A yeast phenomic model for the gene interaction network modulating F508del-CFTR protein biogenesis

To gain insight into the function and evolutionary conservation of a gene interaction network that regulates biogenesis of a misfolded ABC-transporter, we employed yeast genetics to develop a "phenomic" model, in which the F508del-CFTR-equivalent residue of a yeast homolog is mutated (F670del-Yor1), and where the genome is scanned quantitatively for interaction. We first confirmed that F670del-Yor1 undergoes protein misfolding and had reduced half-life, analogous to F508del-CFTR. Gene interaction was then assessed quantitatively by growth curves for all ~5000 double mutants, based on alteration in the dose response to growth inhibition by oligomycin, a toxin extruded from the cell at the plasma membrane by Yor1.From a comparative genomic perspective, yeast gene interaction influencing F670del-Yor1 biogenesis was representative of human homologs previously found to modulate processing of F508del-CFTR in mammalian cells. Additional evolutionarily conserved pathways were implicated by the study, and an F670del-Yor1-specific pro-biogenesis function of the recently discovered ER Membrane Complex (EMC) was evident from the yeast screen. This novel function was validated biochemically by siRNA of an EMC ortholog in a human cell line expressing F508del-CFTR. The precision and accuracy of quantitative high throughput cell array phenotyping (Q-HTCP), which captures tens of thousands of growth curves simultaneously, provided powerful resolution to measure gene interaction on a phenomic scale, based on discrete cell proliferation parameters.We propose phenomic analysis of F670del-Yor1 as a model for investigating gene interaction networks that can modulate cystic fibrosis disease severity. Although the clinical relevance of the F670del-Yor1 gene interaction network for cystic fibrosis remains to be defined, the model appears to be informative with respect to human cell models of F508del-CFTR. Moreover, the general strategy of yeast phenomics can be employed in a systematic mann