised: 04/15/2009] [Accepted: 04/15/2009] [Indexed: 11/20/2022]
Abstract
The transcriptional activator XYR1 is the central regulator that governs cellulolytic and xylanolytic gene expression in Trichoderma reesei. However, despite its biological importance, relatively little is known about its functional binding sequences. In the present study, we investigated the binding characteristics and specific target for XYR1 by using DNase I footprinting analysis and electrophoretic mobility shift assays. We demonstrate that XYR1 can interact not only with the 5'-GGCTAA-3' motif but also with several 5'-GGC(A/T)(3)-3' motifs. In silico analysis revealed that the 5'-GGC(A/T)(3)-3' motifs are widespread as single site in 5'-upstream region of all the XYR1-regulated genes. Furthermore, we defined the important nucleotides within the binding site that contribute to specific interaction with XYR1. Our results suggest that, together with the inverted repeat motifs, the single 5'-GGC(A/T)(4)-3' motifs play important roles as functional XYR1-binding sites in the regulation of cellulase and xylanase gene expression in T. reesei.
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Affiliation(s)
- Takanori Furukawa
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
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Wadman MW, de Vries RP, Kalkhove SIC, Veldink GA, Vliegenthart JFG. Characterization of oxylipins and dioxygenase genes in the asexual fungus Aspergillus niger. BMC Microbiol 2009; 9:59. [PMID: 19309517 PMCID: PMC2666749 DOI: 10.1186/1471-2180-9-59] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 03/23/2009] [Indexed: 11/20/2022] Open
Abstract
Background Aspergillus niger is an ascomycetous fungus that is known to reproduce through asexual spores, only. Interestingly, recent genome analysis of A. niger has revealed the presence of a full complement of functional genes related to sexual reproduction [1]. An example of such genes are the dioxygenase genes which in Aspergillus nidulans, have been shown to be connected to oxylipin production and regulation of both sexual and asexual sporulation [2-4]. Nevertheless, the presence of sex related genes alone does not confirm sexual sporulation in A. niger. Results The current study shows experimentally that A. niger produces the oxylipins 8,11-dihydroxy octadecadienoic acid (8,11-diHOD), 5,8-dihydroxy octadecadienoic acid (5,8-diHOD), lactonized 5,8-diHOD, 8-hydroxy octadecadienoic acid (8-HOD), 10-hydroxy octadecadienoic acid (10-HOD), small amounts of 8-hydroxy octadecamonoenoic acid (8-HOM), 9-hydroxy octadecadienoic acid (9-HOD) and 13-hydroxy octadecadienoic acid (13-HOD). Importantly, this study shows that the A. niger genome contains three putative dioxygenase genes, ppoA, ppoC and ppoD. Expression analysis confirmed that all three genes are indeed expressed under the conditions tested. Conclusion A. niger produces the same oxylipins and has similar dioxygenase genes as A. nidulans. Their presence could point towards the existence of sexual reproduction in A. niger or a broader role for the gene products in physiology, than just sexual development.
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Affiliation(s)
- Mayken W Wadman
- Bioorganic Chemistry, Utrecht University, 3584 CH, Utrecht, the Netherlands.
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Two glucuronoyl esterases of Phanerochaete chrysosporium. Arch Microbiol 2008; 191:133-40. [PMID: 18854978 DOI: 10.1007/s00203-008-0434-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Revised: 09/10/2008] [Accepted: 09/24/2008] [Indexed: 10/21/2022]
Abstract
The white-rot fungus Phanerochaete chrysosporium produces glucuronoyl esterase, a recently discovered carbohydrate esterase, during growth on sugar beet pulp. Two putative genes encoding this enzyme, ge1 and ge2, were isolated and cloned. Heterologous expression in Aspergillus vadensis, Pycnoporus cinnabarinus and Schizophyllum commune resulted in extracellular glucuronoyl esterase activity, demonstrating that these genes encode this enzymatic function. The amino acid sequence of GE1 was used to identify homologous genes in the genomes of twenty-four fungi. Approximately half of the genomes, both from ascomycetes and basidiomycetes, contained putative orthologues, but their presence could not be assigned to any of fungal class or subclass. Comparison of the amino acid sequences of identified and putative glucuronoyl esterases to other types of carbohydrate esterases (CE) confirmed that they form a separate family of CEs. These enzymes are interesting candidates for biotechnological applications such as the separation of lignin and hemicellulose.
