Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments

Daly, Paul; van Munster, Jolanda M.; Blythe, Martin J.; Ibbett, Roger; Kokolski, Matt; Gaddipati, Sanyasi; Lindquist, Erika; Singan, Vasanth R.; Barry, Kerrie W.; Lipzen, Anna; Ngan, Chew Yee; Petzold, Christopher J.; Chan, Leanne Jade G.; Pullan, Steven T.; Delmas, Stéphane; Waldron, Paul R.; Grigoriev, Igor V.; Tucker, Gregory A.; Simmons, Blake A.; Archer, David B.

doi:10.1186/s13068-017-0700-9

Title: Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments

Journal Article · 07 February 2017 · Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-017-0700-9 · OSTI ID:1618669

Daly, Paul; van Munster, Jolanda M.; Blythe, Martin J.; Ibbett, Roger; Kokolski, Matt; Gaddipati, Sanyasi; Lindquist, Erika; Singan, Vasanth R.; Barry, Kerrie W.; Lipzen, Anna; Ngan, Chew Yee; Petzold, Christopher J.; Chan, Leanne Jade G.; Pullan, Steven T.; Delmas, Stéphane; Waldron, Paul R.; Grigoriev, Igor V.; Tucker, Gregory A.; Simmons, Blake A.; Archer, David B.

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. 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. 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.

View Journal Article

Cite

Export

Save

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1618669

Alternate ID(s):: OSTI ID: 1379724

Journal Information:: Biotechnology for Biofuels, Journal Name: Biotechnology for Biofuels Vol. 10 Journal Issue: 1; ISSN 1754-6834

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: Netherlands

Language:: English

Citation Metrics:

Cited by: 14 works

Citation information provided by
Web of Science

References (67)

Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger Ries, Laure; Pullan, Steven T.; Delmas, Stéphane BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-541	journal	January 2013
A comparative systems analysis of polysaccharide-elicited responses in Neurospora crassa reveals carbon source-specific cellular adaptations : Fungal polysaccharide-specific responses revealed Benz, J. Philipp; Chau, Bryant H.; Zheng, Diana Molecular Microbiology, Vol. 91, Issue 2 https://doi.org/10.1111/mmi.12459	journal	December 2013
Enrichment, isolation and characterization of fungi tolerant to 1-ethyl-3-methylimidazolium acetate: Ionic liquid-tolerant fungi Singer, S. W.; Reddy, A. P.; Gladden, J. M. Journal of Applied Microbiology, Vol. 110, Issue 4 https://doi.org/10.1111/j.1365-2672.2011.04959.x	journal	February 2011
CreA modulates the XlnR-induced expression on xylose of Aspergillus niger genes involved in xylan degradation P. de Vries, Ronald; Visser, Jaap; de Graaff, Leo H. Research in Microbiology, Vol. 150, Issue 4 https://doi.org/10.1016/S0923-2508(99)80053-9	journal	May 1999
A broader role for AmyR in Aspergillus niger: regulation of the utilisation of d-glucose or d-galactose containing oligo- and polysaccharides vanKuyk, Patricia A.; Benen, Jaques A. E.; Wösten, Han A. B. Applied Microbiology and Biotechnology, Vol. 93, Issue 1 https://doi.org/10.1007/s00253-011-3550-6	journal	August 2011
Structure of the stationary phase survival protein YuiC from B.subtilis Quay, Doris H. X.; Cole, Ambrose R.; Cryar, Adam BMC Structural Biology, Vol. 15, Issue 1 https://doi.org/10.1186/s12900-015-0039-z	journal	July 2015
Room temperature ionic liquids as emerging solvents for the pretreatment of lignocellulosic biomass Mora-Pale, Mauricio; Meli, Luciana; Doherty, Thomas V. Biotechnology and Bioengineering, Vol. 108, Issue 6 https://doi.org/10.1002/bit.23108	journal	April 2011
Analysis of a conserved cellulase transcriptional regulator reveals inducer-independent production of cellulolytic enzymes in Neurospora crassa Coradetti, Samuel T.; Xiong, Yi; Glass, N. Louise MicrobiologyOpen, Vol. 2, Issue 4 https://doi.org/10.1002/mbo3.94	journal	June 2013
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Kim, Daehwan; Pertea, Geo; Trapnell, Cole Genome Biology, Vol. 14, Issue 4 https://doi.org/10.1186/gb-2013-14-4-r36	journal	January 2013
mProphet: automated data processing and statistical validation for large-scale SRM experiments Reiter, Lukas; Rinner, Oliver; Picotti, Paola Nature Methods, Vol. 8, Issue 5 https://doi.org/10.1038/nmeth.1584	journal	March 2011
Regulation of the α-glucuronidase-encoding gene ( aguA ) from Aspergillus niger Vries, R. de; Vondervoort, P. van de; L., Hendriks Molecular Genetics and Genomics, Vol. 268, Issue 1 https://doi.org/10.1007/s00438-002-0729-7	journal	September 2002
The Aspergillus niger faeB gene encodes a second feruloyl esterase involved in pectin and xylan degradation and is specifically induced in the presence of aromatic compounds de VRIES, Ronald P.; vanKUYK, Patricia A.; Kester, Harry C. M. Biochemical Journal, Vol. 363, Issue 2 https://doi.org/10.1042/bj3630377	journal	April 2002
Efficient biomass pretreatment using ionic liquids derived from lignin and hemicellulose Socha, A. M.; Parthasarathi, R.; Shi, J. Proceedings of the National Academy of Sciences, Vol. 111, Issue 35 https://doi.org/10.1073/pnas.1405685111	journal	August 2014
The Phyre2 web portal for protein modeling, prediction and analysis Kelley, Lawrence A.; Mezulis, Stefans; Yates, Christopher M. Nature Protocols, Vol. 10, Issue 6 https://doi.org/10.1038/nprot.2015.053	journal	May 2015
Understanding changes in lignin of Panicum virgatum and Eucalyptus globulus as a function of ionic liquid pretreatment Varanasi, Patanjali; Singh, Priyanka; Arora, Rohit Bioresource Technology, Vol. 126 https://doi.org/10.1016/j.biortech.2012.08.070	journal	December 2012
Sustainable liquid biofuels from biomass: the writing's on the walls Gomez, Leonardo D.; Steele-King, Clare G.; McQueen-Mason, Simon J. New Phytologist, Vol. 178, Issue 3 https://doi.org/10.1111/j.1469-8137.2008.02422.x	journal	May 2008
Transcriptome and exoproteome analysis of utilization of plant-derived biomass by Myceliophthora thermophila Kolbusz, Magdalena Anna; Di Falco, Marcos; Ishmael, Nadeeza Fungal Genetics and Biology, Vol. 72 https://doi.org/10.1016/j.fgb.2014.05.006	journal	November 2014
The challenge of enzyme cost in the production of lignocellulosic biofuels Klein-Marcuschamer, Daniel; Oleskowicz-Popiel, Piotr; Simmons, Blake A. Biotechnology and Bioengineering, Vol. 109, Issue 4 https://doi.org/10.1002/bit.24370	journal	November 2011
New resources for functional analysis of omics data for the genus Aspergillus Nitsche, Benjamin M.; Crabtree, Jonathan; Cerqueira, Gustavo C. BMC Genomics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2164-12-486	journal	October 2011
Galactose metabolic genes in yeast respond to a ratio of galactose and glucose Escalante-Chong, Renan; Savir, Yonatan; Carroll, Sean M. Proceedings of the National Academy of Sciences, Vol. 112, Issue 5 https://doi.org/10.1073/pnas.1418058112	journal	January 2015
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features Liao, Y.; Smyth, G. K.; Shi, W. Bioinformatics, Vol. 30, Issue 7 https://doi.org/10.1093/bioinformatics/btt656	journal	November 2013
1,4-Benzoquinone Reductase from Phanerochaete chrysosporium: cDNA Cloning and Regulation of Expression Akileswaran, Lakshmi; Brock, Barry J.; Cereghino, Joan Lin Applied and Environmental Microbiology, Vol. 65, Issue 2 https://doi.org/10.1128/AEM.65.2.415-421.1999	journal	February 1999
Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates Häkkinen, Mari; Arvas, Mikko; Oja, Merja Microbial Cell Factories, Vol. 11, Issue 1 https://doi.org/10.1186/1475-2859-11-134	journal	January 2012
dbCAN: a web resource for automated carbohydrate-active enzyme annotation Yin, Yanbin; Mao, Xizeng; Yang, Jincai Nucleic Acids Research, Vol. 40, Issue W1 https://doi.org/10.1093/nar/gks479	journal	May 2012
The transcriptional activator GaaR of Aspergillus niger is required for release and utilization of d- galacturonic acid from pectin Alazi, Ebru; Niu, Jing; Kowalczyk, Joanna E. FEBS Letters, Vol. 590, Issue 12 https://doi.org/10.1002/1873-3468.12211	journal	May 2016
Fungal laccase, manganese peroxidase and lignin peroxidase: Gene expression and regulation Janusz, Grzegorz; Kucharzyk, Katarzyna H.; Pawlik, Anna Enzyme and Microbial Technology, Vol. 52, Issue 1 https://doi.org/10.1016/j.enzmictec.2012.10.003	journal	January 2013
Deconstruction of Lignocellulosic Biomass to Fuels and Chemicals Chundawat, Shishir P. S.; Beckham, Gregg T.; Himmel, Michael E. Annual Review of Chemical and Biomolecular Engineering, Vol. 2, Issue 1, p. 121-145 https://doi.org/10.1146/annurev-chembioeng-061010-114205	journal	July 2011
Mapping the polysaccharide degradation potential of Aspergillus niger Andersen, Mikael R.; Giese, Malene; P., Ronald BMC Genomics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2164-13-313	journal	January 2012
Transcriptional Regulation of Biomass-degrading Enzymes in the Filamentous Fungus Trichoderma reesei Foreman, Pamela K.; Brown, Doug; Dankmeyer, Lydia Journal of Biological Chemistry, Vol. 278, Issue 34, p. 31988-31997 https://doi.org/10.1074/jbc.M304750200	journal	June 2003
Cloning and expression of a second Aspergillus niger pectin lyase gene (pelA): Indications of a pectin lyase gene family in A. niger Harmsen, J. A. M.; Kusters-van Someren, M. A.; Visser, J. Current Genetics, Vol. 18, Issue 2 https://doi.org/10.1007/BF00312604	journal	August 1990
Uncovering the Genome-Wide Transcriptional Responses of the Filamentous Fungus Aspergillus niger to Lignocellulose Using RNA Sequencing Delmas, Stéphane; Pullan, Steven T.; Gaddipati, Sanyasi PLoS Genetics, Vol. 8, Issue 8 https://doi.org/10.1371/journal.pgen.1002875	journal	August 2012
Global potential bioethanol production from wasted crops and crop residues Kim, Seungdo; Dale, Bruce E. Biomass and Bioenergy, Vol. 26, Issue 4, p. 361-375 https://doi.org/10.1016/j.biombioe.2003.08.002	journal	April 2004
Transcriptome analysis of Aspergillus niger grown on sugarcane bagasse de Souza, Wagner R.; de Gouvea, Paula F.; Savoldi, Marcela Biotechnology for Biofuels, Vol. 4, Issue 1 https://doi.org/10.1186/1754-6834-4-40	journal	January 2011
The Transcriptional Activator XlnR Regulates Both Xylanolytic and Endoglucanase Gene Expression inAspergillus niger van Peij, Noël N. M. E.; Gielkens, Marco M. C.; de Vries, Ronald P. Applied and Environmental Microbiology, Vol. 64, Issue 10 https://doi.org/10.1128/AEM.64.10.3615-3619.1998	journal	October 1998
An Evolutionarily Conserved Transcriptional Activator-Repressor Module Controls Expression of Genes for D-Galacturonic Acid Utilization in Aspergillus niger Niu, Jing; Alazi, Ebru; Reid, Ian D. Genetics, Vol. 205, Issue 1 https://doi.org/10.1534/genetics.116.194050	journal	November 2016
Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae Coutinho, Pedro M.; Andersen, Mikael R.; Kolenova, Katarina Fungal Genetics and Biology, Vol. 46, Issue 1 https://doi.org/10.1016/j.fgb.2008.07.020	journal	March 2009
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes Floudas, Dimitrios; Binder, Manfred; Riley, Robert Science, Vol. 336, Issue 6089 https://doi.org/10.1126/science.1221748	journal	June 2012
Gene ontology analysis for RNA-seq: accounting for selection bias Young, Matthew D.; Wakefield, Matthew J.; Smyth, Gordon K. Genome Biology, Vol. 11, Issue 2 https://doi.org/10.1186/gb-2010-11-2-r14	journal	January 2010
Comparative analysis of the Trichoderma reesei transcriptome during growth on the cellulase inducing substrates wheat straw and lactose Bischof, Robert; Fourtis, Lukas; Limbeck, Andreas Biotechnology for Biofuels, Vol. 6, Issue 1 https://doi.org/10.1186/1754-6834-6-127	journal	January 2013
Assessment of the pectin degrading enzyme network of Aspergillus niger by functional genomics Martens-Uzunova, Elena S.; Schaap, Peter J. Fungal Genetics and Biology, Vol. 46, Issue 1 https://doi.org/10.1016/j.fgb.2008.07.021	journal	March 2009
Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger Andersen, Mikael Rørdam; Nielsen, Michael Lynge; Nielsen, Jens Molecular Systems Biology, Vol. 4, Issue 1 https://doi.org/10.1038/msb.2008.12	journal	January 2008
The carbohydrate-active enzymes database (CAZy) in 2013 Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1178	journal	November 2013
Noise-Robust soft Clustering of gene Expression Time-Course data Futschik, Matthias E.; Carlisle, Bronwyn Journal of Bioinformatics and Computational Biology, Vol. 03, Issue 04 https://doi.org/10.1142/S0219720005001375	journal	August 2005
Transition of Cellulose Crystalline Structure and Surface Morphology of Biomass as a Function of Ionic Liquid Pretreatment and Its Relation to Enzymatic Hydrolysis Cheng, Gang; Varanasi, Patanjali; Li, Chenlin Biomacromolecules, Vol. 12, Issue 4 https://doi.org/10.1021/bm101240z	journal	April 2011
The mechanisms of hydrothermal deconstruction of lignocellulose: New insights from thermal–analytical and complementary studies Ibbett, Roger; Gaddipati, Sanyasi; Davies, Scott Bioresource Technology, Vol. 102, Issue 19 https://doi.org/10.1016/j.biortech.2011.06.044	journal	October 2011
