Skip to main content

Research Repository

Advanced Search

Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose

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

Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose Thumbnail


Authors

Jolanda M. van Munster

Paul Daly

Martin J. Blythe

Roger Ibbett

Matt Kokolski

Sanyasi Gaddipati

Erika Lindquist

Vasanth R. Singan

Kerrie W. Barry

Anna Lipzen

Chew Yee Ngan

Christopher J. Petzold

Leanne Jade G. Chan

Mikko Arvas

Roxane Raulo

Steven T. Pullan

Stéphane Delmas

Igor V. Grigoriev

Gregory A. Tucker

Blake A. Simmons

David B. Archer



Abstract

Background
Understanding how fungi degrade lignocellulose is a cornerstone of improving renewables-based biotechnology, in particular for the production of hydrolytic enzymes. Considerable progress has been made in investigating fungal degradation during time-points where CAZyme expression peaks. However, a robust understanding of the fungal survival strategies over its life time on lignocellulose is thereby missed. Here we aimed to uncover the physiological responses of the biotechnological workhorse and enzyme producer Aspergillus niger over its life time to six substrates important for biofuel production.

Results
We analysed the response of A. niger to the feedstock Miscanthus and compared it with our previous study on wheat straw, alone or in combination with hydrothermal or ionic liquid feedstock pretreatments. Conserved (substrate-independent) metabolic responses as well as those affected by pretreatment and feedstock were identified via multivariate analysis of genome-wide transcriptomics combined with targeted transcript and protein analyses and mapping to a metabolic model. Initial exposure to all substrates increased fatty acid beta-oxidation and lipid metabolism transcripts. In a strain carrying a deletion of the ortholog of the Aspergillus nidulans fatty acid beta-oxidation transcriptional regulator farA, there was a reduction in expression of selected lignocellulose degradative CAZyme-encoding genes suggesting that beta-oxidation contributes to adaptation to lignocellulose. Mannan degradation expression was wheat straw feedstock-dependent and pectin degradation was higher on the untreated substrates. In the later life stages, known and novel secondary metabolite gene clusters were activated, which are of high interest due to their potential to synthesize bioactive compounds.

Conclusion
In this study, which includes the first transcriptional response of Aspergilli to Miscanthus, we highlighted that life time as well as substrate composition and structure (via variations in pretreatment and feedstock) influence the fungal responses to lignocellulose. We also demonstrated that the fungal response contains physiological stages that are conserved across substrates and are typically found outside of the conditions with high CAZyme expression, as exemplified by the stages that are dominated by lipid and secondary metabolism.

Citation

van Munster, J. M., Daly, P., Blythe, M. J., Ibbett, R., Kokolski, M., Gaddipati, S., …Archer, D. B. (2020). Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose. Biotechnology for Biofuels, 13(1), Article 69. https://doi.org/10.1186/s13068-020-01702-2

Journal Article Type Article
Acceptance Date Mar 24, 2020
Online Publication Date Apr 13, 2020
Publication Date 2020-12
Deposit Date Apr 20, 2020
Publicly Available Date Mar 29, 2024
Journal Biotechnology for Biofuels
Electronic ISSN 1754-6834
Publisher Springer Verlag
Peer Reviewed Peer Reviewed
Volume 13
Issue 1
Article Number 69
DOI https://doi.org/10.1186/s13068-020-01702-2
Public URL https://nottingham-repository.worktribe.com/output/4315875
Publisher URL https://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/s13068-020-01702-2