title: Metabolic peculiarities of Aspergillus niger disclosed by comparative metabolic genomics.
abstract: BACKGROUND
  Aspergillus niger is an important industrial microorganism for the production of both metabolites, such as citric acid, and proteins, such as fungal enzymes or heterologous proteins. Despite its extensive industrial applications, the genetic inventory of this fungus is only partially understood. The recently released genome sequence opens a new horizon for both scientific studies and biotechnological applications.
  
  
  RESULTS
  Here, we present the first genome-scale metabolic network for A. niger and an in-depth genomic comparison of this species to seven other fungi to disclose its metabolic peculiarities. The raw genomic sequences of A. niger ATCC 9029 were first annotated. The reconstructed metabolic network is based on the annotation of two A. niger genomes, CBS 513.88 and ATCC 9029, including enzymes with 988 unique EC numbers, 2,443 reactions and 2,349 metabolites. More than 1,100 enzyme-coding genes are unique to A. niger in comparison to the other seven fungi. For example, we identified additional copies of genes such as those encoding alternative mitochondrial oxidoreductase and citrate synthase in A. niger, which might contribute to the high citric acid production efficiency of this species. Moreover, nine genes were identified as encoding enzymes with EC numbers exclusively found in A. niger, mostly involved in the biosynthesis of complex secondary metabolites and degradation of aromatic compounds.
  
  
  CONCLUSIONS
  The genome-level reconstruction of the metabolic network and genome-based metabolic comparison disclose peculiarities of A. niger highly relevant to its biotechnological applications and should contribute to future rational metabolic design and systems biology studies of this black mold and related species.
authors.affiliation: Helmholtz Centre for Infection Research, Inhoffenstr., 38124 Braunschweig, Germany.
authors.forename: Jibin
authors.initials: J
authors.lastname: Sun
authors.forename: Xin
authors.initials: X
authors.lastname: Lu
authors.forename: Ursula
authors.initials: U
authors.lastname: Rinas
authors.forename: An Ping
authors.initials: AP
authors.lastname: Zeng
mesh_terms: D001234:Aspergillus niger / Q000235:genetics* / Q000378:metabolism*; D001709:Biotechnology / Q000379:methods; D002950:Citrate (si)-Synthase / Q000378:metabolism; D019343:Citric Acid / Q000378:metabolism; D005656:Fungal Proteins / Q000737:chemistry; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D016678:Genome; D023281:Genomics; D008660:Metabolism; D024101:Mitochondrial Proteins; D008954:Models, Biological; D008957:Models, Genetic; D008962:Models, Theoretical; D010088:Oxidoreductases / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins; D000099188:Alternative Oxidase