Neurospora crassa transcriptomics reveals oxidative stress and plasma membrane homeostasis biology genes as key targets in response to chitosan

Lopez-Moya, Federico; Kowbel, David; Nueda, Ma Jose; Palma-Guerrero, Javier; Glass, N. Louise; Lopez-Llorca, Luis Vicente

doi:10.1039/c5mb00649j

Title: Neurospora crassa transcriptomics reveals oxidative stress and plasma membrane homeostasis biology genes as key targets in response to chitosan

Journal Article · Tue Dec 01 00:00:00 EST 2015 · Molecular BioSystems

DOI:https://doi.org/10.1039/c5mb00649j· OSTI ID:1378742

^[1]; Kowbel, David ^[2]; Nueda, Ma Jose ^[3]; Palma-Guerrero, Javier ^[2]; Glass, N. Louise ^[2]; Lopez-Llorca, Luis Vicente ^[1]

Univ. of Alicante (Spain). Lab. of Plant Pathology, Multidisciplinary Inst. for Environmental Studies (MIES) Ramon Margalef, Dept. of Marine Sciences and Applied Biology
Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
Univ. of Alicante (Spain). Statistics and Operation Research Dept.

Chitosan is a natural polymer with antimicrobial activity. Chitosan causes plasma membrane permeabilization and induction of intracellular reactive oxygen species (ROS) in Neurospora crassa. In this paper, we have determined the transcriptional profile of N. crassa to chitosan and identified the main gene targets involved in the cellular response to this compound. Global network analyses showed membrane, transport and oxidoreductase activity as key nodes affected by chitosan. Activation of oxidative metabolism indicates the importance of ROS and cell energy together with plasma membrane homeostasis in N. crassa response to chitosan. Deletion strain analysis of chitosan susceptibility pointed NCU03639 encoding a class 3 lipase, involved in plasma membrane repair by lipid replacement, and NCU04537 a MFS monosaccharide transporter related to assimilation of simple sugars, as main gene targets of chitosan. NCU10521, a glutathione S-transferase-4 involved in the generation of reducing power for scavenging intracellular ROS is also a determinant chitosan gene target. Ca²⁺ increased tolerance to chitosan in N. crassa. Growth of NCU10610 (fig 1 domain) and SYT1 (a synaptotagmin) deletion strains was significantly increased by Ca²⁺ in the presence of chitosan. Both genes play a determinant role in N. crassa membrane homeostasis. Finally, our results are of paramount importance for developing chitosan as an antifungal.

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Research Organization:: University of California, Berkeley, CA (United States); Univ. of Alicante (Spain)

Sponsoring Organization:: USDOE; National Inst. of Health (NIH) (United States); Ministry of Economy and Competitiveness (Spain)

Grant/Contract Number:: AC02-05CH11231; GM060468; 2011-29297/AGR

OSTI ID:: 1378742

Journal Information:: Molecular BioSystems, Vol. 12, Issue 2; ISSN 1742-206X

Publisher:: Royal Society of ChemistryCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 23 works

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References (58)

