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Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks.
Schäpe, P; Kwon, M J; Baumann, B; Gutschmann, B; Jung, S; Lenz, S; Nitsche, B; Paege, N; Schütze, T; Cairns, T C; Meyer, V.
Afiliación
  • Schäpe P; Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany.
  • Kwon MJ; Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany.
  • Baumann B; Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany.
  • Gutschmann B; Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany.
  • Jung S; Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany.
  • Lenz S; Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany.
  • Nitsche B; Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany.
  • Paege N; Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany.
  • Schütze T; Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany.
  • Cairns TC; Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany.
  • Meyer V; Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany.
Nucleic Acids Res ; 47(2): 559-569, 2019 01 25.
Article en En | MEDLINE | ID: mdl-30496528
A significant challenge in our understanding of biological systems is the high number of genes with unknown function in many genomes. The fungal genus Aspergillus contains important pathogens of humans, model organisms, and microbial cell factories. Aspergillus niger is used to produce organic acids, proteins, and is a promising source of new bioactive secondary metabolites. Out of the 14,165 open reading frames predicted in the A. niger genome only 2% have been experimentally verified and over 6,000 are hypothetical. Here, we show that gene co-expression network analysis can be used to overcome this limitation. A meta-analysis of 155 transcriptomics experiments generated co-expression networks for 9,579 genes (∼65%) of the A. niger genome. By populating this dataset with over 1,200 gene functional experiments from the genus Aspergillus and performing gene ontology enrichment, we could infer biological processes for 9,263 of A. niger genes, including 2,970 hypothetical genes. Experimental validation of selected co-expression sub-networks uncovered four transcription factors involved in secondary metabolite synthesis, which were used to activate production of multiple natural products. This study constitutes a significant step towards systems-level understanding of A. niger, and the datasets can be used to fuel discoveries of model systems, fungal pathogens, and biotechnology.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Aspergillus niger / Regulación Fúngica de la Expresión Génica / Genoma Fúngico / Redes Reguladoras de Genes Tipo de estudio: Prognostic_studies / Systematic_reviews Idioma: En Revista: Nucleic Acids Res Año: 2019 Tipo del documento: Article País de afiliación: Alemania Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Aspergillus niger / Regulación Fúngica de la Expresión Génica / Genoma Fúngico / Redes Reguladoras de Genes Tipo de estudio: Prognostic_studies / Systematic_reviews Idioma: En Revista: Nucleic Acids Res Año: 2019 Tipo del documento: Article País de afiliación: Alemania Pais de publicación: Reino Unido