Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments

Daly, Paul and van Munster, Jolanda M. and Blythe, Martin J. and Ibbett, Roger and Kokolski, Matthew and Gaddipati, Sanyasi and Lindquist, Erika and Singan, Vasanth R. and Barry, Kerrie W. and Lipzen, Anna and Ngan, Chew Yee and Petzold, Christopher J. and Chan, Leanne Jade G. and Pullan, Steven T. and Delmas, Stéphane and Waldron, Paul R. and Grigoriev, Igor V. and Tucker, Gregory A. and Simmons, Blake A. and Archer, David B. (2017) Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments. Biotechnology for Biofuels, 10 (1). 35/1-35/19. ISSN 1754-6834

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Abstract

Background

The capacity of fungi, such as Aspergillus 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 of A. niger to 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 determined A. niger transcript 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.

Item Type: Article
Keywords: Aspergillus niger, Lignocellulose, Ionic liquid and hydrothermal pretreatments, Straw, Transcriptomic responses, CAZy, Hemicellulose, RNA-seq, Targeted proteomics
Schools/Departments: University of Nottingham, UK > Faculty of Medicine and Health Sciences > School of Life Sciences
Identification Number: 10.1186/s13068-017-0700-9
Depositing User: Eprints, Support
Date Deposited: 21 Feb 2017 14:19
Last Modified: 12 Oct 2017 22:17
URI: http://eprints.nottingham.ac.uk/id/eprint/40690

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