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Furukawa T, Shida Y, Kitagami N, Ota Y, Adachi M, Nakagawa S, Shimada R, Kato M, Kobayashi T, Okada H, Ogasawara W, Morikawa Y. Identification of the cis-acting elements involved in regulation of xylanase III gene expression in Trichoderma reesei PC-3-7. Fungal Genet Biol 2008; 45:1094-102. [DOI: 10.1016/j.fgb.2008.03.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 03/19/2008] [Accepted: 03/19/2008] [Indexed: 10/22/2022]
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A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species. Proc Natl Acad Sci U S A 2008; 105:4387-92. [PMID: 18332432 DOI: 10.1073/pnas.0709964105] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The full-genome sequencing of the filamentous fungi Aspergillus nidulans, Aspergillus niger, and Aspergillus oryzae has opened possibilities for studying the cellular physiology of these fungi on a systemic level. As a tool to explore this, we are making available an Affymetrix GeneChip developed for transcriptome analysis of any of the three above-mentioned aspergilli. Transcriptome analysis of triplicate batch cultivations of all three aspergilli on glucose and xylose media was used to validate the performance of the microarray. Gene comparisons of all three species and cross-analysis with the expression data identified 23 genes to be a conserved response across Aspergillus sp., including the xylose transcriptional activator XlnR. A promoter analysis of the up-regulated genes in all three species indicates the conserved XlnR-binding site to be 5'-GGNTAAA-3'. The composition of the conserved gene-set suggests that xylose acts as a molecule, indicating the presence of complex carbohydrates such as hemicellulose, and triggers an array of degrading enzymes. With this case example, we present a validated tool for transcriptome analysis of three Aspergillus species and a methodology for conducting cross-species evolutionary studies within a genus using comparative transcriptomics.
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Regulation of transcription of cellulases- and hemicellulases-encoding genes in Aspergillus niger and Hypocrea jecorina (Trichoderma reesei). Appl Microbiol Biotechnol 2008; 78:211-20. [PMID: 18197406 DOI: 10.1007/s00253-007-1322-0] [Citation(s) in RCA: 182] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 12/06/2007] [Accepted: 12/08/2007] [Indexed: 10/22/2022]
Abstract
The filamentous fungi Aspergillus niger and Hypocrea jecorina (Trichoderma reesei) have been the subject of many studies investigating the mechanism of transcriptional regulation of hemicellulase- and cellulase-encoding genes. The transcriptional regulator XlnR that was initially identified in A. niger as the transcriptional regulator of xylanase-encoding genes controls the transcription of about 20-30 genes encoding hemicellulases and cellulases. The orthologous xyr1 (xylanase regulator 1-encoding) gene product of H. jecorina has a similar function as XlnR, although at points, the mechanisms seems to be different. Specifically in H. jecorina, the interaction of Xyr1 and the co-regulators Ace1 and Ace2 in the regulation of transcription of xylanases and cellulases has been studied. This paper describes the similarities and differences in the transcriptional regulation of expression of hemicellulases and cellulases in A. niger and H. jecorina.
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Cloning, characterisation and expression analysis of α-glucuronidase from the thermophilic fungus Talaromyces emersonii. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2007.05.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Calero-Nieto F, Hera C, Di Pietro A, Orejas M, Roncero MIG. Regulatory elements mediating expression of xylanase genes in Fusarium oxysporum. Fungal Genet Biol 2007; 45:28-34. [PMID: 17664074 DOI: 10.1016/j.fgb.2007.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Revised: 06/06/2007] [Accepted: 06/08/2007] [Indexed: 10/23/2022]
Abstract
The role of DNA regulatory elements mediating activation of the xylanase-encoding gene xyl4 by the transcription factor XlnR in the fungal pathogen Fusarium oxysporum, was studied by in vitro and in vivo functional analysis of the xyl4 promoter. Recombinant XlnR protein specifically bound the sequence GGCTAA in electrophoretic mobility shift assays. Experiments with xyl4 promoter fusions with the lacZ reporter gene showed that the GGCTAA sequence is required for xylan-induced transcriptional activation of xyl4 in F. oxysporum. The results support a model in which the interaction between the transcriptional activator XlnR and an unknown constitutive repressor regulates xylanase gene expression in F. oxysporum.
