Identification and manipulation of Neurospora crassa genes involved in sensitivity to furfural
Abstract
Background: Biofuels derived from lignocellulosic biomass are a viable alternative to fossil fuels required for transportation. Following plant biomass pretreatment, the furan derivative furfural is present at concentrations which are inhibitory to yeasts. Detoxification of furfural is thus important for efficient fermentation. Here, we searched for new genetic attributes in the fungus Neurospora crassa that may be linked to furfural tolerance. The fact that furfural is involved in the natural process of sexual spore germination of N. crassa and that this fungus is highly amenable to genetic manipulations makes it a rational candidate for this study. Results: Both hypothesis-based and unbiased (random promotor mutagenesis) approaches were performed to identify N. crassa genes associated with the response to furfural. Changes in the transcriptional profile following exposure to furfural revealed that the affected processes were, overall, similar to those observed in Saccharomyces cerevisiae. N. crassa was more tolerant (by ~ 30%) to furfural when carboxymethyl cellulose was the main carbon source as opposed to sucrose, indicative of a link between carbohydrate metabolism and furfural tolerance. We also observed increased tolerance in a Δcre-1 mutant (CRE-1 is a key transcription factor that regulates the ability of fungi to utilize non-preferred carbon sources). Inmore »
- Authors:
-
- Hebrew Univ. of Jerusalem, Rehovot (Israel). Dept. of Plant Pathology and Microbiology
- Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
- Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1571949
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Biotechnology for Biofuels
- Additional Journal Information:
- Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1754-6834
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Feldman, Daria, Kowbel, David J., Cohen, Adi, Glass, N. Louise, Hadar, Yitzhak, and Yarden, Oded. Identification and manipulation of Neurospora crassa genes involved in sensitivity to furfural. United States: N. p., 2019.
Web. doi:10.1186/s13068-019-1550-4.
Feldman, Daria, Kowbel, David J., Cohen, Adi, Glass, N. Louise, Hadar, Yitzhak, & Yarden, Oded. Identification and manipulation of Neurospora crassa genes involved in sensitivity to furfural. United States. doi:10.1186/s13068-019-1550-4.
Feldman, Daria, Kowbel, David J., Cohen, Adi, Glass, N. Louise, Hadar, Yitzhak, and Yarden, Oded. Wed .
"Identification and manipulation of Neurospora crassa genes involved in sensitivity to furfural". United States. doi:10.1186/s13068-019-1550-4. https://www.osti.gov/servlets/purl/1571949.
@article{osti_1571949,
title = {Identification and manipulation of Neurospora crassa genes involved in sensitivity to furfural},
author = {Feldman, Daria and Kowbel, David J. and Cohen, Adi and Glass, N. Louise and Hadar, Yitzhak and Yarden, Oded},
abstractNote = {Background: Biofuels derived from lignocellulosic biomass are a viable alternative to fossil fuels required for transportation. Following plant biomass pretreatment, the furan derivative furfural is present at concentrations which are inhibitory to yeasts. Detoxification of furfural is thus important for efficient fermentation. Here, we searched for new genetic attributes in the fungus Neurospora crassa that may be linked to furfural tolerance. The fact that furfural is involved in the natural process of sexual spore germination of N. crassa and that this fungus is highly amenable to genetic manipulations makes it a rational candidate for this study. Results: Both hypothesis-based and unbiased (random promotor mutagenesis) approaches were performed to identify N. crassa genes associated with the response to furfural. Changes in the transcriptional profile following exposure to furfural revealed that the affected processes were, overall, similar to those observed in Saccharomyces cerevisiae. N. crassa was more tolerant (by ~ 30%) to furfural when carboxymethyl cellulose was the main carbon source as opposed to sucrose, indicative of a link between carbohydrate metabolism and furfural tolerance. We also observed increased tolerance in a Δcre-1 mutant (CRE-1 is a key transcription factor that regulates the ability of fungi to utilize non-preferred carbon sources). In addition, analysis of aldehyde dehydrogenase mutants showed that ahd-2 (NCU00378) was involved in tolerance to furfural as well as the predicted membrane transporter NCU05580 (flr-1), a homolog of FLR1 in S. cerevisiae. Further to the rational screening, an unbiased approach revealed additional genes whose inactivation conferred increased tolerance to furfural: (i) NCU02488, which affected the abundance of the non-anchored cell wall protein NCW-1 (NCU05137), and (ii) the zinc finger protein NCU01407. Conclusions:We identified attributes in N. crassa associated with tolerance or degradation of furfural, using complementary research approaches. The manipulation of the genes involved in furan sensitivity can provide a means for improving the production of biofuel producing strains. Similar research approaches can be utilized in N. crassa and other filamentous fungi to identify additional attributes relevant to other furans or toxic chemicals.},
doi = {10.1186/s13068-019-1550-4},
journal = {Biotechnology for Biofuels},
number = 1,
volume = 12,
place = {United States},
year = {2019},
month = {9}
}
Works referenced in this record:
Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa
journal, September 2017
- Samal, Areejit; Craig, James P.; Coradetti, Samuel T.
