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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

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 facilitatedmore » 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.« less

Authors:
 [1];  [2];  [3];  [3];  [3];  [3];  [4];  [4];  [4];  [4];  [4];  [5];  [5];  [6];  [7];  [3];  [4];  [3];  [5];  [3]
  1. Univ. of Nottingham, Nottingham (United Kingdom); Utrecht Univ., Utrecht (The Netherlands)
  2. Univ. of Nottingham, Nottingham (United Kingdom); Univ. of Manchester, Manchester (United Kingdom)
  3. Univ. of Nottingham, Nottingham (United Kingdom)
  4. U.S. Dept. of Energy Joint Genome Institute, Walnut Creek, CA (United States)
  5. Joint BioEnergy Institute, Emeryville, CA (United States)
  6. Univ. of Nottingham, Nottingham (United Kingdom); Public Health England, Salisbury (United Kingdom)
  7. Univ. of Nottingham, Nottingham (United Kingdom); Sorbonne Univ., Paris (France)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1379724
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Biotechnology for Biofuels
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1754-6834
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; Aspergillus niger; Lignocellulose; Ionic liquid and hydrothermal pretreatments; Straw; Transcriptomic responses; CAZy; Hemicellulose; RNA-seq; Targeted proteomics

Citation Formats

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, Stephane, Waldron, Paul R., Grigoriev, Igor V., Tucker, Gregory A., Simmons, Blake A., and Archer, David B. Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments. United States: N. p., 2017. Web. doi:10.1186/s13068-017-0700-9.
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, Stephane, 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. United States. doi:10.1186/s13068-017-0700-9.
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, Stephane, Waldron, Paul R., Grigoriev, Igor V., Tucker, Gregory A., Simmons, Blake A., and Archer, David B. Tue . "Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments". United States. doi:10.1186/s13068-017-0700-9. https://www.osti.gov/servlets/purl/1379724.
@article{osti_1379724,
title = {Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments},
author = {Daly, Paul and van Munster, Jolanda M. and Blythe, Martin J. and Ibbett, Roger and Kokolski, Matt 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, Stephane and Waldron, Paul R. and Grigoriev, Igor V. and Tucker, Gregory A. and Simmons, Blake A. and Archer, David B.},
abstractNote = {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.},
doi = {10.1186/s13068-017-0700-9},
journal = {Biotechnology for Biofuels},
number = 1,
volume = 10,
place = {United States},
year = {Tue Feb 07 00:00:00 EST 2017},
month = {Tue Feb 07 00:00:00 EST 2017}
}

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