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Title: Deletion of either the regulatory gene ara1 or metabolic gene xki1 in Trichoderma reesei leads to increased CAZyme gene expression on crude plant biomass

Abstract

Background:Trichoderma reesei is one of the major producers of enzymes for the conversion of plant biomass to sustainable fuels and chemicals. Crude plant biomass can induce the production of CAZymes in T. reesei, but there is limited understanding of how the transcriptional response to crude plant biomass is regulated. In addition, it is unknown whether induction on untreated recalcitrant crude plant biomass (with a large diversity of inducers) can be sustained for longer. We investigated the transcriptomic response of T. reesei to the two industrial feedstocks, corn stover (CS) and soybean hulls (SBH), over time (4 h, 24 h and 48 h), and its regulatory basis using transcription factor deletion mutants (Δxyr1 and Δara1). We also investigated whether deletion of a xylulokinase gene (Δxki1) from the pentose catabolic pathway that converts potential inducers could lead to increased CAZyme gene expression. Results:By analyzing the transcriptomic responses using clustering as well as differential and cumulative expression of plant biomass degrading CAZymes, we found that corn stover induced a broader range and higher expression of CAZymes in T. reesei, while SBH induced more pectinolytic and mannanolytic transcripts. XYR1 was the major TF regulating CS utilization, likely due to the significant amount of d-xylose in this substrate.more » In contrast, ARA1 had a stronger effect on SBH utilization, which correlates with a higher abundance of l-arabinose in SBH that activates ARA1. Blocking pentose catabolism by deletion of xki1 led to higher expression of CAZyme encoding genes on both substrates at later time points. Surprisingly, this was also observed for Δara1 at later time points. Many of these genes were XYR1 regulated, suggesting that inducers for this regulator accumulated over time on both substrates. Conclusion:Our data demonstrates the complexity of the regulatory system related to plant biomass degradation in T. reesei and the effect the feedstock composition has on this. Furthermore, this dataset provides leads to improve the efficiency of a T. reesei enzyme cocktail, such as by the choice of substrate or by deleting xki1 to obtain higher production of plant biomass degrading CAZymes.« less

Authors:
 [1];  [1];  [1];  [1];  [2];  [2];  [2];  [2];  [3];  [4];  [1]; ORCiD logo [1]
  1. Utrecht Univ. (The Netherlands)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
  4. Inst. of Chemical, Environmental and Bioscience Engineering, Vienna (Austria)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); Netherlands Organization for Scientific Research (NWO)
OSTI Identifier:
1581318
Grant/Contract Number:  
AC02-05CH11231; 016.130.609; 824.15.023
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Biotechnology for Biofuels
Additional Journal Information:
Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1754-6834
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; plant biomass degradation; trichoderma reesei; xylan; cellulose; CAZymes; xyr1

