title: qPCA: a scalable assay to measure the perturbation of protein-protein interactions in living cells.
abstract: One of the most important challenges in systems biology is to understand how cells respond to genetic and environmental perturbations. Here we show that the yeast DHFR-PCA, coupled with high-resolution growth profiling (DHFR-qPCA), is a straightforward assay to study the modulation of protein-protein interactions (PPIs) in vivo as a response to genetic, metabolic and drug perturbations. Using the canonical Protein Kinase A (PKA) pathway as a test system, we show that changes in PKA activity can be measured in living cells as a modulation of the interaction between its regulatory (Bcy1) and catalytic (Tpk1 and Tpk2) subunits in response to changes in carbon metabolism, caffeine and methyl methanesulfonate (MMS) treatments and to modifications in the dosage of its enzymatic regulators, the phosphodiesterases. Our results show that the DHFR-qPCA is easily implementable and amenable to high-throughput. The DHFR-qPCA will pave the way to the study of the effects of drug, genetic and environmental perturbations on in vivo PPI networks, thus allowing the exploration of new spaces of the eukaryotic interactome.
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada.
authors.forename: Luca
authors.initials: L
authors.lastname: Freschi
authors.forename: Francisco
authors.initials: F
authors.lastname: Torres-Quiroz
authors.forename: Alexandre K
authors.initials: AK
authors.lastname: Dubé
authors.forename: Christian R
authors.initials: CR
authors.lastname: Landry
mesh_terms: D000465:Algorithms; D000818:Animals; D017868:Cyclic AMP-Dependent Protein Kinases / Q000235:genetics / Q000378:metabolism; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D005816:Genetic Complementation Test / Q000379:methods; D055442:Metabolome / Q000187:drug effects / Q000235:genetics; D008727:Methotrexate / Q000494:pharmacology; D051379:Mice; D025941:Protein Interaction Mapping / Q000379:methods*; D015398:Signal Transduction / Q000187:drug effects / Q000235:genetics; D049490:Systems Biology / Q000379:methods*; D013762:Tetrahydrofolate Dehydrogenase / Q000235:genetics / Q000378:metabolism*; D015003:Yeasts / Q000166:cytology / Q000235:genetics / Q000378:metabolism
chemical_list: D005656:Fungal Proteins; D013762:Tetrahydrofolate Dehydrogenase; D017868:Cyclic AMP-Dependent Protein Kinases; D008727:Methotrexate