Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing
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 h...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
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Public Library of Science
2012
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| Online Access: | https://eprints.nottingham.ac.uk/2586/ |
| _version_ | 1848790823782580224 |
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| author | 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. |
| author_facet | 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. |
| author_sort | Delmas, Stéphane |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-14T18:18:44Z |
| format | Article |
| id | nottingham-2586 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T18:18:44Z |
| publishDate | 2012 |
| publisher | Public Library of Science |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-25862020-05-04T16:33:50Z https://eprints.nottingham.ac.uk/2586/ 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. 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. Public Library of Science 2012-08-09 Article PeerReviewed 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. and Archer, David B. (2012) Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing. PLoS Genetics, 8 (8). e1002875/1-e1002875/13. ISSN 1553-7390 http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002875 doi:10.1371/journal.pgen.1002875 doi:10.1371/journal.pgen.1002875 |
| spellingShingle | 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. Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing |
| title | Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing |
| title_full | Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing |
| title_fullStr | Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing |
| title_full_unstemmed | Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing |
| title_short | Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing |
| title_sort | uncovering the genome-wide transcriptional responses of the filamentous fungus aspergillus niger to lignocellulose using rna sequencing |
| url | https://eprints.nottingham.ac.uk/2586/ https://eprints.nottingham.ac.uk/2586/ https://eprints.nottingham.ac.uk/2586/ |