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation Merico, Daniele; Isserlin, Ruth; Stueker, Oliver PLoS ONE, Vol. 5, Issue 11 https://doi.org/10.1371/journal.pone.0013984	journal	November 2010
The fungicidal effect of chitosan on fungi of varying cell wall composition Allan, Carolyn R.; Hadwiger, Lee A. Experimental Mycology, Vol. 3, Issue 3 https://doi.org/10.1016/S0147-5975(79)80054-7	journal	September 1979
Identification and Characterization of LFD-2, a Predicted Fringe Protein Required for Membrane Integrity during Cell Fusion in Neurospora crassa Palma-Guerrero, Javier; Zhao, Jiuhai; Gonçalves, A. Pedro Eukaryotic Cell, Vol. 14, Issue 3 https://doi.org/10.1128/EC.00233-14	journal	January 2015
NADPH Oxidases NOX-1 and NOX-2 Require the Regulatory Subunit NOR-1 To Control Cell Differentiation and Growth in Neurospora crassa Cano-Domínguez, Nallely; Álvarez-Delfín, Karen; Hansberg, Wilhelm Eukaryotic Cell, Vol. 7, Issue 8 https://doi.org/10.1128/EC.00137-08	journal	June 2008
Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series Nueda, M. J.; Tarazona, S.; Conesa, A. Bioinformatics, Vol. 30, Issue 18 https://doi.org/10.1093/bioinformatics/btu333	journal	June 2014
Carbon and nitrogen limitation increase chitosan antifungal activity in Neurospora crassa and fungal human pathogens Lopez-Moya, Federico; Colom-Valiente, Maria F.; Martinez-Peinado, Pascual Fungal Biology, Vol. 119, Issue 2-3 https://doi.org/10.1016/j.funbio.2014.12.003	journal	March 2015
Azoles: Mode of Antifungal Action and Resistance Development. Effect of Miconazole on Endogenous Reactive Oxygen Species Production in Candida albicans Francois, Isabelle; Cammue, Bruno; Borgers, Marcel Anti-Infective Agents in Medicinal Chemistry, Vol. 5, Issue 1 https://doi.org/10.2174/187152106774755554	journal	January 2006
Reduced glutathione export during programmed cell death of Neurospora crassa Fernandes, Andreia S.; Castro, Ana; Videira, Arnaldo Apoptosis, Vol. 18, Issue 8 https://doi.org/10.1007/s10495-013-0858-y	journal	May 2013
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Langmead, Ben; Trapnell, Cole; Pop, Mihai Genome Biology, Vol. 10, Issue 3 https://doi.org/10.1186/gb-2009-10-3-r25	journal	January 2009
Variable selection for multifactorial genomic data Tarazona, Sonia; Prado-López, Sonia; Dopazo, Joaquín Chemometrics and Intelligent Laboratory Systems, Vol. 110, Issue 1 https://doi.org/10.1016/j.chemolab.2011.10.012	journal	January 2012
Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics Jaime, Maria DLA; Lopez-Llorca, Luis; Conesa, Ana BMC Genomics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2164-13-267	journal	January 2012
Discovering gene expression patterns in time course microarray experiments by ANOVA–SCA Nueda, María José; Conesa, Ana; Westerhuis, Johan A. Bioinformatics, Vol. 23, Issue 14 https://doi.org/10.1093/bioinformatics/btm251	journal	May 2007
TopHat: discovering splice junctions with RNA-Seq Trapnell, Cole; Pachter, Lior; Salzberg, Steven L. Bioinformatics, Vol. 25, Issue 9 https://doi.org/10.1093/bioinformatics/btp120	journal	March 2009
The Saccharomyces cerevisiae PRM1 Homolog in Neurospora crassa Is Involved in Vegetative and Sexual Cell Fusion Events but Also Has Postfertilization Functions Fleißner, André; Diamond, Spencer; Glass, N. Louise Genetics, Vol. 181, Issue 2 https://doi.org/10.1534/genetics.108.096149	journal	December 2008
A review of chitin and chitosan applications Ravi Kumar, Majeti N. V. Reactive and Functional Polymers, Vol. 46, Issue 1, p. 1-27 https://doi.org/10.1016/S1381-5148(00)00038-9	journal	November 2000