Citation Formats

Benocci, Tiziano, Aguilar-Pontes, Maria Victoria, Kun, Roland Sándor, Lubbers, Ronnie J. M., Lail, Kathleen, Wang, Mei, Lipzen, Anna, Ng, Vivian, Grigoriev, Igor V., Seiboth, Bernhard, Daly, Paul, and de Vries, Ronald P. Deletion of either the regulatory gene ara1 or metabolic gene xki1 in Trichoderma reesei leads to increased CAZyme gene expression on crude plant biomass. United States: N. p., 2019. Web. doi:10.1186/s13068-019-1422-y.
Benocci, Tiziano, Aguilar-Pontes, Maria Victoria, Kun, Roland Sándor, Lubbers, Ronnie J. M., Lail, Kathleen, Wang, Mei, Lipzen, Anna, Ng, Vivian, Grigoriev, Igor V., Seiboth, Bernhard, Daly, Paul, & de Vries, Ronald P. Deletion of either the regulatory gene ara1 or metabolic gene xki1 in Trichoderma reesei leads to increased CAZyme gene expression on crude plant biomass. United States. https://doi.org/10.1186/s13068-019-1422-y
Benocci, Tiziano, Aguilar-Pontes, Maria Victoria, Kun, Roland Sándor, Lubbers, Ronnie J. M., Lail, Kathleen, Wang, Mei, Lipzen, Anna, Ng, Vivian, Grigoriev, Igor V., Seiboth, Bernhard, Daly, Paul, and de Vries, Ronald P. 2019. "Deletion of either the regulatory gene ara1 or metabolic gene xki1 in Trichoderma reesei leads to increased CAZyme gene expression on crude plant biomass". United States. https://doi.org/10.1186/s13068-019-1422-y. https://www.osti.gov/servlets/purl/1581318.
@article{osti_1581318,
title = {Deletion of either the regulatory gene ara1 or metabolic gene xki1 in Trichoderma reesei leads to increased CAZyme gene expression on crude plant biomass},
author = {Benocci, Tiziano and Aguilar-Pontes, Maria Victoria and Kun, Roland Sándor and Lubbers, Ronnie J. M. and Lail, Kathleen and Wang, Mei and Lipzen, Anna and Ng, Vivian and Grigoriev, Igor V. and Seiboth, Bernhard and Daly, Paul and de Vries, Ronald P.},
abstractNote = {Background:Trichoderma reesei is one of the major producers of enzymes for the conversion of plant biomass to sustainable fuels and chemicals. Crude plant biomass can induce the production of CAZymes in T. reesei, but there is limited understanding of how the transcriptional response to crude plant biomass is regulated. In addition, it is unknown whether induction on untreated recalcitrant crude plant biomass (with a large diversity of inducers) can be sustained for longer. We investigated the transcriptomic response of T. reesei to the two industrial feedstocks, corn stover (CS) and soybean hulls (SBH), over time (4 h, 24 h and 48 h), and its regulatory basis using transcription factor deletion mutants (Δxyr1 and Δara1). We also investigated whether deletion of a xylulokinase gene (Δxki1) from the pentose catabolic pathway that converts potential inducers could lead to increased CAZyme gene expression. Results:By analyzing the transcriptomic responses using clustering as well as differential and cumulative expression of plant biomass degrading CAZymes, we found that corn stover induced a broader range and higher expression of CAZymes in T. reesei, while SBH induced more pectinolytic and mannanolytic transcripts. XYR1 was the major TF regulating CS utilization, likely due to the significant amount of d-xylose in this substrate. In contrast, ARA1 had a stronger effect on SBH utilization, which correlates with a higher abundance of l-arabinose in SBH that activates ARA1. Blocking pentose catabolism by deletion of xki1 led to higher expression of CAZyme encoding genes on both substrates at later time points. Surprisingly, this was also observed for Δara1 at later time points. Many of these genes were XYR1 regulated, suggesting that inducers for this regulator accumulated over time on both substrates. Conclusion:Our data demonstrates the complexity of the regulatory system related to plant biomass degradation in T. reesei and the effect the feedstock composition has on this. Furthermore, this dataset provides leads to improve the efficiency of a T. reesei enzyme cocktail, such as by the choice of substrate or by deleting xki1 to obtain higher production of plant biomass degrading CAZymes.},
doi = {10.1186/s13068-019-1422-y},
url = {https://www.osti.gov/biblio/1581318}, journal = {Biotechnology for Biofuels},
issn = {1754-6834},
number = 1,
volume = 12,
place = {United States},
year = {Tue Apr 09 00:00:00 EDT 2019},
month = {Tue Apr 09 00:00:00 EDT 2019}
}

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Cited by: 7 works
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Works referenced in this record:

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Comparative analysis of basidiomycete transcriptomes reveals a core set of expressed genes encoding plant biomass degrading enzymes
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Plant biomass degradation by fungi
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A novel l -arabinose-responsive regulator discovered in the rice-blast fungus Pyricularia oryzae ( Magnaporthe oryzae )
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Fungal arabinan and l-arabinose metabolism
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Aspergillus niger RhaR, a regulator involved in l-rhamnose release and catabolism
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A versatile transformation system for the cellulolytic filamentous fungus Trichoderma reesei
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Fermentation of soybean hulls to ethanol while preserving protein value
journal, July 2009


Xyr1 receives the lactose induction signal and regulates lactose metabolism in Hypocrea jecorina
journal, July 2007


Plant biomass degradation by fungi
journal, November 2014


Lignin in straw of herbaceous crops
journal, November 2008


Gene targeting in a nonhomologous end joining deficient Hypocrea jecorina
journal, January 2009


The Post-genomic Era of Trichoderma reesei : What's Next?
journal, December 2016


Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi
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L-Arabinose and D-Xylose Catabolism in Aspergillus niger
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Trichoderma reesei RUT-C30 - thirty years of strain improvement
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Isolation and characterization of two specific regulatory Aspergillus niger mutants shows antagonistic regulation of arabinan and xylan metabolism
journal, May 2003


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Xyr1 (Xylanase Regulator 1) Regulates both the Hydrolytic Enzyme System and d-Xylose Metabolism in Hypocrea jecorina
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RNA Sequencing Reveals Xyr1 as a Transcription Factor Regulating Gene Expression beyond Carbohydrate Metabolism
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Mapping the polysaccharide degradation potential of Aspergillus niger
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Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates
journal, January 2012


A versatile toolkit for high throughput functional genomics with Trichoderma reesei
journal, January 2012


Enhancement of fermentable sugar yields by α-xylosidase supplementation of commercial cellulases
journal, January 2013


Cellulases and beyond: the first 70 years of the enzyme producer Trichoderma reesei
journal, June 2016


The Relation Between Promoter Chromatin Status, Xyr1 and Cellulase Expression in Trichoderma reesei
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Works referencing / citing this record: