Figure 3
Overview of microarray analysis in the three mutants in the logarithmic (left) and stationary (right) phase of growth. (A) Venn diagrams showing numbers of genes differentially expressed in the indicated mutants and having at least a two-fold change with cut-off p ≤ 0.05 compared to the wild-type both in exponential and stationary phase. Numbers represent genes changed exclusively in one mutant, while the numbers in the intersections represent those occurring between each two or among all the three mutants. Pairwise numbers show genes regulated in one mutant. “+”: up-regulation; “-”: down-regulation. (B) Functional categories of regulated genes based on clusters of orthologous groups (COGs) both in exponential and stationary phase. Functional categories were determined using COG for D. shibae provided by IMG (http://img.jgi.doe.gov/). The bars represent the number of regulated genes within a given category. ctrA: red; cckA: green; chpT: blue. (Genes that were not assigned in COG are not included here but shown in Additional file 1: Table S1). (C) Sequence logo of the putative CtrA binding site in the D. shibae genome. This motif logo was plotted using Weblogo (weblogo.berkeley.edu). (D) Heat map showing gene expression of (anti-)sigma factors. The color bar represents the expression level in log2 scale. Red indicates relatively high expression levels; blue indicates relatively low expression levels. (E) A putative CtrA binding site located in the promoter region of rpoH 1 .