Figure 2

A systematic screen for genes involved in Cu-dependent growth. (A) Schematic of the experimental workflow. A complete pool of homozygous deletion mutants and a smaller pool of respiration deficient strains (see Methods) were grown under respiratory conditions in the presence and absence of CuSO₄. Comparison of CuSO₄-treated and -untreated samples, identified 105 and 79 strains where Cu’s effect on growth was increased or decreased, respectively (see Methods). (B) Heatmap depicting log2 ratios of CuSO₄-treated and -untreated samples (see legend below) for the 184 strains identified in (A). Yellow indicates greater Cu-dependent growth and blue indicates reduced Cu-dependent growth. Dendrograms depict the results from hierarchical clustering of genes (y-axis) and experiments (x-axis). (C) Network illustrating overrepresented Gene Ontology categories (nodes) among the 105 strains with an enhanced response to copper. This gene list was analyzed, and the network image created, using the BiNGO plugin for Cytoscape [38] (see Methods). Representative nodes are circled and labelled with those genes identified in the screen. (D) Dotplots of log2-transformed microarray fluorescence intensities for a select set of deletion strains. Triplicate data points for YPD and the non-fermentable carbon source in which the greatest copper response was observed are shown for copper-treated (green) and -untreated (blue) conditions. YPE, YPG, and YPL refer to data from the complete homozygous deletion pool experiment; YPE* refers to the respiration defective pool.