Distinct Signaling Roles of Ceramide Species in Yeast Revealed Through Systematic Perturbation and Systems Biology Analyses
Unraveling Ceramide Signaling Specificity
The extensive biochemical complexity of the ceramide class of lipids, with more than 30 species in yeast and hundreds in mammals, creates challenges for discerning the specific functions of individual species of ceramide or subgroups of these lipids. Montefusco et al. took a systems biology approach to tackle the functional complexity of ceramide-regulated events in yeast using a biosynthetic inhibitor to limit the number of species produced. The authors clustered changes in lipid abundance with functionally related transcriptional changes in yeast subjected to heat stress to identify changes in gene expression that correlated with specific classes of ceramides. Mapping of the lipid-correlated transcriptional profiles to transcription factors identified putative transcriptional modules regulated by changes in ceramide abundance, and two of these modules were experimentally verified in yeast. Thus, this approach and the data set will help unravel specificity in ceramide-mediated regulatory events.
Abstract
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.
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Supplementary Material
Summary
Fig. S1. The effect of myristate on the lipidomic profile, including the effect on sphingoids.
Fig. S2. Validation of lipid-specific growth phenotypes in triplicate.
Table S1. Lipidomics data under all combinations of treatments (xlxs).
Table S2. Microarray data heat stress (xlxs).
Table S3. Microarray data under all combinations of treatments (xlxs).
Table S4. List of lipid-gene pairs showing significant association measured by MIC (xlxs).
Table S5. List of lipid-gene pairs showing significant Pearson correlations (xlxs).
Table S6. List of lipid-gene pairs showing significant associations measured using Bayesian regression (xlxs).
Table S7. All treatments tested for fatty acid–specific growth defects.
Table S8. Yeast strains used in this study.
Resources
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Information & Authors
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Published In
Science Signaling
Volume 6 | Issue 299
October 2013
October 2013
Copyright
Copyright © 2013, American Association for the Advancement of Science.
Submission history
Received: 15 July 2013
Accepted: 10 October 2013
Acknowledgments
We acknowledge the Medical University of South Carolina (MUSC) Lipidomics facility as well as the MUSC ProteoGenomics facility for their services. We would also like to thank L. A. Cowart for commenting on the manuscript and C. Mao for providing the plasmid overexpressing YDC1 and for his suggestions and comments. Funding: This work is partially supported by NIH grants R01LM 010144, R01LM011155 (X.L.), R01LM010020 (G.F.C.), and R01GM063265 (Y.A.H.). Author contributions: Y.A.H. and X.L. conceived and directed the study; D.J.M., N.M., and B.N. performed yeast experiments, lipidomics, microarray data collection, and yeast validation experiments; L.C., S.L., G.F.C., and X.L. performed data analysis and modeling; and D.J.M., L.C., N.M., X.L., and Y.A.H. drafted and edited the manuscript. Competing interests: The authors declare that they have no competing interests. Data and materials availability: Data are available as supplementary tables and from http://www.dbmi.pitt.edu/publications/YeastCeramideSignaling.
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