- Biotechnology for Biofuels, Vol. 10, Issue 1
Characterization of indole-3-pyruvic acid pathway-mediated biosynthesis of auxin in Neurospora crassa
journal, February 2018
- Sardar, Puspendu; Kempken, Frank
- PLOS ONE, Vol. 13, Issue 2
Performances of Lactobacillus brevis for Producing Lactic Acid from Hydrolysate of Lignocellulosics
journal, November 2009
- Guo, Wei; Jia, Wendi; Li, Yin
- Applied Biochemistry and Biotechnology, Vol. 161, Issue 1-8
Inhibition of ethanol-producing yeast and bacteria by degradation products produced during pre-treatment of biomass
journal, August 2004
- Klinke, H. B.; Thomsen, A. B.; Ahring, B. K.
- Applied Microbiology and Biotechnology, Vol. 66, Issue 1, p. 10-26
ManR, a Transcriptional Regulator of the β-Mannan Utilization System, Controls the Cellulose Utilization System in <i>Aspergillus oryzae</i>
journal, January 2013
- Ogawa, Masahiro; Kobayashi, Tetsuo; Koyama, Yasuji
- Bioscience, Biotechnology, and Biochemistry, Vol. 77, Issue 2
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
journal, May 2010
- Trapnell, Cole; Williams, Brian A.; Pertea, Geo
- Nature Biotechnology, Vol. 28, Issue 5
Bioconversion of dilute-acid pretreated sorghum bagasse to ethanol by Neurospora crassa
journal, May 2012
- Dogaris, Ioannis; Gkounta, Olga; Mamma, Diomi
- Applied Microbiology and Biotechnology, Vol. 95, Issue 2
Differential expression analysis for sequence count data
journal, October 2010
- Anders, Simon; Huber, Wolfgang
- Genome Biology, Vol. 11, Issue 10
Multiple gene-mediated NAD(P)H-dependent aldehyde reduction is a mechanism of in situ detoxification of furfural and 5-hydroxymethylfurfural by Saccharomyces cerevisiae
journal, September 2008
- Lewis Liu, Z.; Moon, Jaewoong; Andersh, Brad J.
- Applied Microbiology and Biotechnology, Vol. 81, Issue 4, p. 743-753
Fungal pretreatment of lignocellulosic biomass
journal, November 2012
- Wan, Caixia; Li, Yebo
- Biotechnology Advances, Vol. 30, Issue 6
Fast and accurate long-read alignment with Burrows–Wheeler transform
journal, January 2010
- Li, Heng; Durbin, Richard
- Bioinformatics, Vol. 26, Issue 5
Cellulosic Biofuels
journal, June 2009
- Carroll, Andrew; Somerville, Chris
- Annual Review of Plant Biology, Vol. 60, Issue 1
Microbial transformation of furfural to furfuryl alcohol by saccharomyces cerevisiae: Biotransformation of Furfural to Furfuryl Alcohol
journal, January 1992
- Villa, G. P.; Bartroli, R.; López, R.
- Acta Biotechnologica, Vol. 12, Issue 6
Molecular mechanisms of yeast tolerance and in situ detoxification of lignocellulose hydrolysates
journal, March 2011
- Liu, Z. Lewis
- Applied Microbiology and Biotechnology, Vol. 90, Issue 3
Strains of Neurospora Collected from Nature
journal, June 1976
- Perkins, David D.; Turner, Barbara C.; Barry, Edward G.
- Evolution, Vol. 30, Issue 2
A proteomic and genetic analysis of the Neurospora crassa conidia cell wall proteins identifies two glycosyl hydrolases involved in cell wall remodeling
journal, September 2016
- Ao, Jie; Aldabbous, Mash’el; Notaro, Marysa J.
- Fungal Genetics and Biology, Vol. 94
FungiDB: an integrated functional genomics database for fungi
journal, November 2011
- Stajich, J. E.; Harris, T.; Brunk, B. P.
- Nucleic Acids Research, Vol. 40, Issue D1
Neurospora from natural populations: Toward the population biology of a haploid eukaryote
journal, June 1988
- Perkins, David D.; Turner, Barbara C.
- Experimental Mycology, Vol. 12, Issue 2
Chitin synthase 1 plays a major role in cell wall biogenesis in Neurospora crassa.
journal, December 1991
- Yarden, O.; Yanofsky, C.
- Genes & Development, Vol. 5, Issue 12b
SAMBLASTER: fast duplicate marking and structural variant read extraction
journal, May 2014
- Faust, G. G.; Hall, I. M.
- Bioinformatics, Vol. 30, Issue 17
Human liver mitochondrial aldehyde dehydrogenase: Three-dimensional structure and the restoration of solubility and activity of chimeric forms
journal, January 1999
- Ni, Li; Zhou, Jianzhong; Weiner, Henry
- Protein Science, Vol. 8, Issue 12
Induction of lignocellulose-degrading enzymes in Neurospora crassa by cellodextrins
journal, April 2012
- Znameroski, E. A.; Coradetti, S. T.; Roche, C. M.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 16
Mechanism of formation of 2-furaldehyde from d-xylose
journal, September 1991
- Antal, Michael Jerry; Leesomboon, Tongchit; Mok, William S.
