Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae

Pedro M. Coutinho, Mikael R. Andersen, Katarina Kolenova, Patricia A. vanKuyk, Isabelle Benoit, Birgit S. Gruben, Blanca Trejo-Aguilar, Hans Visser, Piet van Solingen, Tiina Pakula, Bernard Seiboth, Evy Battaglia, Guillermo Aguilar-Osorio, Jan F. de Jong, Robin A. Ohm, Mariana Aguilar, Bernard Henrissat, Jens Nielsen, Henrik Stålbrand, Ronald P. de Vries (Corresponding Author)

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Abstract

The plant polysaccharide degradative potential of Aspergillus nidulans was analysed in detail and compared to that of Aspergillus niger and Aspergillus oryzae using a combination of bioinformatics, physiology and transcriptomics. Manual verification indicated that 28.4% of the A. nidulans ORFs analysed in this study do not contain a secretion signal, of which 40% may be secreted through a non-classical method. While significant differences were found between the species in the numbers of ORFs assigned to the relevant CAZy families, no significant difference was observed in growth on polysaccharides. Growth differences were observed between the Aspergilli and Podospora anserina, which has a more different genomic potential for polysaccharide degradation, suggesting that large genomic differences are required to cause growth differences on polysaccharides. Differences were also detected between the Aspergilli in the presence of putative regulatory sequences in the promoters of the ORFs of this study and correlation of the presence of putative XlnR binding sites to induction by xylose was detected for A. niger. These data demonstrate differences at genome content, substrate specificity of the enzymes and gene regulation in these three Aspergilli, which likely reflect their individual adaptation to their natural biotope.

Original languageEnglish
Pages (from-to)S161-S169
Number of pages9
JournalFungal Genetics and Biology
Volume46
Issue number1, Supplement
DOIs
Publication statusPublished - 2009
MoE publication typeA1 Journal article-refereed

Fingerprint

Aspergillus oryzae
Aspergillus nidulans
Aspergillus niger
Polysaccharides
Aspergillus
Open Reading Frames
Growth
Podospora
Xylose
Substrate Specificity
Computational Biology
Binding Sites
Genome
Enzymes
Genes

Keywords

  • Aspergillus
  • Plant polysaccharide degradation
  • CAZy
  • Promoter analysis
  • Micro array analysis
  • XlnR
  • Substrate specificity

Cite this

Coutinho, P. M., Andersen, M. R., Kolenova, K., vanKuyk, P. A., Benoit, I., Gruben, B. S., ... de Vries, R. P. (2009). Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae. Fungal Genetics and Biology, 46(1, Supplement), S161-S169. https://doi.org/10.1016/j.fgb.2008.07.020
Coutinho, Pedro M. ; Andersen, Mikael R. ; Kolenova, Katarina ; vanKuyk, Patricia A. ; Benoit, Isabelle ; Gruben, Birgit S. ; Trejo-Aguilar, Blanca ; Visser, Hans ; van Solingen, Piet ; Pakula, Tiina ; Seiboth, Bernard ; Battaglia, Evy ; Aguilar-Osorio, Guillermo ; de Jong, Jan F. ; Ohm, Robin A. ; Aguilar, Mariana ; Henrissat, Bernard ; Nielsen, Jens ; Stålbrand, Henrik ; de Vries, Ronald P. / Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae. In: Fungal Genetics and Biology. 2009 ; Vol. 46, No. 1, Supplement. pp. S161-S169.
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Coutinho, PM, Andersen, MR, Kolenova, K, vanKuyk, PA, Benoit, I, Gruben, BS, Trejo-Aguilar, B, Visser, H, van Solingen, P, Pakula, T, Seiboth, B, Battaglia, E, Aguilar-Osorio, G, de Jong, JF, Ohm, RA, Aguilar, M, Henrissat, B, Nielsen, J, Stålbrand, H & de Vries, RP 2009, 'Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae', Fungal Genetics and Biology, vol. 46, no. 1, Supplement, pp. S161-S169. https://doi.org/10.1016/j.fgb.2008.07.020

Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae. / Coutinho, Pedro M.; Andersen, Mikael R.; Kolenova, Katarina; vanKuyk, Patricia A.; Benoit, Isabelle; Gruben, Birgit S.; Trejo-Aguilar, Blanca; Visser, Hans; van Solingen, Piet; Pakula, Tiina; Seiboth, Bernard; Battaglia, Evy; Aguilar-Osorio, Guillermo; de Jong, Jan F.; Ohm, Robin A.; Aguilar, Mariana; Henrissat, Bernard; Nielsen, Jens; Stålbrand, Henrik; de Vries, Ronald P. (Corresponding Author).