Ca 2+ homeostasis in the budding yeast Saccharomyces cerevisiae : Impact of ER/Golgi Ca 2+ storage D’hooge, Petra; Coun, Catherina; Van Eyck, Vincent Cell Calcium, Vol. 58, Issue 2 https://doi.org/10.1016/j.ceca.2015.05.004	journal	August 2015
Early Colony Establishment in Neurospora crassa Requires a MAP Kinase Regulatory Network Leeder, Abigail C.; Jonkers, Wilfried; Li, Jingyi Genetics, Vol. 195, Issue 3 https://doi.org/10.1534/genetics.113.156984	journal	September 2013
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles Subramanian, A.; Tamayo, P.; Mootha, V. K. Proceedings of the National Academy of Sciences, Vol. 102, Issue 43, p. 15545-15550 https://doi.org/10.1073/pnas.0506580102	journal	September 2005
Activation of stress signalling pathways enhances tolerance of fungi to chemical fungicides and antifungal proteins Hayes, Brigitte M. E.; Anderson, Marilyn A.; Traven, Ana Cellular and Molecular Life Sciences, Vol. 71, Issue 14 https://doi.org/10.1007/s00018-014-1573-8	journal	February 2014
Extracellular calcium triggers unique transcriptional programs and modulates staurosporine-induced cell death in Neurospora crassa Goncalves, Pedro; Monteiro, Joao; Lucchi, Chiara Microbial Cell, Vol. 1, Issue 9 https://doi.org/10.15698/mic2014.09.165	journal	September 2014
WoLF PSORT: protein localization predictor Horton, P.; Park, K. -J.; Obayashi, T. Nucleic Acids Research, Vol. 35, Issue Web Server https://doi.org/10.1093/nar/gkm259	journal	May 2007
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Edgar, R. Nucleic Acids Research, Vol. 30, Issue 1 https://doi.org/10.1093/nar/30.1.207	journal	January 2002
maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments Conesa, A.; Nueda, M. J.; Ferrer, A. Bioinformatics, Vol. 22, Issue 9 https://doi.org/10.1093/bioinformatics/btl056	journal	February 2006
Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project Dunlap, Jay C.; Borkovich, Katherine A.; Henn, Matthew R. Fungal Genomics https://doi.org/10.1016/S0065-2660(06)57002-6	book	March 2007
Cross-talk between calcium and reactive oxygen species signaling Yan, Yuan; Wei, Chao-liang; Zhang, Wan-rui Acta Pharmacologica Sinica, Vol. 27, Issue 7 https://doi.org/10.1111/j.1745-7254.2006.00390.x	journal	July 2006
Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method Livak, Kenneth J.; Schmittgen, Thomas D. Methods, Vol. 25, Issue 4 https://doi.org/10.1006/meth.2001.1262	journal	December 2001
Antifungal activity of oligochitosans (short chain chitosans) against some Candida species and clinical isolates of Candida albicans: Molecular weight–activity relationship Kulikov, Sergey N.; Lisovskaya, Svetlana A.; Zelenikhin, Pavel V. European Journal of Medicinal Chemistry, Vol. 74 https://doi.org/10.1016/j.ejmech.2013.12.017	journal	March 2014
Role of Glutathione S -Transferases in Protection against Lipid Peroxidation: OVEREXPRESSION OF hGSTA2-2 IN K562 CELLS PROTECTS AGAINST HYDROGEN PEROXIDE-INDUCED APOPTOSIS AND INHIBITS JNK AND CASPASE 3 ACTIVATION Yang, Yusong; Cheng, Ji-Zhong; Singhal, Sharad S. Journal of Biological Chemistry, Vol. 276, Issue 22 https://doi.org/10.1074/jbc.M100551200	journal	March 2001
Secreted lipases supply fatty acids for yeast growth in the absence of de novo fatty acid synthesis Nguyen, Long Nam; Gacser, Attila; Nosanchuk, Joshua D. Virulence, Vol. 2, Issue 6 https://doi.org/10.4161/viru.2.6.18244	journal	November 2011