- Carbohydrate Research, Vol. 217
Overexpression of Saccharomyces cerevisiae transcription factor and multidrug resistance genes conveys enhanced resistance to lignocellulose-derived fermentation inhibitors
journal, February 2010
- Alriksson, Björn; Horváth, Ilona Sárvári; Jönsson, Leif J.
- Process Biochemistry, Vol. 45, Issue 2
Exploring the tolerance of marine yeast to inhibitory compounds for improving bioethanol production
journal, January 2019
- Greetham, Darren; Zaky, Abdelrahman Saleh; Du, Chenyu
- Sustainable Energy & Fuels, Vol. 3, Issue 6
Using a model filamentous fungus to unravel mechanisms of lignocellulose deconstruction
journal, January 2013
- Znameroski, Elizabeth A.; Glass, N. Louise
- Biotechnology for Biofuels, Vol. 6, Issue 1
Conversion of furfural to furoic acid and furfuryl alcohol by Neurospora ascospores
journal, January 1970
- Eilers, Frederick I.; Sussman, Alfred S.
- Planta, Vol. 94, Issue 4
SpeedSeq: ultra-fast personal genome analysis and interpretation
journal, August 2015
- Chiang, Colby; Layer, Ryan M.; Faust, Gregory G.
- Nature Methods, Vol. 12, Issue 10
Transcriptome profiling of Zymomonas mobilis under furfural stress
journal, May 2012
- He, Ming-xiong; Wu, Bo; Shui, Zong-xia
- Applied Microbiology and Biotechnology, Vol. 95, Issue 1
GFP as a tool to analyze the organization, dynamics and function of nuclei and microtubules in Neurospora crassa
journal, October 2004
- Freitag, Michael; Hickey, Patrick C.; Raju, Namboori B.
- Fungal Genetics and Biology, Vol. 41, Issue 10
AP1-mediated Multidrug Resistance in Saccharomyces cerevisiae Requires FLR1 Encoding a Transporter of the Major Facilitator Superfamily
journal, August 1997
- Alarco, Anne-Marie; Balan, Inga; Talibi, Driss
- Journal of Biological Chemistry, Vol. 272, Issue 31
Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae
journal, January 2010
- Ma, Menggen; Liu, Z. Lewis
- BMC Genomics, Vol. 11, Issue 1
A 5-hydroxymethyl furfural reducing enzyme encoded by theSaccharomyces cerevisiae ADH6 gene conveys HMF tolerance
journal, January 2006
- Petersson, Anneli; Almeida, João R. M.; Modig, Tobias
- Yeast, Vol. 23, Issue 6, p. 455-464
Pretreatment of Lignocellulosic Wastes to Improve Ethanol and Biogas Production: A Review
journal, September 2008
- Taherzadeh, Mohammad; Karimi, Keikhosro
- International Journal of Molecular Sciences, Vol. 9, Issue 9, p. 1621-1651
The generation of fermentation inhibitors during dilute acid hydrolysis of softwood
journal, February 1999
- Larsson, Simona; Palmqvist, Eva; Hahn-Hägerdal, Bärbel
- Enzyme and Microbial Technology, Vol. 24, Issue 3-4
Comparative Proteomic Analysis of Tolerance and Adaptation of Ethanologenic Saccharomyces cerevisiae to Furfural, a Lignocellulosic Inhibitory Compound
journal, April 2009
- Lin, F. -M.; Qiao, B.; Yuan, Y. -J.
- Applied and Environmental Microbiology, Vol. 75, Issue 11
Inhibition effects of furfural on alcohol dehydrogenase, aldehyde dehydrogenase and pyruvate dehydrogenase
journal, April 2002
- Modig, Tobias; LidÉN, Gunnar; Taherzadeh, Mohammad J.
- Biochemical Journal, Vol. 363, Issue 3
Open source clustering software
journal, February 2004
- de Hoon, M. J. L.; Imoto, S.; Nolan, J.
- Bioinformatics, Vol. 20, Issue 9
Analysis of a conserved cellulase transcriptional regulator reveals inducer-independent production of cellulolytic enzymes in Neurospora crassa
journal, June 2013
- Coradetti, Samuel T.; Xiong, Yi; Glass, N. Louise
- MicrobiologyOpen, Vol. 2, Issue 4
Transcriptional profiling reveals molecular basis and novel genetic targets for improved resistance to multiple fermentation inhibitors in Saccharomyces cerevisiae
journal, January 2016
- Chen, Yingying; Sheng, Jiayuan; Jiang, Tao
- Biotechnology for Biofuels, Vol. 9, Issue 1
Silencing of NADPH-Dependent Oxidoreductase Genes (yqhD and dkgA) in Furfural-Resistant Ethanologenic Escherichia coli
journal, May 2009
- Miller, E. N.; Jarboe, L. R.; Yomano, L. P.
- Applied and Environmental Microbiology, Vol. 75, Issue 13, p. 4315-4323
Neurospora crassa transcriptomics reveals oxidative stress and plasma membrane homeostasis biology genes as key targets in response to chitosan
journal, January 2016
- Lopez-Moya, Federico; Kowbel, David; Nueda, Ma José
- Molecular BioSystems, Vol. 12, Issue 2
TopHat: discovering splice junctions with RNA-Seq
journal, March 2009
- Trapnell, Cole; Pachter, Lior; Salzberg, Steven L.