In: Fungal Genetics and Biology, Vol. 46, No. 1, Supplement, 2009, p. S161-S169.

Research output: Contribution to journalArticleScientificpeer-review

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T1 - Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae

AU - Coutinho, Pedro M.

AU - Andersen, Mikael R.

AU - Kolenova, Katarina

AU - vanKuyk, Patricia A.

AU - Benoit, Isabelle

AU - Gruben, Birgit S.

AU - Trejo-Aguilar, Blanca

AU - Visser, Hans

AU - van Solingen, Piet

AU - Pakula, Tiina

AU - Seiboth, Bernard

AU - Battaglia, Evy

AU - Aguilar-Osorio, Guillermo

AU - de Jong, Jan F.

AU - Ohm, Robin A.

AU - Aguilar, Mariana

AU - Henrissat, Bernard

AU - Nielsen, Jens

AU - Stålbrand, Henrik

AU - de Vries, Ronald P.

PY - 2009

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N2 - The plant polysaccharide degradative potential of Aspergillus nidulans was analysed in detail and compared to that of Aspergillus niger and Aspergillus oryzae using a combination of bioinformatics, physiology and transcriptomics. Manual verification indicated that 28.4% of the A. nidulans ORFs analysed in this study do not contain a secretion signal, of which 40% may be secreted through a non-classical method. While significant differences were found between the species in the numbers of ORFs assigned to the relevant CAZy families, no significant difference was observed in growth on polysaccharides. Growth differences were observed between the Aspergilli and Podospora anserina, which has a more different genomic potential for polysaccharide degradation, suggesting that large genomic differences are required to cause growth differences on polysaccharides. Differences were also detected between the Aspergilli in the presence of putative regulatory sequences in the promoters of the ORFs of this study and correlation of the presence of putative XlnR binding sites to induction by xylose was detected for A. niger. These data demonstrate differences at genome content, substrate specificity of the enzymes and gene regulation in these three Aspergilli, which likely reflect their individual adaptation to their natural biotope.

AB - The plant polysaccharide degradative potential of Aspergillus nidulans was analysed in detail and compared to that of Aspergillus niger and Aspergillus oryzae using a combination of bioinformatics, physiology and transcriptomics. Manual verification indicated that 28.4% of the A. nidulans ORFs analysed in this study do not contain a secretion signal, of which 40% may be secreted through a non-classical method. While significant differences were found between the species in the numbers of ORFs assigned to the relevant CAZy families, no significant difference was observed in growth on polysaccharides. Growth differences were observed between the Aspergilli and Podospora anserina, which has a more different genomic potential for polysaccharide degradation, suggesting that large genomic differences are required to cause growth differences on polysaccharides. Differences were also detected between the Aspergilli in the presence of putative regulatory sequences in the promoters of the ORFs of this study and correlation of the presence of putative XlnR binding sites to induction by xylose was detected for A. niger. These data demonstrate differences at genome content, substrate specificity of the enzymes and gene regulation in these three Aspergilli, which likely reflect their individual adaptation to their natural biotope.

KW - Aspergillus

KW - Plant polysaccharide degradation

KW - CAZy

KW - Promoter analysis

KW - Micro array analysis

KW - XlnR

KW - Substrate specificity

U2 - 10.1016/j.fgb.2008.07.020

DO - 10.1016/j.fgb.2008.07.020

M3 - Article

VL - 46

SP - S161-S169

JO - Fungal Genetics and Biology

JF - Fungal Genetics and Biology

SN - 1087-1845

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