Lipid signalling in pathogenic fungi: Lipid signalling Singh, Arpita; Del Poeta, Maurizio Cellular Microbiology, Vol. 13, Issue 2 https://doi.org/10.1111/j.1462-5822.2010.01550.x	journal	December 2010
Cytoscape 2.8: new features for data integration and network visualization Smoot, M. E.; Ono, K.; Ruscheinski, J. Bioinformatics, Vol. 27, Issue 3 https://doi.org/10.1093/bioinformatics/btq675	journal	December 2010
Structure of a lipid-bound extended synaptotagmin indicates a role in lipid transfer Schauder, Curtis M.; Wu, Xudong; Saheki, Yasunori Nature, Vol. 510, Issue 7506 https://doi.org/10.1038/nature13269	journal	May 2014
Membrane fluidity determines sensitivity of filamentous fungi to chitosan Palma-Guerrero, J.; Lopez-Jimenez, J. A.; Pérez-Berná, A. J. Molecular Microbiology, Vol. 75, Issue 4 https://doi.org/10.1111/j.1365-2958.2009.07039.x	journal	February 2010
Dynamic binding mode of a Synaptotagmin-1–SNARE complex in solution Brewer, Kyle D.; Bacaj, Taulant; Cavalli, Andrea Nature Structural & Molecular Biology, Vol. 22, Issue 7 https://doi.org/10.1038/nsmb.3035	journal	June 2015
Reactive oxygen species-inducing antifungal agents and their activity against fungal biofilms Delattin, Nicolas; Cammue, Bruno PA; Thevissen, Karin Future Medicinal Chemistry, Vol. 6, Issue 1 https://doi.org/10.4155/fmc.13.189	journal	January 2014
Damage control: cellular mechanisms of plasma membrane repair Andrews, Norma W.; Almeida, Patricia E.; Corrotte, Matthias Trends in Cell Biology, Vol. 24, Issue 12 https://doi.org/10.1016/j.tcb.2014.07.008	journal	December 2014
A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors Colot, H. V.; Park, G.; Turner, G. E. Proceedings of the National Academy of Sciences, Vol. 103, Issue 27 https://doi.org/10.1073/pnas.0601456103	journal	June 2006
Oxylipins in fungi: Fungal oxylipins Brodhun, Florian; Feussner, Ivo FEBS Journal, Vol. 278, Issue 7 https://doi.org/10.1111/j.1742-4658.2011.08027.x	journal	February 2011
Changes in the Proteome of Candida albicans in Response to Azole, Polyene, and Echinocandin Antifungal Agents Hoehamer, C. F.; Cummings, E. D.; Hilliard, G. M. Antimicrobial Agents and Chemotherapy, Vol. 54, Issue 5 https://doi.org/10.1128/AAC.00756-09	journal	February 2010
Identification of protein coding regions by database similarity search Gish, Warren; States, David J. Nature Genetics, Vol. 3, Issue 3 https://doi.org/10.1038/ng0393-266	journal	March 1993
Mitochondria Influence CDR1 Efflux Pump Activity, Hog1-Mediated Oxidative Stress Pathway, Iron Homeostasis, and Ergosterol Levels in Candida albicans Thomas, Edwina; Roman, Elvira; Claypool, Steven Antimicrobial Agents and Chemotherapy, Vol. 57, Issue 11 https://doi.org/10.1128/AAC.00889-13	journal	August 2013
Transport and incorporation of N-acetyl-D-glucosamine in Bacillus subtilis. Mobley, H. L.; Doyle, R. J.; Streips, U. N. Journal of Bacteriology, Vol. 150, Issue 1 https://doi.org/10.1128/JB.150.1.8-15.1982	journal	January 1982
Functional assessment of time course microarray data Nueda, María; Sebastián, Patricia; Tarazona, Sonia BMC Bioinformatics, Vol. 10, Issue Suppl 6 https://doi.org/10.1186/1471-2105-10-S6-S9	journal	January 2009
Transcriptional Response of Saccharomyces cerevisiae to the Plasma Membrane-Perturbing Compound Chitosan Zakrzewska, Anna; Boorsma, Andre; Brul, Stanley Eukaryotic Cell, Vol. 4, Issue 4 https://doi.org/10.1128/EC.4.4.703-715.2005	journal	April 2005
