Systems biological analysis of osmotically induced gene expression in C. elegans

An integrated genomic understanding of the mechanisms by which animal cells sense osmotic stress and regulate osmosensitive gene expression is lacking. C. elegans provides a number of experimental advantages for developing a systems biological level description of osmosensitive gene expression. Using genome‐wide microarrays, we identified 372 genes that exhibit robust transcriptional regulation following exposure to hyperosmotic stress. Transgenic worms expressing GFP reporters for three upregulated genes show increased GFP expression under hypertonic conditions. One of these genes, gpdh‐1 , catalyzes the rate‐limiting step in biosynthesis of the compatible organic osmolyte glycerol. gpdh‐1::GFP reporter worms express GFP only following exposure to hyperosmotic environments. We inhibited the expression of ~16,000 genes by RNAi feeding methods and identified 105 gene inactivations that cause constitutive expression of the gpdh‐1 reporter in the absence of hyperosmotic stress. Integration of our RNAi and gene expression data with the genome‐wide C. elegans protein‐protein interaction map revealed a highly interconnected network of 371 genes that is enriched for proteins involved in protein homeostasis. These included genes required for protein degradation, folding, and synthesis. We propose that disruption of protein homeostasis, which is a major consequence of hyperosmotic stress, activates osmosensitive gene expression. We are currently using RNAi methods to test the functional significance of this gene network in the cellular osmotic stress response.