- Bioinformatics, Vol. 25, Issue 9
Carbon source affects PKA-dependent polarity of Neurospora crassa in a CRE-1-dependent and independent manner
journal, February 2008
- Ziv, Carmit; Gorovits, Rena; Yarden, Oded
- Fungal Genetics and Biology, Vol. 45, Issue 2
LUMPY: a probabilistic framework for structural variant discovery
journal, January 2014
- Layer, Ryan M.; Chiang, Colby; Quinlan, Aaron R.
- Genome Biology, Vol. 15, Issue 6
Detoxification of 5-hydroxymethylfurfural by the Pleurotus ostreatus lignolytic enzymes aryl alcohol oxidase and dehydrogenase
journal, April 2015
- Feldman, Daria; Kowbel, David J.; Glass, N. Louise
- Biotechnology for Biofuels, Vol. 8, Issue 1
MindTheGap: integrated detection and assembly of short and long insertions
journal, August 2014
- Rizk, G.; Gouin, A.; Chikhi, R.
- Bioinformatics, Vol. 30, Issue 24
Computational Method to Predict Mitochondrially Imported Proteins and their Targeting Sequences
journal, November 1996
- Claros, Manuel G.; Vincens, Pierre
- European Journal of Biochemistry, Vol. 241, Issue 3
Protein Subcellular Localization Prediction with wolf Psort
conference, November 2011
- Horton, Paul; Park, Keun-Joon; Obayashi, Takeshi
- Proceedings of the 4th Asia-Pacific Bioinformatics Conference
The Fungal Genetics Stock Center: a repository for 50 years of fungal genetics research
journal, January 2010
- McCluskey, K.; Wiest, A.; Plamann, M.
- Journal of Biosciences, Vol. 35, Issue 1
Transcriptome shifts in response to furfural and acetic acid in Saccharomyces cerevisiae
journal, March 2010
- Li, Bing-Zhi; Yuan, Ying-Jin
- Applied Microbiology and Biotechnology, Vol. 86, Issue 6
The Tandem Repeats Enabling Reversible Switching between the Two Phases of β-Lactamase Substrate Spectrum
journal, September 2014
- Yi, Hyojeong; Song, Han; Hwang, Junghyun
- PLoS Genetics, Vol. 10, Issue 9
Regulation of cellulolytic genes by McmA, the SRF-MADS box protein in Aspergillus nidulans
journal, February 2013
- Yamakawa, Yohei; Endo, Yoshikazu; Li, Nuo
- Biochemical and Biophysical Research Communications, Vol. 431, Issue 4
Furfural Formation and Behavior
journal, February 1948
- Dunlop, A. P.
- Industrial & Engineering Chemistry, Vol. 40, Issue 2
Strains of Neurospora Collected from Nature
journal, June 1976
- Perkins, David D.; Turner, Barbara C.; Barry, Edward G.
- Evolution, Vol. 30, Issue 2
Metabolic effects of furaldehydes and impacts on biotechnological processes
journal, January 2009
- Almeida, João R. M.; Bertilsson, Magnus; Gorwa-Grauslund, Marie F.
- Applied Microbiology and Biotechnology, Vol. 82, Issue 4
Regulation of Neurospora crassa cell wall remodeling via the cot-1 pathway is mediated by gul-1
journal, June 2016
- Herold, Inbal; Yarden, Oded
- Current Genetics, Vol. 63, Issue 1
Neurospora from Natural Populations: A Global Study
journal, March 2001
- Turner, Barbara C.; Perkins, David D.; Fairfield, Ann
- Fungal Genetics and Biology, Vol. 32, Issue 2
Biotechnological strategies to overcome inhibitors in lignocellulose hydrolysates for ethanol production: review
journal, May 2010
- Parawira, W.; Tekere, M.
- Critical Reviews in Biotechnology, Vol. 31, Issue 1
Identification and characterization of the furfural and 5-(hydroxymethyl)furfural degradation pathways of Cupriavidus basilensis HMF14
journal, March 2010
- Koopman, F.; Wierckx, N.; de Winde, J. H.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 11
Lessons from the Genome Sequence of Neurospora crassa: Tracing the Path from Genomic Blueprint to Multicellular Organism
journal, March 2004
- Borkovich, K. A.; Alex, L. A.; Yarden, O.
- Microbiology and Molecular Biology Reviews, Vol. 68, Issue 1
Comparative proteomic analysis of a new adaptive Pichia Stipitis strain to furfural, a lignocellulosic inhibitory compound
journal, January 2013
- Hao, Xue-Cai; Yang, Xiu-Shan; Wan, Ping
- Biotechnology for Biofuels, Vol. 6, Issue 1
The genome sequence of the filamentous fungus Neurospora crassa
journal, April 2003
- Galagan, James E.; Calvo, Sarah E.; Borkovich, Katherine A.
