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

Daly, Paul; van Munster, Jolanda M.; Blythe, Martin J.; Ibbett, Roger; Kokolski, Matthew; Gaddipati, Sanyasi; Lindquist, Erika; Singan, Vasanth R.; Barry, Kerrie W.; Lipzen, Anna; Ngan, Chew Yee; Petzold, Christopher J.; Chan, Leanne Jade G.; Pullan, Steven T.; Delmas, St�phane; Waldron, Paul R.; Grigoriev, Igor V.; Tucker, Gregory A.; Simmons, Blake A.; Archer, David B.

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


Authors

Paul Daly

Jolanda M. van Munster

Martin J. Blythe

Roger Ibbett

Matthew Kokolski

Sanyasi Gaddipati

Erika Lindquist

Vasanth R. Singan

Kerrie W. Barry

Anna Lipzen

Chew Yee Ngan

Christopher J. Petzold

Leanne Jade G. Chan

Steven T. Pullan

St�phane Delmas

Paul R. Waldron

Igor V. Grigoriev

Gregory A. Tucker

Blake A. Simmons

David B. Archer



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.

Citation

Daly, P., van Munster, J. M., Blythe, M. J., Ibbett, R., Kokolski, M., Gaddipati, S., Lindquist, E., Singan, V. R., Barry, K. W., Lipzen, A., Ngan, C. Y., Petzold, C. J., Chan, L. J. G., Pullan, S. T., Delmas, S., Waldron, P. R., Grigoriev, I. V., Tucker, G. A., Simmons, B. A., & Archer, D. 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), Article 35. https://doi.org/10.1186/s13068-017-0700-9

Journal Article Type Article
Acceptance Date Jan 5, 2017
Publication Date Feb 7, 2017
Deposit Date Feb 21, 2017
Publicly Available Date Feb 21, 2017
Journal Biotechnology for Biofuels
Electronic ISSN 1754-6834
Publisher Springer Verlag
Peer Reviewed Peer Reviewed
Volume 10
Issue 1
Article Number 35
DOI https://doi.org/10.1186/s13068-017-0700-9
Keywords Aspergillus niger, Lignocellulose, Ionic liquid and hydrothermal pretreatments, Straw, Transcriptomic responses, CAZy, Hemicellulose, RNA-seq, Targeted proteomics
Public URL https://nottingham-repository.worktribe.com/output/847155
Publisher URL http://dx.doi.org/10.1186/s13068-017-0700-9
Contract Date Feb 21, 2017

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