Expression ofAspergillus nigerCAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments.
BACKGROUND
The capacity of fungi, such asAspergillus niger,to degrade lignocellulose is harnessed in biotechnology to generate biofuels and high-value compounds from renewable feedstocks. Most feedstocks are currently pretreated to increase enzymatic digestibility: improving our understanding of the transcriptomic responses of fungi to pretreated lignocellulosic substrates could help to improve the mix of activities and reduce the production costs of commercial lignocellulose saccharifying cocktails.


RESULTS
We investigated the responses ofA. nigerto untreated, ionic liquid and hydrothermally pretreated wheat straw over a 5-day time course using RNA-seq and targeted proteomics. The ionic liquid pretreatment altered the cellulose crystallinity while retaining more of the hemicellulosic sugars than the hydrothermal pretreatment. Ionic liquid pretreatment of straw led to a dynamic induction and repression of genes, which was correlated with the higher levels of pentose sugars saccharified from the ionic liquid-pretreated straw. Hydrothermal pretreatment of straw led to reduced levels of transcripts of genes encoding carbohydrate-active enzymes as well as the derived proteins and enzyme activities. Both pretreatments abolished the expression of a large set of genes encoding pectinolytic enzymes. These reduced levels could be explained by the removal of parts of the lignocellulose by the hydrothermal pretreatment. The time course also facilitated identification of temporally limited gene induction patterns.


CONCLUSIONS
The presented transcriptomic and biochemical datasets demonstrate that pretreatments caused modifications of the lignocellulose, to both specific structural features as well as the organisation of the overall lignocellulosic structure, that determinedA. nigertranscript levels. The experimental setup allowed reliable detection of substrate-specific gene expression patterns as well as hitherto non-expressed genes. Our data suggest beneficial effects of using untreated and IL-pretreated straw, but not HT-pretreated straw, as feedstock for CAZyme production.
School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK.|Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.
Paul
P
Daly
School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK.|Chemical Biology, Manchester Institute for Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK.
Jolanda M
JM
van Munster
Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK.
Martin J
MJ
Blythe
School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK.
Roger
R
Ibbett
School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK.
Matt
M
Kokolski
School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK.
Sanyasi
S
Gaddipati
US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA.
Erika
E
Lindquist
US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA.
Vasanth R
VR
Singan
US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA.
Kerrie W
KW
Barry
US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA.
Anna
A
Lipzen
US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA.
Chew Yee
CY
Ngan
Joint BioEnergy Institute, Emeryville, CA 94608 USA.
Christopher J
CJ
Petzold
Joint BioEnergy Institute, Emeryville, CA 94608 USA.
Leanne Jade G
LJG
Chan
School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK.|TB Programme, Microbiology Services, Public Health England, Salisbury, UK.
Steven T
ST
Pullan
School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK.|UPMC, Univ. Paris 06, CNRS UMR7238, Sorbonne Universités, 15 rue de l'Ecole de Médecine, 75270 Paris, France.
Stéphane
S
Delmas
School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK.
Paul R
PR
Waldron
US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA.
Igor V
IV
Grigoriev
School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK.
Gregory A
GA
Tucker
Joint BioEnergy Institute, Emeryville, CA 94608 USA.
Blake A
BA
Simmons
School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK.
David B
DB
Archer
Aspergillus niger; CAZy; Hemicellulose; Ionic liquid and hydrothermal pretreatments; Lignocellulose; RNA-seq; Straw; Targeted proteomics; Transcriptomic responses