- Nature, Vol. 422, Issue 6934
High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states
journal, February 2013
- Blecher-Gonen, Ronnie; Barnett-Itzhaki, Zohar; Jaitin, Diego
- Nature Protocols, Vol. 8, Issue 3
Understanding physiological responses to pre-treatment inhibitors in ethanologenic fermentations
journal, February 2012
- Taylor, Mark P.; Mulako, Inonge; Tuffin, Marla
- Biotechnology Journal, Vol. 7, Issue 9, p. 1169-1181
Genomic adaptation of ethanologenic yeast to biomass conversion inhibitors
journal, October 2006
- Liu, Z. Lewis
- Applied Microbiology and Biotechnology, Vol. 73, Issue 1
Resistance of Saccharomyces cerevisiae to High Concentrations of Furfural Is Based on NADPH-Dependent Reduction by at Least Two Oxireductases
journal, October 2009
- Heer, D.; Heine, D.; Sauer, U.
- Applied and Environmental Microbiology, Vol. 75, Issue 24
Fermentation of lignocellulosic hydrolysates. II: inhibitors and mechanisms of inhibition
journal, August 2000
- Palmqvist, Eva; Hahn-Hägerdal, Bärbel
- Bioresource Technology, Vol. 74, Issue 1, p. 25-33
Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi
journal, April 2012
- Coradetti, S. T.; Craig, J. P.; Xiong, Y.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 19
Insight into progress in pre-treatment of lignocellulosic biomass
journal, March 2017
- Bhutto, Abdul Waheed; Qureshi, Khadija; Harijan, Khanji
- Energy, Vol. 122
Identification of the CRE-1 Cellulolytic Regulon in Neurospora crassa
journal, September 2011
- Sun, Jianping; Glass, N. Louise
- PLoS ONE, Vol. 6, Issue 9
Life-history ofNeurospora intermedia in a sugar cane field
journal, March 1996
- Pandit, Alka; Maheshwari, Ramesh
- Journal of Biosciences, Vol. 21, Issue 1
Plant Cell Wall Deconstruction by Ascomycete Fungi
journal, September 2013
- Glass, N. Louise; Schmoll, Monika; Cate, Jamie H. D.
- Annual Review of Microbiology, Vol. 67, Issue 1
Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa
journal, December 2009
- Tian, Chaoguang; Beeson, William T.; Iavarone, Anthony T.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 52
Mutational Analysis of the Glycosylphosphatidylinositol (GPI) Anchor Pathway Demonstrates that GPI-Anchored Proteins Are Required for Cell Wall Biogenesis and Normal Hyphal Growth in Neurospora crassa
journal, March 2006
- Bowman, Shaun M.; Piwowar, Amy; Al Dabbous, Mash'el
- Eukaryotic Cell, Vol. 5, Issue 3, p. 587-600
Chemical Activation of Ascospore Germination in Neurospora crassa1
journal, January 1948
- Emerson, Mary R.
- Journal of Bacteriology, Vol. 55, Issue 3
Works referencing / citing this record:
Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae
journal, January 2010
- Ma, Menggen; Liu, Z. Lewis
- BMC Genomics, Vol. 11, Issue 1
Detoxification of 5-hydroxymethylfurfural by the Pleurotus ostreatus lignolytic enzymes aryl alcohol oxidase and dehydrogenase
journal, April 2015
- Feldman, Daria; Kowbel, David J.; Glass, N. Louise
- Biotechnology for Biofuels, Vol. 8, Issue 1
MindTheGap: integrated detection and assembly of short and long insertions
journal, August 2014
- Rizk, G.; Gouin, A.; Chikhi, R.
- Bioinformatics, Vol. 30, Issue 24
Biotechnological strategies to overcome inhibitors in lignocellulose hydrolysates for ethanol production: review
journal, May 2010
- Parawira, W.; Tekere, M.
- Critical Reviews in Biotechnology, Vol. 31, Issue 1
Transcriptome shifts in response to furfural and acetic acid in Saccharomyces cerevisiae
journal, March 2010
- Li, Bing-Zhi; Yuan, Ying-Jin
- Applied Microbiology and Biotechnology, Vol. 86, Issue 6
The genome sequence of the filamentous fungus Neurospora crassa
journal, April 2003
- Galagan, James E.; Calvo, Sarah E.; Borkovich, Katherine A.
- Nature, Vol. 422, Issue 6934
High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states
journal, February 2013
- Blecher-Gonen, Ronnie; Barnett-Itzhaki, Zohar; Jaitin, Diego
- Nature Protocols, Vol. 8, Issue 3
The generation of fermentation inhibitors during dilute acid hydrolysis of softwood
journal, February 1999
- Larsson, Simona; Palmqvist, Eva; Hahn-Hägerdal, Bärbel
- Enzyme and Microbial Technology, Vol. 24, Issue 3-4
Chitin synthase 1 plays a major role in cell wall biogenesis in Neurospora crassa.
journal, December 1991
- Yarden, O.; Yanofsky, C.
- Genes & Development, Vol. 5, Issue 12b
Identification and characterization of the furfural and 5-(hydroxymethyl)furfural degradation pathways of Cupriavidus basilensis HMF14
journal, March 2010
- Koopman, F.; Wierckx, N.; de Winde, J. H.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 11
TopHat: discovering splice junctions with RNA-Seq
journal, March 2009
- Trapnell, Cole; Pachter, Lior; Salzberg, Steven L.
