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Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing

Delmas, Stéphane; Pullan, Steven T.; Gaddipati, Sanyasi; Kokolski, Matthew; Malla, Sunir; Blythe, Martin J.; Ibbett, Roger; Campbell, Maria; Liddell, Susan; Aboobaker, Aziz; Tucker, Gregory A.; Archer, David B.

Authors

Stéphane Delmas

Steven T. Pullan

Sanyasi Gaddipati

Matthew Kokolski

Sunir Malla

Martin J. Blythe

Roger Ibbett

Maria Campbell

Susan Liddell

Aziz Aboobaker

Gregory A. Tucker

David B. Archer



Abstract

A key challenge in the production of second generation biofuels is the conversion of lignocellulosic substrates into fermentable sugars. Enzymes, particularly those from fungi, are a central part of this process, and many have been isolated and characterised. However, relatively little is known of how fungi respond to lignocellulose and produce the enzymes necessary for dis-assembly of plant biomass. We studied the physiological response of the fungus Aspergillus niger when exposed to wheat straw as a model lignocellulosic substrate. Using RNA sequencing we showed that, 24 hours after exposure to straw, gene expression of known and presumptive plant cell wall–degrading enzymes represents a huge investment for the cells (about 20% of the total mRNA). Our results also uncovered new esterases and surface interacting proteins that might form part of the fungal arsenal of enzymes for the degradation of plant biomass. Using transcription factor deletion mutants (xlnR and creA) to study the response to both lignocellulosic substrates and low carbon source concentrations, we showed that a subset of genes coding for degradative enzymes is induced by starvation. Our data support a model whereby this subset of enzymes plays a scouting role under starvation conditions, testing for available complex polysaccharides and liberating inducing sugars, that triggers the subsequent induction of the majority of hydrolases. We also showed that antisense transcripts are abundant and that their expression can be regulated by growth conditions.

Journal Article Type Article
Publication Date Aug 9, 2012
Journal PLoS Genetics
Print ISSN 1553-7390
Electronic ISSN 1553-7390
Publisher Public Library of Science
Peer Reviewed Peer Reviewed
Volume 8
Issue 8
Article Number e1002875
Institution Citation Delmas, S., Pullan, S. T., Gaddipati, S., Kokolski, M., Malla, S., Blythe, M. J., …Archer, D. B. (2012). Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing. PLoS Genetics, 8(8), doi:10.1371/journal.pgen.1002875
DOI https://doi.org/10.1371/journal.pgen.1002875
Publisher URL http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002875
Copyright Statement Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0

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Copyright Statement
Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0



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