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Affiliation(s)
- Fernando Calero-Nieto
- Departamento de Genética, Universidad de Córdoba, Campus Universitario de Rabanales, Edif C5, E-14071 Córdoba, Spain
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de Jong JF, Deelstra HJ, Wösten HAB, Lugones LG. RNA-mediated gene silencing in monokaryons and dikaryons of Schizophyllum commune. Appl Environ Microbiol 2006; 72:1267-9. [PMID: 16461675 PMCID: PMC1392905 DOI: 10.1128/aem.72.2.1267-1269.2006] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Disruption of genes by homologous recombination occurs at a low frequency in the basidiomycete Schizophyllum commune. For instance, the SC3 and SC15 genes were inactivated at frequencies of 1 and 5%, respectively. As an alternative to disruption, we used gene silencing through the introduction of a hairpin construct. The SC15 gene, which encodes an abundantly secreted structural protein, was silenced at a frequency of 80% in monokaryons of S. commune after introduction of a hairpin construct of the gene. Silencing also occurred in dikaryons in which one of the partners was not a silenced strain. The silencing mechanism resembles RNAi in other filamentous fungi and is a powerful tool for the functional analysis of genes expressed in monokaryons or dikaryons.
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Affiliation(s)
- Jan F de Jong
- Microbiology, Institute of Biomembranes, University of Utrecht, Padualaan 8, NL-3584 CH Utrecht, The Netherlands
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Aro N, Pakula T, Penttilä M. Transcriptional regulation of plant cell wall degradation by filamentous fungi. FEMS Microbiol Rev 2004; 29:719-39. [PMID: 16102600 DOI: 10.1016/j.femsre.2004.11.006] [Citation(s) in RCA: 274] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2004] [Revised: 10/29/2004] [Accepted: 11/01/2004] [Indexed: 11/22/2022] Open
Abstract
Plant cell wall consists mainly of the large biopolymers cellulose, hemicellulose, lignin and pectin. These biopolymers are degraded by many microorganisms, in particular filamentous fungi, with the aid of extracellular enzymes. Filamentous fungi have a key role in degradation of the most abundant biopolymers found in nature, cellulose and hemicelluloses, and therefore are essential for the maintenance of the global carbon cycle. The production of plant cell wall degrading enzymes, cellulases, hemicellulases, ligninases and pectinases, is regulated mainly at the transcriptional level in filamentous fungi. The genes are induced in the presence of the polymers or molecules derived from the polymers and repressed under growth conditions where the production of these enzymes is not necessary, such as on glucose. The expression of the genes encoding the enzymes is regulated by various environmental and cellular factors, some of which are common while others are more unique to either a certain fungus or a class of enzymes. This review summarises our current knowledge on the transcriptional regulation, focusing on the recently characterized transcription factors that regulate genes coding for enzymes involved in the breakdown of plant cell wall biopolymers.
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Affiliation(s)
- Nina Aro
- VTT Biotechnology, Espoo, Finland.
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Abstract
Hemicellulases are a diverse group of enzymes that hydrolyze hemicelluloses--one of the most abundant groups of polysaccharide in nature. These enzymes have many biotechnological applications and their structure/function relationships are a subject of intense research. During the past year, new high-resolution structures of catalytic and non-catalytic domains of hemicellulases have been elucidated, and, together with biochemical studies, they reveal the principles of catalysis and specificity for these enzymes.
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Affiliation(s)
- Dalia Shallom
- Department of Food Engineering and Biotechnology and Institute of Catalysis, Science and Technology, Technion, Haifa 32000, Israel
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