Expression profiling of pectinolytic genes from Aspergillus niger de Vries, Ronald P.; Jansen, Jenny; Aguilar, Guillermo FEBS Letters, Vol. 530, Issue 1-3 https://doi.org/10.1016/S0014-5793(02)03391-4	journal	September 2002
An NADH:Quinone Oxidoreductase Active during Biodegradation by the Brown-Rot Basidiomycete Gloeophyllum trabeum Jensen, K. A.; Ryan, Z. C.; Vanden Wymelenberg, A. Applied and Environmental Microbiology, Vol. 68, Issue 6 https://doi.org/10.1128/AEM.68.6.2699-2703.2002	journal	June 2002
Cloning and Characterization of a Gene Coding for a Major Extracellular Chitosanase from the Koji Mold Aspergillus oryzae Sugita, Akihiro; Sugii, Ayako; Sato, Kazuaki Bioscience, Biotechnology, and Biochemistry, Vol. 76, Issue 1 https://doi.org/10.1271/bbb.110605	journal	January 2012
Structural reorganisation of cellulose fibrils in hydrothermally deconstructed lignocellulosic biomass and relationships with enzyme digestibility Ibbett, Roger; Gaddipati, Sanyasi; Hill, Sandra Biotechnology for Biofuels, Vol. 6, Issue 1 https://doi.org/10.1186/1754-6834-6-33	journal	January 2013
mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support Strasser, Kimchi; McDonnell, Erin; Nyaga, Carol Database, Vol. 2015 https://doi.org/10.1093/database/bav008	journal	January 2015
Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88 Pel, Herman J.; de Winde, Johannes H.; Archer, David B. Nature Biotechnology, Vol. 25, Issue 2, p. 221-231 https://doi.org/10.1038/nbt1282	journal	January 2007
Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88 Andersen, M. R.; Salazar, M. P.; Schaap, P. J. Genome Research, Vol. 21, Issue 6, p. 885-897 https://doi.org/10.1101/gr.112169.110	journal	May 2011
Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization Mewis, Keith; Lenfant, Nicolas; Lombard, Vincent Applied and Environmental Microbiology, Vol. 82, Issue 6 https://doi.org/10.1128/AEM.03453-15	journal	January 2016
Transcriptomic responses of mixed cultures of ascomycete fungi to lignocellulose using dual RNA-seq reveal inter-species antagonism and limited beneficial effects on CAZyme expression Daly, Paul; van Munster, Jolanda M.; Kokolski, Matthew Fungal Genetics and Biology, Vol. 102 https://doi.org/10.1016/j.fgb.2016.04.005	journal	May 2017
Ab initio phasing of a nucleoside hydrolase-related hypothetical protein from Saccharophagus degradans that is associated with carbohydrate metabolism Hehemann, Jan-Hendrik; Marsters, Candace; Boraston, Alisdair B. Proteins: Structure, Function, and Bioinformatics, Vol. 79, Issue 10 https://doi.org/10.1002/prot.23126	journal	August 2011
The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger van Munster, Jolanda M.; Daly, Paul; Delmas, Stéphane Fungal Genetics and Biology, Vol. 72 https://doi.org/10.1016/j.fgb.2014.04.006	journal	November 2014
Plant Cell Wall Deconstruction by Ascomycete Fungi Glass, N. Louise; Schmoll, Monika; Cate, Jamie H. D. Annual Review of Microbiology, Vol. 67, Issue 1 https://doi.org/10.1146/annurev-micro-092611-150044	journal	September 2013
The Aspergillus niger multicopper oxidase family: analysis and overexpression of laccase-like encoding genes Tamayo Ramos, Juan A.; Barends, Sharief; Verhaert, Raymond MD Microbial Cell Factories, Vol. 10, Issue 1 https://doi.org/10.1186/1475-2859-10-78	journal	January 2011
An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data Braaksma, Machtelt; Martens-Uzunova, Elena S.; Punt, Peter J. BMC Genomics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2164-11-584	journal	January 2010
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 de Souza, Wagner Rodrigo; Maitan-Alfenas, Gabriela Piccolo; de Gouvêa, Paula Fagundes Fungal Genetics and Biology, Vol. 60 https://doi.org/10.1016/j.fgb.2013.07.007	journal	November 2013
Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa Tian, Chaoguang; Beeson, William T.; Iavarone, Anthony T. Proceedings of the National Academy of Sciences, Vol. 106, Issue 52 https://doi.org/10.1073/pnas.0906810106	journal	December 2009
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Love, Michael I.; Huber, Wolfgang; Anders, Simon Genome Biology, Vol. 15, Issue 12 https://doi.org/10.1186/s13059-014-0550-8	journal	December 2014
RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger Pullan, Steven T.; Daly, Paul; Delmas, Stéphane Fungal Biology and Biotechnology, Vol. 1, Issue 1 https://doi.org/10.1186/s40694-014-0003-x	journal	November 2014
Pretreatment of Lignocellulosic Wastes to Improve Ethanol and Biogas Production: A Review Taherzadeh, Mohammad; Karimi, Keikhosro International Journal of Molecular Sciences, Vol. 9, Issue 9, p. 1621-1651 https://doi.org/10.3390/ijms9091621	journal	September 2008
Cloning and characterization of Aspergillus niger genes encoding an α-galactosidase and a β-mannosidase involved in galactomannan degradation : α-Galactosidase and β-mannosidase from Ademark, Pia; de Vries, Ronald P.; Hägglund, Per European Journal of Biochemistry, Vol. 268, Issue 10 https://doi.org/10.1046/j.1432-1327.2001.02188.x	journal	May 2001
Cloning of the Aspergillus niger gene encoding α-l-arabinofuranosidase A Flipphi, Michel J. A.; Visser, Jaap; van der Veen, Peter Applied Microbiology and Biotechnology, Vol. 39, Issue 3 https://doi.org/10.1007/BF00192088	journal	June 1993
Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes Levasseur, Anthony; Drula, Elodie; Lombard, Vincent Biotechnology for Biofuels, Vol. 6, Issue 1, Article No. 41 https://doi.org/10.1186/1754-6834-6-41	journal	January 2013

Cited By (8)

Carbon sources and XlnR-dependent transcriptional landscape of CAZymes in the industrial fungus Talaromyces versatilis: when exception seems to be the rule Llanos, Agustina; Déjean, Sébastien; Neugnot-Roux, Virginie Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1062-8	journal	January 2019
Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose van Munster, Jolanda M.; Daly, Paul; Blythe, Martin J. Biotechnology for Biofuels, Vol. 13, Issue 1 https://doi.org/10.1186/s13068-020-01702-2	journal	April 2020
Mild hydrothermal pretreatment of sugarcane bagasse enhances the production of holocellulases by Aspergillus niger de Oliveira Gorgulho Silva, Caio; de Castro Moreira dos Santos Júnior, Agenor; Santana, Renata Henrique Journal of Industrial Microbiology & Biotechnology, Vol. 46, Issue 11 https://doi.org/10.1007/s10295-019-02207-0	journal	June 2019
Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation Daly, Paul; Peng, Mao; Mitchell, Hugh D. Environmental Microbiology, Vol. 22, Issue 3 https://doi.org/10.1111/1462-2920.14907	journal	August 2019
Phenotypic plasticity and the evolution of azole resistance in Aspergillus fumigatus; an expression profile of clinical isolates upon exposure to itraconazole Hokken, Margriet W. J.; Zoll, Jan; Coolen, Jordy P. M. BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-018-5255-z	journal	January 2019
Systems metabolic engineering for citric acid production by Aspergillus niger in the post-genomic era Tong, Zhenyu; Zheng, Xiaomei; Tong, Yi Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1064-6	journal	February 2019
Regulators of plant biomass degradation in ascomycetous fungi Benocci, Tiziano; Aguilar-Pontes, Maria Victoria; Zhou, Miaomiao Biotechnology for Biofuels, Vol. 10, Issue 1 https://doi.org/10.1186/s13068-017-0841-x	journal	June 2017
Genome-wide annotation, comparison and functional genomics of carbohydrate-active enzymes in legumes infecting Fusarium oxysporum formae speciales Roy, Abhijeet; Jayaprakash, Aiswarya; T., Raja Rajeswary Taylor & Francis https://doi.org/10.6084/m9.figshare.11512848	text	January 2020