- Bioinformatics, Vol. 25, Issue 9
Identification of the CRE-1 Cellulolytic Regulon in Neurospora crassa
journal, September 2011
- Sun, Jianping; Glass, N. Louise
- PLoS ONE, Vol. 6, Issue 9
Pretreatment of Lignocellulosic Wastes to Improve Ethanol and Biogas Production: A Review
journal, September 2008
- Taherzadeh, Mohammad; Karimi, Keikhosro
- International Journal of Molecular Sciences, Vol. 9, Issue 9, p. 1621-1651
The Tandem Repeats Enabling Reversible Switching between the Two Phases of β-Lactamase Substrate Spectrum
journal, September 2014
- Yi, Hyojeong; Song, Han; Hwang, Junghyun
- PLoS Genetics, Vol. 10, Issue 9
Neurospora from natural populations: Toward the population biology of a haploid eukaryote
journal, June 1988
- Perkins, David D.; Turner, Barbara C.
- Experimental Mycology, Vol. 12, Issue 2
Inhibition effects of furfural on alcohol dehydrogenase, aldehyde dehydrogenase and pyruvate dehydrogenase
journal, April 2002
- Modig, Tobias; LidÉN, Gunnar; Taherzadeh, Mohammad J.
- Biochemical Journal, Vol. 363, Issue 3
Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi
journal, April 2012
- Coradetti, S. T.; Craig, J. P.; Xiong, Y.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 19
Open source clustering software
journal, February 2004
- de Hoon, M. J. L.; Imoto, S.; Nolan, J.
- Bioinformatics, Vol. 20, Issue 9
Human liver mitochondrial aldehyde dehydrogenase: Three-dimensional structure and the restoration of solubility and activity of chimeric forms
journal, January 1999
- Ni, Li; Zhou, Jianzhong; Weiner, Henry
- Protein Science, Vol. 8, Issue 12
Mutational Analysis of the Glycosylphosphatidylinositol (GPI) Anchor Pathway Demonstrates that GPI-Anchored Proteins Are Required for Cell Wall Biogenesis and Normal Hyphal Growth in Neurospora crassa
journal, March 2006
- Bowman, Shaun M.; Piwowar, Amy; Al Dabbous, Mash'el
- Eukaryotic Cell, Vol. 5, Issue 3, p. 587-600
Carbon source affects PKA-dependent polarity of Neurospora crassa in a CRE-1-dependent and independent manner
journal, February 2008
- Ziv, Carmit; Gorovits, Rena; Yarden, Oded
- Fungal Genetics and Biology, Vol. 45, Issue 2
Insight into progress in pre-treatment of lignocellulosic biomass
journal, March 2017
- Bhutto, Abdul Waheed; Qureshi, Khadija; Harijan, Khanji
- Energy, Vol. 122
Analysis of a conserved cellulase transcriptional regulator reveals inducer-independent production of cellulolytic enzymes in Neurospora crassa
journal, June 2013
- Coradetti, Samuel T.; Xiong, Yi; Glass, N. Louise
- MicrobiologyOpen, Vol. 2, Issue 4
Strains of Neurospora Collected from Nature
journal, June 1976
- Perkins, David D.; Turner, Barbara C.; Barry, Edward G.
- Evolution, Vol. 30, Issue 2
Multiple gene-mediated NAD(P)H-dependent aldehyde reduction is a mechanism of in situ detoxification of furfural and 5-hydroxymethylfurfural by Saccharomyces cerevisiae
journal, September 2008
- Lewis Liu, Z.; Moon, Jaewoong; Andersh, Brad J.
- Applied Microbiology and Biotechnology, Vol. 81, Issue 4, p. 743-753
Transcriptional profiling reveals molecular basis and novel genetic targets for improved resistance to multiple fermentation inhibitors in Saccharomyces cerevisiae
journal, January 2016
- Chen, Yingying; Sheng, Jiayuan; Jiang, Tao
- Biotechnology for Biofuels, Vol. 9, Issue 1
Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa
journal, December 2009
- Tian, Chaoguang; Beeson, William T.; Iavarone, Anthony T.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 52
Understanding physiological responses to pre-treatment inhibitors in ethanologenic fermentations
journal, February 2012
- Taylor, Mark P.; Mulako, Inonge; Tuffin, Marla
- Biotechnology Journal, Vol. 7, Issue 9, p. 1169-1181
Fungal pretreatment of lignocellulosic biomass
journal, November 2012
- Wan, Caixia; Li, Yebo
- Biotechnology Advances, Vol. 30, Issue 6
Life-history ofNeurospora intermedia in a sugar cane field
journal, March 1996
- Pandit, Alka; Maheshwari, Ramesh
- Journal of Biosciences, Vol. 21, Issue 1
Silencing of NADPH-Dependent Oxidoreductase Genes (yqhD and dkgA) in Furfural-Resistant Ethanologenic Escherichia coli
journal, May 2009
- Miller, E. N.; Jarboe, L. R.; Yomano, L. P.
- Applied and Environmental Microbiology, Vol. 75, Issue 13, p. 4315-4323
Plant Cell Wall Deconstruction by Ascomycete Fungi
journal, September 2013
- Glass, N. Louise; Schmoll, Monika; Cate, Jamie H. D.
