Aspergillus niger: Mapping fungal specific zinc-finger transcription factors to gene co-expression networks

Benjamin M Nitsche1, Vera Meyer1, Arthur FJ Ram

Author address: 

1Leiden Universitiy, Institute of Biology, Section of Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, The Netherlands 2Kluyver Centre for Genomics of Industrial Fermentation, Sylviusweg 72, 2333 BE Leiden, The Netherlands

Abstract: 

Aspergillus niger is a saprophytic filamentous fungus with a long history in industrial production of organic acids such as citric and gluconic acid as well as various enzymes like glycoamylases and pectinases. Furthermore, A. niger is an important multi-cellular model organism to study for example the establishment of cell polarity or protein secretion and it is used for the discovery of new anti-fungal drugs. A. niger can easily be genetically modified and cultivated under defined growth conditions in bioreactors. DSM published its 33.9 million base pair genome in February 2007 and an Affymetrix DNA microarray platform with more than 14.000 annotated open reading frames (ORFs) and genetic elements was designed. Among the predicted ORFs, over 300 fungal specific zinc-finger transcription factors (TFs) have been annotated. The function of most of these TFs remains unknown. In the current study we, have built gene co-expression networks from a dataset of about 100 Affymetrix microarrays covering more than 30 different growth conditions including those which induce stress related to secretion, maintenance of polarity, cell wall integrity, carbon-source utilization and starvation. Exemplarily for a wide range of applications, we show mapping of putative TFs with unknown functions to these networks. Allocation of TFs to functionally enriched gene clusters can serve as an indication for their regulatory role and thereby give valuable leads for further experimental studies.
2010

abstract No: 

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Full conference title: 

10th EUROPEAN CONFERENCE ON FUNGAL GENETICS
    • ECFG 10th (2010)