title: Short- and long-term dynamic responses of the metabolic network and gene expression in yeast to a transient change in the nutrient environment.
abstract: Quantitative data on the dynamic changes in the transcriptome and the metabolome of yeast in response to an impulse-like perturbation in nutrient availability was integrated with the metabolic pathway information in order to elucidate the long-term dynamic re-organization of the cells. This study revealed that, in addition to the dynamic re-organization of the de novo biosynthetic pathways, salvage pathways were also re-organized in a time-dependent manner upon catabolite repression. The transcriptional and the metabolic responses observed for nitrogen catabolite repression were not as severe as those observed for carbon catabolite repression. Selective up- or down regulation of a single member of a paralogous gene pair during the response to the relaxation from nutritional limitation was identified indicating a differentiation of functions among paralogs. Our study highlighted the role of inosine accumulation and recycling in energy homeostasis and indicated possible bottlenecks in the process.
authors.affiliation: Department of Chemical Engineering, Bogazici University, Istanbul, Turkey. duygu.dikicioglu@boun.edu.tr
authors.forename: Duygu
authors.initials: D
authors.lastname: Dikicioglu
authors.forename: Warwick B
authors.initials: WB
authors.lastname: Dunn
authors.forename: Douglas B
authors.initials: DB
authors.lastname: Kell
authors.forename: Betul
authors.initials: B
authors.lastname: Kirdar
authors.forename: Stephen G
authors.initials: SG
authors.lastname: Oliver
mesh_terms: D002244:Carbon / Q000378:metabolism; D057465:Catabolite Repression / Q000235:genetics / Q000502:physiology; D004734:Energy Metabolism / Q000235:genetics / Q000502:physiology; D005492:Folic Acid / Q000378:metabolism; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal / Q000235:genetics / Q000502:physiology*; D005947:Glucose / Q000378:metabolism; D005998:Glycine / Q000378:metabolism; D007288:Inosine / Q000378:metabolism; D053858:Metabolic Networks and Pathways / Q000235:genetics / Q000502:physiology*; D009584:Nitrogen / Q000378:metabolism; D009711:Nucleotides / Q000378:metabolism; D000644:Quaternary Ammonium Compounds / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D012694:Serine / Q000378:metabolism; D049490:Systems Biology / Q000379:methods*; D059467:Transcriptome / Q000235:genetics / Q000502:physiology
chemical_list: D009711:Nucleotides; D000644:Quaternary Ammonium Compounds; D012694:Serine; D007288:Inosine; D002244:Carbon; D005492:Folic Acid; D005947:Glucose; D009584:Nitrogen; D005998:Glycine