title: Genome-wide metabolic re-annotation of Ashbya gossypii: new insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis.
abstract: BACKGROUND
  Ashbya gossypii is an industrially relevant microorganism traditionally used for riboflavin production. Despite the high gene homology and gene order conservation comparatively with Saccharomyces cerevisiae, it presents a lower level of genomic complexity. Its type of growth, placing it among filamentous fungi, questions how close it really is from the budding yeast, namely in terms of metabolism, therefore raising the need for an extensive and thorough study of its entire metabolism. This work reports the first manual enzymatic genome-wide re-annotation of A. gossypii as well as the first annotation of membrane transport proteins.
  
  
  RESULTS
  After applying a developed enzymatic re-annotation pipeline, 847 genes were assigned with metabolic functions. Comparatively to KEGG's annotation, these data corrected the function for 14% of the common genes and increased the information for 52 genes, either completing existing partial EC numbers or adding new ones. Furthermore, 22 unreported enzymatic functions were found, corresponding to a significant increase in the knowledge of the metabolism of this organism. The information retrieved from the metabolic re-annotation and transport annotation was used for a comprehensive analysis of A. gossypii's metabolism in comparison to the one of S. cerevisiae (post-WGD - whole genome duplication) and Kluyveromyces lactis (pre-WGD), suggesting some relevant differences in several parts of their metabolism, with the majority being found for the metabolism of purines, pyrimidines, nitrogen and lipids. A considerable number of enzymes were found exclusively in A. gossypii comparatively with K. lactis (90) and S. cerevisiae (13). In a similar way, 176 and 123 enzymatic functions were absent on A. gossypii comparatively to K. lactis and S. cerevisiae, respectively, confirming some of the well-known phenotypes of this organism.
  
  
  CONCLUSIONS
  This high quality metabolic re-annotation, together with the first membrane transporters annotation and the metabolic comparative analysis, represents a new important tool for the study and better understanding of A. gossypii's metabolism.
authors.forename: Daniel
authors.initials: D
authors.lastname: Gomes
authors.forename: Tatiana Q
authors.initials: TQ
authors.lastname: Aguiar
authors.forename: Oscar
authors.initials: O
authors.lastname: Dias
authors.forename: Eugénio C
authors.initials: EC
authors.lastname: Ferreira
authors.forename: Lucília
authors.initials: L
authors.lastname: Domingues
authors.affiliation: CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal. irocha@deb.uminho.pt.
authors.forename: Isabel
authors.initials: I
authors.lastname: Rocha
mesh_terms: D055169:Eremothecium / Q000145:classification / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism*; D016681:Genome, Fungal / Q000235:genetics; D023281:Genomics; D007716:Kluyveromyces / Q000145:classification / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism; D026901:Membrane Transport Proteins / Q000235:genetics / Q000378:metabolism; D058977:Molecular Sequence Annotation / Q000379:methods*; D010802:Phylogeny; D012441:Saccharomyces cerevisiae / Q000145:classification / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism
chemical_list: D026901:Membrane Transport Proteins