Humboldt-Universität zu Berlin - Mikrobiologie

Escherichia coli genes under the control of the general stress sigma factor σ^S (RpoS) identified by microarray analysis

A detailed description of the strains, procedures and microarrays used was published:

Weber, H., T. Polen, J. Heuveling, V. Wendisch, and R. Hengge (2005) Genome-wide analysis of the general stress response network in Escherichia coli: σ^S-dependent genes, promoters and sigma factor selectivity. J. Bacteriol. 187, 1591-1603.

Three different growth and stress conditions that are known to result in high cellular σ^S levels were used for RNA preparation:

1. growth in LB medium to an OD578 of 4.0 (this corresponds to transition into stationary phase);
2. growth in minimal medium to which 0.3 M NaCl was added at an OD578 of 0.3 (cells were harvested 20 min after this hyperosmotic shift);
3. growth in LB medium which was acidified by the addition of MES at an OD578 of 0.4 (cells were harvested 40 min after this shift to pH5).

We identified a total of 481 genes, which exhibited more than two-fold higher expression in the rpoS+ strain than in the rpoS mutant (Fig. 1). Only 140 of these positively σ^S-controlled genes were found under all three growth and stress conditions (Fig. 1). These genes are refer to as the “core” set of σ^S-controlled genes. The other 341 genes revealed their σ^S-dependence only under one or two of the growth and stress conditions used (with genes in all possible combinatorial groups; Fig. 1). The table shows expression ratios for rpoS+ and rpoS- strains of all σ^S-controlled genes (not only “core“ genes).