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

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

doi:10.1186/s13068-017-0700-9

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

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

^*Corresponding author for this work

Research & Development Institute Scientific Leaders

Research output: Contribution to journal › Article › peer-review

16 Citations (Scopus)

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.

Original language	English
Article number	35
Journal	Biotechnology for Biofuels
Volume	10
Issue number	1
DOIs	https://doi.org/10.1186/s13068-017-0700-9
Publication status	Published - 7 Feb 2017

Bibliographical note

Funding Information:
We gratefully acknowledge the support from the Biotechnology and Biological Sciences Research Council (BBSRC) (Grant refs. BB/G01616X/1 and BB/ K01434X/1). This work was part of the DOE Joint BioEnergy Institute (http:// www.jbei.org) supported by the U. S. Department of Energy, Office of Science, Office of Biological and Environmental Research, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U. S. Department of Energy. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

Publisher Copyright:
© 2017 The Author(s).

Keywords

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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1186/s13068-017-0700-9

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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), [35]. https://doi.org/10.1186/s13068-017-0700-9

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

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.",

keywords = "Aspergillus niger, CAZy, Hemicellulose, Ionic liquid and hydrothermal pretreatments, Lignocellulose, RNA-seq, Straw, Targeted proteomics, Transcriptomic responses",

author = "Paul Daly and {Van Munster}, {Jolanda M.} and Blythe, {Martin J.} and Roger Ibbett and Matt Kokolski and Sanyasi Gaddipati and Erika Lindquist and Singan, {Vasanth R.} and Barry, {Kerrie W.} and Anna Lipzen and Ngan, {Chew Yee} and Petzold, {Christopher J.} and Chan, {Leanne Jade G.} and Pullan, {Steven T.} and St{\'e}phane Delmas and Waldron, {Paul R.} and Grigoriev, {Igor V.} and Tucker, {Gregory A.} and Simmons, {Blake A.} and Archer, {David B.}",

note = "Funding Information: We gratefully acknowledge the support from the Biotechnology and Biological Sciences Research Council (BBSRC) (Grant refs. BB/G01616X/1 and BB/ K01434X/1). This work was part of the DOE Joint BioEnergy Institute (http:// www.jbei.org) supported by the U. S. Department of Energy, Office of Science, Office of Biological and Environmental Research, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U. S. Department of Energy. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Publisher Copyright: {\textcopyright} 2017 The Author(s).",

year = "2017",

month = feb,

day = "7",

doi = "10.1186/s13068-017-0700-9",

language = "English",

volume = "10",

journal = "Biotechnology for Biofuels",

issn = "1754-6834",

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Daly, P, Van Munster, JM, Blythe, MJ, Ibbett, R, Kokolski, M, Gaddipati, S, Lindquist, E, Singan, VR, Barry, KW, Lipzen, A, Ngan, CY, Petzold, CJ, Chan, LJG, Pullan, ST, Delmas, S, Waldron, PR, Grigoriev, IV, Tucker, GA, Simmons, BA & Archer, DB 2017, 'Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments', Biotechnology for Biofuels, vol. 10, no. 1, 35. https://doi.org/10.1186/s13068-017-0700-9

TY - JOUR

T1 - Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments

AU - Daly, Paul

AU - Van Munster, Jolanda M.

AU - Blythe, Martin J.

AU - Ibbett, Roger

AU - Kokolski, Matt

AU - Gaddipati, Sanyasi

AU - Lindquist, Erika

AU - Singan, Vasanth R.

AU - Barry, Kerrie W.

AU - Lipzen, Anna

AU - Ngan, Chew Yee

AU - Petzold, Christopher J.

AU - Chan, Leanne Jade G.

AU - Pullan, Steven T.

AU - Delmas, Stéphane

AU - Waldron, Paul R.

AU - Grigoriev, Igor V.

AU - Tucker, Gregory A.

AU - Simmons, Blake A.

AU - Archer, David B.

N1 - Funding Information: We gratefully acknowledge the support from the Biotechnology and Biological Sciences Research Council (BBSRC) (Grant refs. BB/G01616X/1 and BB/ K01434X/1). This work was part of the DOE Joint BioEnergy Institute (http:// www.jbei.org) supported by the U. S. Department of Energy, Office of Science, Office of Biological and Environmental Research, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U. S. Department of Energy. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Publisher Copyright: © 2017 The Author(s).

PY - 2017/2/7

Y1 - 2017/2/7

N2 - 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.

AB - 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.

KW - Aspergillus niger

KW - CAZy

KW - Hemicellulose

KW - Ionic liquid and hydrothermal pretreatments

KW - Lignocellulose

KW - RNA-seq

KW - Straw

KW - Targeted proteomics

KW - Transcriptomic responses

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U2 - 10.1186/s13068-017-0700-9

DO - 10.1186/s13068-017-0700-9

M3 - Article

AN - SCOPUS:85013997142

SN - 1754-6834

VL - 10

JO - Biotechnology for Biofuels

JF - Biotechnology for Biofuels

IS - 1

M1 - 35

ER -

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

Abstract

Bibliographical note

Keywords

UN SDGs

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