The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation
Figure 9
Gene Expression of D. vulgaris Expansions
Gene expression profiles across a compendium of experimental stress response conditions (NaCl, heat shock, cold shock, nitrite, and oxygen) were monitored using DNA microarrays, and shown next to a phylogenetic NJ tree (with 1,000 bootstraps, generated using the MEGA3 software package [28]) of all HPK domains in D. vulgaris. Blue colors indicate down-regulated genes (relative to unperturbed cells), and red colors indicate up-regulated genes. No significant excess correlation in gene expression was observed for genes within each cluster (compared with randomly chosen pairs of genes) using a Student's t-test to compare mean correlations or the Kolmogorov-Smirnov test to compare distributions. The domain structure of each gene in the three LSEs is shown to the right. Gene names are provided for all genes, and MicrobesOnline accession numbers are provided in parentheses for genes in each of the major clusters for comparison with Figure 8. Bootstrap values are provided for each of the major clusters, and the amino acid sequence of the “H-Box” motif for genes in each cluster is shown. A more detailed description of the experiments performed is given in Methods.