- Annual Review of Microbiology, Vol. 67, Issue 1
Exploring the tolerance of marine yeast to inhibitory compounds for improving bioethanol production
journal, January 2019
- Greetham, Darren; Zaky, Abdelrahman Saleh; Du, Chenyu
- Sustainable Energy & Fuels, Vol. 3, Issue 6
ManR, a Transcriptional Regulator of the β-Mannan Utilization System, Controls the Cellulose Utilization System in <i>Aspergillus oryzae</i>
journal, January 2013
- Ogawa, Masahiro; Kobayashi, Tetsuo; Koyama, Yasuji
- Bioscience, Biotechnology, and Biochemistry, Vol. 77, Issue 2
Comparative proteomic analysis of a new adaptive Pichia Stipitis strain to furfural, a lignocellulosic inhibitory compound
journal, January 2013
- Hao, Xue-Cai; Yang, Xiu-Shan; Wan, Ping
- Biotechnology for Biofuels, Vol. 6, Issue 1
Mechanism of formation of 2-furaldehyde from d-xylose
journal, September 1991
- Antal, Michael Jerry; Leesomboon, Tongchit; Mok, William S.
- Carbohydrate Research, Vol. 217
Furfural Formation and Behavior
journal, February 1948
- Dunlop, A. P.
- Industrial & Engineering Chemistry, Vol. 40, Issue 2
Lessons from the Genome Sequence of Neurospora crassa: Tracing the Path from Genomic Blueprint to Multicellular Organism
journal, March 2004
- Borkovich, K. A.; Alex, L. A.; Yarden, O.
- Microbiology and Molecular Biology Reviews, Vol. 68, Issue 1
LUMPY: a probabilistic framework for structural variant discovery
journal, January 2014
- Layer, Ryan M.; Chiang, Colby; Quinlan, Aaron R.
- Genome Biology, Vol. 15, Issue 6
The Fungal Genetics Stock Center: a repository for 50 years of fungal genetics research
journal, January 2010
- McCluskey, K.; Wiest, A.; Plamann, M.
- Journal of Biosciences, Vol. 35, Issue 1
Resistance of Saccharomyces cerevisiae to High Concentrations of Furfural Is Based on NADPH-Dependent Reduction by at Least Two Oxireductases
journal, October 2009
- Heer, D.; Heine, D.; Sauer, U.
- Applied and Environmental Microbiology, Vol. 75, Issue 24
Inhibition of ethanol-producing yeast and bacteria by degradation products produced during pre-treatment of biomass
journal, August 2004
- Klinke, H. B.; Thomsen, A. B.; Ahring, B. K.
- Applied Microbiology and Biotechnology, Vol. 66, Issue 1, p. 10-26
Fast and accurate long-read alignment with Burrows–Wheeler transform
journal, January 2010
- Li, Heng; Durbin, Richard
- Bioinformatics, Vol. 26, Issue 5
AP1-mediated Multidrug Resistance in Saccharomyces cerevisiae Requires FLR1 Encoding a Transporter of the Major Facilitator Superfamily
journal, August 1997
- Alarco, Anne-Marie; Balan, Inga; Talibi, Driss
- Journal of Biological Chemistry, Vol. 272, Issue 31
Cellulosic Biofuels
journal, June 2009
- Carroll, Andrew; Somerville, Chris
- Annual Review of Plant Biology, Vol. 60, Issue 1
SpeedSeq: ultra-fast personal genome analysis and interpretation
journal, August 2015
- Chiang, Colby; Layer, Ryan M.; Faust, Gregory G.
- Nature Methods, Vol. 12, Issue 10
GFP as a tool to analyze the organization, dynamics and function of nuclei and microtubules in Neurospora crassa
journal, October 2004
- Freitag, Michael; Hickey, Patrick C.; Raju, Namboori B.
- Fungal Genetics and Biology, Vol. 41, Issue 10
Overexpression of Saccharomyces cerevisiae transcription factor and multidrug resistance genes conveys enhanced resistance to lignocellulose-derived fermentation inhibitors
journal, February 2010
- Alriksson, Björn; Horváth, Ilona Sárvári; Jönsson, Leif J.
- Process Biochemistry, Vol. 45, Issue 2
A proteomic and genetic analysis of the Neurospora crassa conidia cell wall proteins identifies two glycosyl hydrolases involved in cell wall remodeling
journal, September 2016
- Ao, Jie; Aldabbous, Mash’el; Notaro, Marysa J.
- Fungal Genetics and Biology, Vol. 94
FungiDB: an integrated functional genomics database for fungi
journal, November 2011
- Stajich, J. E.; Harris, T.; Brunk, B. P.
