title: RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates inAspergillus niger.
abstract: BACKGROUND
  Saprobic fungi are the predominant industrial sources of Carbohydrate Active enZymes (CAZymes) used for the saccharification of lignocellulose during the production of second generation biofuels. The production of more effective enzyme cocktails is a key objective for efficient biofuel production. To achieve this objective, it is crucial to understand the response of fungi to lignocellulose substrates. Our previous study used RNA-seq to identify the genes induced inAspergillus nigerin response to wheat straw, a biofuel feedstock, and showed that the range of genes induced was greater than previously seen with simple inducers.
  
  
  RESULTS
  In this work we used RNA-seq to identify the genes induced inA. nigerin response to short rotation coppice willow and compared this with the response to wheat straw from our previous study, at the same time-point. The response to willow showed a large increase in expression of genes encoding CAZymes. Genes encoding the major activities required to saccharify lignocellulose were induced on willow such as endoglucanases, cellobiohydrolases and xylanases. The transcriptome response to willow had many similarities with the response to straw with some significant differences in the expression levels of individual genes which are discussed in relation to differences in substrate composition or other factors. Differences in transcript levels include higher levels on wheat straw from genes encoding enzymes classified as members of GH62 (an arabinofuranosidase) and CE1 (a feruloyl esterase) CAZy families whereas two genes encoding endoglucanases classified as members of the GH5 family had higher transcript levels when exposed to willow. There were changes in the cocktail of enzymes secreted byA. nigerwhen cultured with willow or straw. Assays for particular enzymes as well as saccharification assays were used to compare the enzyme activities of the cocktails. Wheat straw induced an enzyme cocktail that saccharified wheat straw to a greater extent than willow. Genes not encoding CAZymes were also induced on willow such as hydrophobins as well as genes of unknown function. Several genes were identified as promising targets for future study.
  
  
  CONCLUSIONS
  By comparing this first study of the global transcriptional response of a fungus to willow with the response to straw, we have shown that the inducing lignocellulosic substrate has a marked effect upon the range of transcripts and enzymes expressed byA. niger. The use by industry of complex substrates such as wheat straw or willow could benefit efficient biofuel production.
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
authors.forename: Steven T
authors.initials: ST
authors.lastname: Pullan
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Daly
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Delmas
authors.affiliation: School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
authors.forename: Roger
authors.initials: R
authors.lastname: Ibbett
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
authors.forename: Matthew
authors.initials: M
authors.lastname: Kokolski
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
authors.forename: Almar
authors.initials: A
authors.lastname: Neiteler
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
authors.forename: Jolanda M
authors.initials: JM
authors.lastname: van Munster
authors.affiliation: Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
authors.forename: Raymond
authors.initials: R
authors.lastname: Wilson
authors.affiliation: Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Blythe
authors.affiliation: School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
authors.forename: Sanyasi
authors.initials: S
authors.lastname: Gaddipati
authors.affiliation: School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Tucker
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
authors.forename: David B
authors.initials: DB
authors.lastname: Archer
keywords: Aspergillus; Biofuels; RNA-seq; Transcriptome; Wheat straw; Willow