FIG.1.

Hierarchical cluster analysis of gene expression changes in response to sodium acetate, sodium propionate, sodium chloride, and CCCP. Gene expression data from 27 microarray experiments (columns) and 179 genes (lines) are represented. Microarray experiments involved comparing gene expression by E. coli MG1655 on LB medium (reference) to gene expression 5 min (Ac_pulse_#I and II) and 50 min (Ac_50 min_#I to VI) after the addition of acetate, after adaptation to acetate (Ac_adapt_#I to IV), 5 min after the addition of propionate (Prop_pulse), after adaptation to propionate (Prop_adapt_#I to III), after adaptation to increased sodium chloride concentrations (NaCl_#I to III), and 5 min (CCCP_pulse_#I and II) and 3 h (CCCP_adapt_#I and II) after the addition of CCCP. Gene expression after the adaptation of MG1655 to acetate was compared directly to that after adaptation to propionate (Ac_vs_Prop_adapt_#I to III). Gene expression by the lrhA disruption strain IMW331 on LB medium (reference) was compared to gene expression after adaptation to acetate (Ac_adapt_delta_LrhA). Green indicates decreased RNA levels and red indicates increased RNA levels in the test culture compared to the reference culture. (A) Graph depicting the whole cluster (see the text for details). Subclusters 1 and 2 are highlighted in red, and subcluster 3 is highlighted in green. The scale bar indicates color coding of the RNA levels. (B to D) Subclusters 1 to 3, respectively, from panel A with corresponding gene names.