Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network

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.

doi:10.1186/s12864-019-6235-7

Title: Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network

Journal Article · Thu Nov 14 00:00:00 EST 2019 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-019-6235-7· OSTI ID:1591830

Khosravi, Claire ^[1]; Kowalczyk, Joanna E. ^[1]; Chroumpi, Tania ^[1]; Battaglia, Evy ^[1]; Aguilar Pontes, Maria-Victoria ^[1]; Peng, Mao ^[1]; Wiebenga, Ad ^[1]; Ng, Vivian ^[2]; Lipzen, Anna ^[2]; He, Guifen ^[2]; Bauer, Diane ^[2]; Grigoriev, Igor V. ^[3];

^[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)

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.

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

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1591830

Journal Information:: BMC Genomics, Vol. 20, Issue 1; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 4 works

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59 BASIC BIOLOGICAL SCIENCES
transcriptomics
Aspergillus Niger
XlnR
XkiA
gene expression

Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.c.4740287.v1 The current record is supplemented by this collection	collection	January 2019
MOESM9 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309247 The current record is supplemented by this dataset	dataset	January 2019
MOESM3 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309202 The current record is supplemented by this dataset	dataset	January 2019
MOESM4 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309208 The current record is supplemented by this dataset	dataset	January 2019
MOESM6 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309223.v1 The current record is supplemented by this dataset	dataset	January 2019
MOESM5 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309217.v1 The current record is supplemented by this dataset	dataset	January 2019
MOESM3 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309202.v1 The current record is supplemented by this dataset	dataset	January 2019
MOESM2 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309190 The current record is supplemented by this dataset	dataset	January 2019
MOESM8 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309238.v1 The current record is supplemented by this text	text	January 2019
MOESM8 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309238 The current record is supplemented by this text	text	January 2019
MOESM2 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309190.v1 The current record is supplemented by this dataset	dataset	January 2019
MOESM6 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309223 The current record is supplemented by this dataset	dataset	January 2019
MOESM9 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309247.v1 The current record is supplemented by this dataset	dataset	January 2019
MOESM1 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309181 The current record is supplemented by this dataset	dataset	January 2019
MOESM10 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309172.v1 The current record is supplemented by this text	text	January 2019
MOESM7 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309229 The current record is supplemented by this dataset	dataset	January 2019
Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.c.4740287 The current record is supplemented by this collection	collection	January 2019
MOESM1 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309181.v1 The current record is supplemented by this dataset	dataset	January 2019
MOESM10 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309172 The current record is supplemented by this text	text	January 2019
MOESM4 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309208.v1 The current record is supplemented by this dataset	dataset	January 2019
MOESM7 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309229.v1 The current record is supplemented by this dataset	dataset	January 2019
MOESM5 of Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network Khosravi, Claire; Kowalczyk, Joanna; Chroumpi, Tania https://doi.org/10.6084/m9.figshare.10309217 The current record is supplemented by this dataset	dataset	January 2019

Title: Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network

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