Constructed Aspergillus niger gene co-expression networks relate to biological processes

Robert A. van den Berg1, Machtelt Braaksma2, Douwe van der Veen3, Mariet J. van der Werf2, Peter J. Punt2, John van der Oost3, Leo H. de Graaff3

Author address: 

1 SymBioSys, Katholieke Universiteit Leuven, Leuven, Belgium 2 TNO Quality of Life, Zeist, The Netherlands 3 Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands


The fungus Aspergillus niger has been studied in considerable detail with respect to various industrial applications. Although its central metabolic pathways are relatively well understood, the mechanisms that control the adaptation of its metabolism are understood poorly. In this study, clustering of coexpressed genes has been performed on the basis of DNA microarray data sets from two experimental approaches. In one approach, low amounts of inducer caused a relatively mild perturbation, while in the other approach the imposed environmental conditions including carbon source starvation caused severe perturbed stress. Evolutionary conserved genes were used to construct gene co-expression networks for both the individual and combined data sets. Comparative analysis revealed the existence of modules, some of which are present in all three networks. In addition, experimental condition-specific modules were identified. Module-derived consensus expression profiles enabled the integration of all protein-coding A. niger genes to the coexpression analysis, including hypothetical and poorly conserved genes. Conserved sequence motifs were detected in the upstream region of genes that cluster in some modules, e.g., the binding site for the amino acid metabolism-related transcription factor CpcA as well as for the fatty acid metabolism related transcription factors, FarA and FarB. Moreover, not previously described putative transcription factor binding sites were discovered for two modules: the motif 5'-CGACAA is overrepresented in the module containing genes encoding cytosolic ribosomal proteins, while the motif 5'-GGCCGCG is overrepresented in genes related to 'gene expression', such as RNA helicases and translation initiation factors

abstract No: 


Full conference title: 

    • ECFG 10th (2010)