Short- and long-term dynamic responses of the metabolic network and gene expression in yeast to a transient change in the nutrient environment

Mol Biosyst. 2012 Jun;8(6):1760-74. doi: 10.1039/c2mb05443d. Epub 2012 Apr 11.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carbon / metabolism
  • Catabolite Repression / genetics
  • Catabolite Repression / physiology
  • Energy Metabolism / genetics
  • Energy Metabolism / physiology
  • Folic Acid / metabolism
  • Gene Expression Profiling
  • Gene Expression Regulation, Fungal / genetics
  • Gene Expression Regulation, Fungal / physiology*
  • Glucose / metabolism
  • Glycine / metabolism
  • Inosine / metabolism
  • Metabolic Networks and Pathways / genetics
  • Metabolic Networks and Pathways / physiology*
  • Nitrogen / metabolism
  • Nucleotides / metabolism
  • Quaternary Ammonium Compounds / metabolism
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae / physiology*
  • Serine / metabolism
  • Systems Biology / methods*
  • Transcriptome / genetics
  • Transcriptome / physiology

Substances

  • Nucleotides
  • Quaternary Ammonium Compounds
  • Serine
  • Inosine
  • Carbon
  • Folic Acid
  • Glucose
  • Nitrogen
  • Glycine