Membrane Organization and Cell Fusion During Mating in Fission Yeast Requires Multipass Membrane Protein Prm1 Curto, M. -Ángeles; Sharifmoghadam, Mohammad Reza; Calpena, Eduardo Genetics, Vol. 196, Issue 4 https://doi.org/10.1534/genetics.113.159558	journal	February 2014
Involvement of mitochondrial proteins in calcium signaling and cell death induced by staurosporine in Neurospora crassa Gonçalves, A. Pedro; Cordeiro, J. Miguel; Monteiro, João Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1847, Issue 10 https://doi.org/10.1016/j.bbabio.2015.05.011	journal	October 2015
Chitosan permeabilizes the plasma membrane and kills cells of Neurospora crassa in an energy dependent manner Palma-Guerrero, J.; Huang, I. -C.; Jansson, H. -B. Fungal Genetics and Biology, Vol. 46, Issue 8 https://doi.org/10.1016/j.fgb.2009.02.010	journal	August 2009
Fig1p Facilitates Ca ²⁺ Influx and Cell Fusion during Mating of Saccharomyces cerevisiae Muller, Eric M.; Mackin, Nancy A.; Erdman, Scott E. Journal of Biological Chemistry, Vol. 278, Issue 40 https://doi.org/10.1074/jbc.M304089200	journal	July 2003
CZT-1 Is a Novel Transcription Factor Controlling Cell Death and Natural Drug Resistance in Neurospora crassa Gonçalves, A. Pedro; Hall, Charles; Kowbel, David J. G3: Genes\|Genomes\|Genetics, Vol. 4, Issue 6 https://doi.org/10.1534/g3.114.011312	journal	April 2014
Rotenone Enhances the Antifungal Properties of Staurosporine Castro, Ana; Lemos, Catarina; Falcão, Artur Eukaryotic Cell, Vol. 9, Issue 6 https://doi.org/10.1128/EC.00003-10	journal	April 2010
NADPH oxidases regulate septin-mediated cytoskeletal remodeling during plant infection by the rice blast fungus Ryder, L. S.; Dagdas, Y. F.; Mentlak, T. A. Proceedings of the National Academy of Sciences, Vol. 110, Issue 8 https://doi.org/10.1073/pnas.1217470110	journal	February 2013
HMMER web server: interactive sequence similarity searching Finn, R. D.; Clements, J.; Eddy, S. R. Nucleic Acids Research, Vol. 39, Issue suppl https://doi.org/10.1093/nar/gkr367	journal	May 2011
Identification and characterization of LFD1, a novel protein involved in membrane merger during cell fusion in N eurospora crassa : The role of LFD1 in cell fusion Palma-Guerrero, Javier; Leeder, Abigail C.; Welch, Juliet Molecular Microbiology, Vol. 92, Issue 1 https://doi.org/10.1111/mmi.12545	journal	March 2014
Role of Fig1, a Component of the Low-Affinity Calcium Uptake System, in Growth and Sexual Development of Filamentous Fungi Cavinder, Brad; Trail, Frances Eukaryotic Cell, Vol. 11, Issue 8 https://doi.org/10.1128/EC.00007-12	journal	May 2012
Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics Conesa, Ana; Götz, Stefan International Journal of Plant Genomics, Vol. 2008 https://doi.org/10.1155/2008/619832	journal	January 2008
Antifungal Agents: Mode of Action, Mechanisms of Resistance, and Correlation of These Mechanisms with Bacterial Resistance Ghannoum, Mahmoud A.; Rice, Louis B. Clinical Microbiology Reviews, Vol. 12, Issue 4 https://doi.org/10.1128/CMR.12.4.501	journal	October 1999
Genome-wide Expression Profiling of the Response to Polyene, Pyrimidine, Azole, and Echinocandin Antifungal Agents in Saccharomyces cerevisiae Agarwal, Ameeta K.; Rogers, P. David; Baerson, Scott R. Journal of Biological Chemistry, Vol. 278, Issue 37 https://doi.org/10.1074/jbc.M306291200	journal	June 2003
INDUCTION OF ad-3 MUTANTS OF NEUROSPORA CRASSA BY 2-AMINOPURINE Brockman, H. E.; de Serres, F. J. Genetics, Vol. 48, Issue 4 https://doi.org/10.1093/genetics/48.4.597	journal	April 1963

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