Stable isotope labeling by amino acids combined with mass spectrometry is a widely used methodology to quantitatively examine metabolic and signaling pathways in yeast, fruit flies, plants, cell cultures and mice. We have recently shown that C. elegans can be completely labeled with heavy-labeled lysine by feeding worms on prelabeled lysine auxotroph Escherichia coli for just one generation, and used this combined with high resolution mass spectrometry to identify novel genes regulated by nuclear hormone receptor 49 (Fredens et al., 2011, Nature Methods). We have used this methodology to examine how the multicellular organism C. elegans responds to knock down of SBP-1, a basic helix-loop-helix (bHLH) transcription factor homologous to the mammalian Sterol Regulatory Element Binding Proteins (SREBP), which is known as a master regulator of expression of lipogenic genes in eukaryotes. We have identified and quantified several thousands proteins, and among these identified several proteins that either become up-or down regulated in response to RNAi against SBP-1. As expected, several of the down-regulated proteins we identified are involved in the biosynthesis of fatty acids and glycerolipids, however, our results also indicate that SBP-1 regulate the transcription of genes involved in ceramide synthesis. Additionally, we identified a large number of proteins involved in nucleotide-, carbohydrate- and amino acid metabolism to be down regulated upon SBP-1 knock down, which is paralleled by changes in cellular metabolites determined by metabolomics and lipidomics. Collectively, our findings suggest that SBP-1/SREBP not only regulate the expression of lipogenic genes, but also the expression of other biosynthetic pathways. We therefore hypothesize that SBP-1 is a general transcriptional regulator of biosynthetic pathways in C. elegans.
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