Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network
Abstract
BACKGROUND: Enzymatic plant biomass degradation by fungi is a highly complex process and one of the leading challenges in developing a biobased economy. Some industrial fungi (e.g. Aspergillus niger) have a long history of use with respect to plant biomass degradation and for that reason have become 'model' species for this topic. A. niger is a major industrial enzyme producer that has a broad ability to degrade plant based polysaccharides. A. niger wild-type, the (hemi-)cellulolytic regulator (xlnR) and xylulokinase (xkiA1) mutant strains were grown on a monocot (corn stover, CS) and dicot (soybean hulls, SBH) substrate. The xkiA1 mutant is unable to utilize the pentoses D-xylose and L-arabinose and the polysaccharide xylan, and was previously shown to accumulate inducers for the (hemi-)cellulolytic transcriptional activator XlnR and the arabinanolytic transcriptional activator AraR in the presence of pentoses, resulting in overexpression of their target genes. The xlnR mutant has reduced growth on xylan and down-regulation of its target genes. The mutants therefore have a similar phenotype on xylan, but an opposite transcriptional effect. D-xylose and L-arabinose are the most abundant monosaccharides after D-glucose in nearly all plant-derived biomass materials. In this study we evaluated the effect of the xlnR and xkiA1 mutationmore »
- Authors:
-
[1]
- Utrecht Univ. (The Netherlands)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1591830
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Genomics
- Additional Journal Information:
- Journal Volume: 20; Journal Issue: 1; Journal ID: ISSN 1471-2164
- Publisher:
- Springer
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; transcriptomics; Aspergillus Niger; XlnR; XkiA; gene expression
Citation Formats
Khosravi, Claire, Kowalczyk, Joanna E., Chroumpi, Tania, Battaglia, Evy, Aguilar Pontes, Maria-Victoria, Peng, Mao, Wiebenga, Ad, Ng, Vivian, Lipzen, Anna, He, Guifen, Bauer, Diane, Grigoriev, Igor V., and de Vries, Ronald P. Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network. United States: N. p., 2019.
Web. doi:10.1186/s12864-019-6235-7.
Khosravi, Claire, Kowalczyk, Joanna E., Chroumpi, Tania, Battaglia, Evy, Aguilar Pontes, Maria-Victoria, Peng, Mao, Wiebenga, Ad, Ng, Vivian, Lipzen, Anna, He, Guifen, Bauer, Diane, Grigoriev, Igor V., & de Vries, Ronald P. Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network. United States. https://doi.org/10.1186/s12864-019-6235-7
Khosravi, Claire, Kowalczyk, Joanna E., Chroumpi, Tania, Battaglia, Evy, Aguilar Pontes, Maria-Victoria, Peng, Mao, Wiebenga, Ad, Ng, Vivian, Lipzen, Anna, He, Guifen, Bauer, Diane, Grigoriev, Igor V., and de Vries, Ronald P. Thu .
"Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network". United States. https://doi.org/10.1186/s12864-019-6235-7. https://www.osti.gov/servlets/purl/1591830.
@article{osti_1591830,
title = {Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network},
author = {Khosravi, Claire and Kowalczyk, Joanna E. and Chroumpi, Tania and Battaglia, Evy and Aguilar Pontes, Maria-Victoria and Peng, Mao and Wiebenga, Ad and Ng, Vivian and Lipzen, Anna and He, Guifen and Bauer, Diane and Grigoriev, Igor V. and de Vries, Ronald P.},
abstractNote = {BACKGROUND: Enzymatic plant biomass degradation by fungi is a highly complex process and one of the leading challenges in developing a biobased economy. Some industrial fungi (e.g. Aspergillus niger) have a long history of use with respect to plant biomass degradation and for that reason have become 'model' species for this topic. A. niger is a major industrial enzyme producer that has a broad ability to degrade plant based polysaccharides. A. niger wild-type, the (hemi-)cellulolytic regulator (xlnR) and xylulokinase (xkiA1) mutant strains were grown on a monocot (corn stover, CS) and dicot (soybean hulls, SBH) substrate. The xkiA1 mutant is unable to utilize the pentoses D-xylose and L-arabinose and the polysaccharide xylan, and was previously shown to accumulate inducers for the (hemi-)cellulolytic transcriptional activator XlnR and the arabinanolytic transcriptional activator AraR in the presence of pentoses, resulting in overexpression of their target genes. The xlnR mutant has reduced growth on xylan and down-regulation of its target genes. The mutants therefore have a similar phenotype on xylan, but an opposite transcriptional effect. D-xylose and L-arabinose are the most abundant monosaccharides after D-glucose in nearly all plant-derived biomass materials. In this study we evaluated the effect of the xlnR and xkiA1 mutation during growth on two pentose-rich substrates by transcriptome analysis. RESULTS: Particular attention was given to CAZymes, metabolic pathways and transcription factors related to the plant biomass degradation. Genes coding for the main enzymes involved in plant biomass degradation were down-regulated at the beginning of the growth on CS and SBH. However, at a later time point, significant differences were found in the expression profiles of both mutants on CS compared to SBH. CONCLUSION: This study demonstrates the high complexity of the plant biomass degradation process by fungi, by showing that mutant strains with fairly straightforward phenotypes on pure mono- and polysaccharides, have much less clear-cut phenotypes and transcriptomes on crude plant biomass.},
doi = {10.1186/s12864-019-6235-7},
journal = {BMC Genomics},
number = 1,
volume = 20,
place = {United States},
year = {Thu Nov 14 00:00:00 EST 2019},
month = {Thu Nov 14 00:00:00 EST 2019}
}
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