- Nucleic Acids Research, Vol. 40, Issue D1
Regulation of Neurospora crassa cell wall remodeling via the cot-1 pathway is mediated by gul-1
journal, June 2016
- Herold, Inbal; Yarden, Oded
- Current Genetics, Vol. 63, Issue 1
Genomic adaptation of ethanologenic yeast to biomass conversion inhibitors
journal, October 2006
- Liu, Z. Lewis
- Applied Microbiology and Biotechnology, Vol. 73, Issue 1
A 5-hydroxymethyl furfural reducing enzyme encoded by theSaccharomyces cerevisiae ADH6 gene conveys HMF tolerance
journal, January 2006
- Petersson, Anneli; Almeida, João R. M.; Modig, Tobias
- Yeast, Vol. 23, Issue 6, p. 455-464
Induction of lignocellulose-degrading enzymes in Neurospora crassa by cellodextrins
journal, April 2012
- Znameroski, E. A.; Coradetti, S. T.; Roche, C. M.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 16
Differential expression analysis for sequence count data
journal, October 2010
- Anders, Simon; Huber, Wolfgang
- Genome Biology, Vol. 11, Issue 10
Regulation of cellulolytic genes by McmA, the SRF-MADS box protein in Aspergillus nidulans
journal, February 2013
- Yamakawa, Yohei; Endo, Yoshikazu; Li, Nuo
- Biochemical and Biophysical Research Communications, Vol. 431, Issue 4
Neurospora from Natural Populations: A Global Study
journal, March 2001
- Turner, Barbara C.; Perkins, David D.; Fairfield, Ann
- Fungal Genetics and Biology, Vol. 32, Issue 2
Characterization of indole-3-pyruvic acid pathway-mediated biosynthesis of auxin in Neurospora crassa
journal, February 2018
- Sardar, Puspendu; Kempken, Frank
- PLOS ONE, Vol. 13, Issue 2
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
journal, May 2010
- Trapnell, Cole; Williams, Brian A.; Pertea, Geo
- Nature Biotechnology, Vol. 28, Issue 5
Metabolic effects of furaldehydes and impacts on biotechnological processes
journal, January 2009
- Almeida, João R. M.; Bertilsson, Magnus; Gorwa-Grauslund, Marie F.
- Applied Microbiology and Biotechnology, Vol. 82, Issue 4
Performances of Lactobacillus brevis for Producing Lactic Acid from Hydrolysate of Lignocellulosics
journal, November 2009
- Guo, Wei; Jia, Wendi; Li, Yin
- Applied Biochemistry and Biotechnology, Vol. 161, Issue 1-8
Bioconversion of dilute-acid pretreated sorghum bagasse to ethanol by Neurospora crassa
journal, May 2012
- Dogaris, Ioannis; Gkounta, Olga; Mamma, Diomi
- Applied Microbiology and Biotechnology, Vol. 95, Issue 2
Molecular mechanisms of yeast tolerance and in situ detoxification of lignocellulose hydrolysates
journal, March 2011
- Liu, Z. Lewis
- Applied Microbiology and Biotechnology, Vol. 90, Issue 3
Comparative Proteomic Analysis of Tolerance and Adaptation of Ethanologenic Saccharomyces cerevisiae to Furfural, a Lignocellulosic Inhibitory Compound
journal, April 2009
- Lin, F. -M.; Qiao, B.; Yuan, Y. -J.
- Applied and Environmental Microbiology, Vol. 75, Issue 11
Transcriptome profiling of Zymomonas mobilis under furfural stress
journal, May 2012
- He, Ming-xiong; Wu, Bo; Shui, Zong-xia
- Applied Microbiology and Biotechnology, Vol. 95, Issue 1
Neurospora crassa transcriptomics reveals oxidative stress and plasma membrane homeostasis biology genes as key targets in response to chitosan
journal, January 2016
- Lopez-Moya, Federico; Kowbel, David; Nueda, Ma José
- Molecular BioSystems, Vol. 12, Issue 2
Microbial transformation of furfural to furfuryl alcohol by saccharomyces cerevisiae: Biotransformation of Furfural to Furfuryl Alcohol
journal, January 1992
- Villa, G. P.; Bartroli, R.; López, R.
- Acta Biotechnologica, Vol. 12, Issue 6
SAMBLASTER: fast duplicate marking and structural variant read extraction
journal, May 2014
- Faust, G. G.; Hall, I. M.
- Bioinformatics, Vol. 30, Issue 17
Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa
journal, September 2017
- Samal, Areejit; Craig, James P.; Coradetti, Samuel T.
- Biotechnology for Biofuels, Vol. 10, Issue 1
Using a model filamentous fungus to unravel mechanisms of lignocellulose deconstruction
journal, January 2013
- Znameroski, Elizabeth A.; Glass, N. Louise
- Biotechnology for Biofuels, Vol. 6, Issue 1
Fermentation of lignocellulosic hydrolysates. II: inhibitors and mechanisms of inhibition
journal, August 2000
- Palmqvist, Eva; Hahn-Hägerdal, Bärbel
- Bioresource Technology, Vol. 74, Issue 1, p. 25-33
Conversion of furfural to furoic acid and furfuryl alcohol by Neurospora ascospores
journal, January 1970
- Eilers, Frederick I.; Sussman, Alfred S.
- Planta, Vol. 94, Issue 4
Protein Subcellular Localization Prediction with wolf Psort
conference, November 2011
- Horton, Paul; Park, Keun-Joon; Obayashi, Takeshi
- Proceedings of the 4th Asia-Pacific Bioinformatics Conference
Computational Method to Predict Mitochondrially Imported Proteins and their Targeting Sequences
journal, November 1996
- Claros, Manuel G.; Vincens, Pierre
- European Journal of Biochemistry, Vol. 241, Issue 3