We investigated the global landscape of Ca²⁺ homeostasis in budding yeast based on high-dimensional chemical-genetic interaction profiles. The morphological responses of 62 Ca²⁺-sensitive (cls) mutants were quantitatively analyzed with the image processing program CalMorph after exposure to a high concentration of Ca²⁺ After a generalized linear model was applied, an analysis of covariance model was used to detect significant Ca²⁺-cls interactions. We found that high-dimensional, morphological Ca²⁺-cls interactions were mixed with positive (86%) and negative (14%) chemical-genetic interactions, whereas one-dimensional fitness Ca²⁺-cls interactions were all negative in principle. Clustering analysis with the interaction profiles revealed nine distinct gene groups, six of which were functionally associated. In addition, characterization of Ca²⁺-cls interactions revealed that morphology-based negative interactions are unique signatures of sensitized cellular processes and pathways. Principal component analysis was used to discriminate between suppression and enhancement of the Ca²⁺-sensitive phenotypes triggered by inactivation of calcineurin, a Ca²⁺-dependent phosphatase. Finally, similarity of the interaction profiles was used to reveal a connected network among the Ca²⁺ homeostasis units acting in different cellular compartments. Our analyses of high-dimensional chemical-genetic interaction profiles provide novel insights into the intracellular network of yeast Ca²⁺ homeostasis.

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Ghanegolmohammadi F, Yoshida M, Ohnuki S, Sukegawa Y, Okada H, Obara K, Kihara A, Suzuki K, Kojima T, Yachie N, ... Show all

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