Distinct signaling roles of ceramide species in yeast revealed through systematic perturbation and systems biology analyses

Sci Signal. 2013 Oct 29;6(299):rs14. doi: 10.1126/scisignal.2004515.


Ceramide, the central molecule of sphingolipid metabolism, is an important bioactive molecule that participates in various cellular regulatory events and that has been implicated in disease. Deciphering ceramide signaling is challenging because multiple ceramide species exist, and many of them may have distinct functions. We applied systems biology and molecular approaches to perturb ceramide metabolism in the yeast Saccharomyces cerevisiae and inferred causal relationships between ceramide species and their potential targets by combining lipidomic, genomic, and transcriptomic analyses. We found that during heat stress, distinct metabolic mechanisms controlled the abundance of different groups of ceramide species and provided experimental support for the importance of the dihydroceramidase Ydc1 in mediating the decrease in dihydroceramides during heat stress. Additionally, distinct groups of ceramide species, with different N-acyl chains and hydroxylations, regulated different sets of functionally related genes, indicating that the structural complexity of these lipids produces functional diversity. The transcriptional modules that we identified provide a resource to begin to dissect the specific functions of ceramides.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amidohydrolases / genetics
  • Amidohydrolases / metabolism
  • Ceramidases / genetics
  • Ceramidases / metabolism
  • Ceramides / chemistry
  • Ceramides / metabolism*
  • Cluster Analysis
  • Gene Expression Regulation, Fungal
  • Gene Ontology
  • Hot Temperature
  • Lipid Metabolism / genetics
  • Molecular Structure
  • Mutation
  • Oligonucleotide Array Sequence Analysis
  • Reverse Transcriptase Polymerase Chain Reaction
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • Signal Transduction*
  • Sphingolipids / chemistry
  • Sphingolipids / metabolism
  • Stress, Physiological / genetics
  • Systems Biology / methods*
  • Transcriptome / genetics


  • Ceramides
  • Saccharomyces cerevisiae Proteins
  • Sphingolipids
  • dihydroceramide
  • Amidohydrolases
  • alkaline dihydroceramidase, S cerevisiae
  • Ceramidases