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, Matt; 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, Stéphane; Waldron, Paul R.; Grigoriev, Igor V.; Tucker, Gregory A.; Simmons, Blake A.; Archer, David B.

doi:10.1186/s13068-017-0700-9

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

Journal Article · Tue Feb 07 00:00:00 EST 2017 · Biotechnology for Biofuels

DOI:https://doi.org/10.1186/s13068-017-0700-9· OSTI ID:1618669

Daly, Paul; van Munster, Jolanda M.; 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.; Pullan, Steven T.; Delmas, Stéphane; Waldron, Paul R.; Grigoriev, Igor V.; Tucker, Gregory A.; Simmons, Blake A.; Archer, David B.

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. 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. 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.

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Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1618669

Alternate ID(s):: OSTI ID: 1379724

Journal Information:: Biotechnology for Biofuels, Journal Name: Biotechnology for Biofuels Vol. 10 Journal Issue: 1; ISSN 1754-6834

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: Netherlands

Language:: English

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Cited by: 13 works

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Related Subjects

09 BIOMASS FUELS
Aspergillus niger
Lignocellulose
Ionic liquid and hydrothermal pretreatments
Straw
Transcriptomic responses
CAZy
Hemicellulose
RNA-seq
Targeted proteomics

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments [Supplementary Data] Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393 The current record is supplemented by this dataset	dataset	February 2017
Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments [Supplemental Data] Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM3 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d1.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM1 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d10.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM14 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d11.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM5 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d12.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM2 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d13.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM10 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d14.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM7 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d2.v1 The current record is supplemented by this figure	figure	February 2017
MOESM6 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d3.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM11 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d4.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM8 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d5.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM13 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d6.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM4 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d7.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM9 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d8.v1 The current record is supplemented by this dataset	dataset	February 2017
MOESM12 of Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments Daly, Paul; Munster, Jolanda; Blythe, Martin https://doi.org/10.6084/m9.figshare.c.3685393_d9.v1 The current record is supplemented by this dataset	dataset	February 2017