FIG. 3.

DNA macroarray analysis of pH-responsive gene expression. One hundred one putative pH-responsive genes were identified based on array analyses of wild-type strain J99, grown at pH 7.0 and pH 5.0. Scatterplots depict expression of these 101 genes in the wild-type strain and three isogenic mutant strains, each grown at pH 7.0 and pH 5.0. Mean normalized signal intensities for the 101 genes are shown. Mean normalized signal intensities for 1,681 genes on the arrays are represented by the diagonal lines. Differential expression of a given gene at pH 5.0 versus pH 7.0 is reflected by deviation of a point from the diagonal line. The variance in pH 5/pH 7 expression ratios was higher in the wild-type strain (top left panel) than in the HP0165 or HP1364 mutant strains (variance of 1.2 versus 0.4 and 0.4, respectively). Coordinates representing expression of ureA and HP1432 are indicated.