Genome-Wide Analysis of the General Stress Response Network in Escherichia coli: capital sigma super(S)-Dependent Genes, Promoters, and Sigma Factor Selectivity

The capital sigma super(S) (or RpoS) subunit of RNA polymerase is the master regulator of the general stress response in Escherichia coli. While nearly absent in rapidly growing cells, capital sigma super(S) is strongly induced during entry into stationary phase and/or many other stress conditions and is essential for the expression of multiple stress resistances. Genome-wide expression profiling data presented here indicate that up to 10% of the E. coli genes are under direct or indirect control of capital sigma super(S) and that capital sigma super(S) should be considered a second vegetative sigma factor with a major impact not only on stress tolerance but on the entire cell physiology under nonoptimal growth conditions. This large data set allowed us to unequivocally identify a capital sigma super(S) consensus promoter in silico. Moreover, our results suggest that capital sigma super(S)-dependent genes represent a regulatory network with complex internal control (as exemplified by the acid resistance genes). This network also exhibits extensive regulatory overlaps with other global regulons (e.g., the cyclic AMP receptor protein regulon). In addition, the global regulatory protein Lrp was found to affect capital sigma super(S) and/or capital sigma super(70) selectivity of many promoters. These observations indicate that certain modules of the capital sigma super(S)-dependent general stress response can be temporarily recruited by stress-specific regulons, which are controlled by other stress-responsive regulators that act together with capital sigma super(70) RNA polymerase. Thus, not only the expression of genes within a regulatory network but also the architecture of the network itself can be subject to regulation.