Linked Research (16)

Similar Records

Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose

Journal Article · 2020 · Biotechnology for Biofuels · OSTI ID:1618778

van Munster, Jolanda M.; Daly, Paul; Blythe, Martin J.; +18 more

Deletion of either the regulatory gene ara1 or metabolic gene xki1 in Trichoderma reesei leads to increased CAZyme gene expression on crude plant biomass

Journal Article · 2019 · Biotechnology for Biofuels · OSTI ID:1581318

Benocci, Tiziano; Aguilar-Pontes, Maria Victoria; Kun, Roland Sándor; +9 more

Development of an E. coli strain for one-pot biofuel production from ionic liquid pretreated cellulose and switchgrass

Journal Article · 2016 · Green Chemistry · OSTI ID:1378746

Frederix, Marijke; Mingardon, Florence; Hu, Matthew; +6 more

Related Subjects

09 BIOMASS FUELS
Aspergillus niger
Lignocellulose
Ionic liquid and hydrothermal pretreatments
Straw
Transcriptomic responses
CAZy
Hemicellulose
RNA-seq
Targeted proteomics

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments [Supplementary Data] Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393 The current record is supplemented by this dataset	dataset	February 2017
Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments [Supplemental Data] Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM3 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d1.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM1 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d10.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM14 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d11.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM5 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d12.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM2 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d13.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM10 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d14.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM7 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d2.v1 The current record is supplemented by this figure	figure	February 2017
MOESM6 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d3.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM11 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d4.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM8 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d5.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM13 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d6.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM4 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d7.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM9 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d8.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM12 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d9.v1 The current record is supplemented by this dataset	dataset	February 2017