Regulon and promoter analysis of the E-coli heat-shock factor, σ32, reveals a multifaceted cellular response to heat stress

The heat-shock response (HSR), a universal cellular response to heat, is crucial for cellular adaptation. In Escherichia coli, the HSR is mediated by the alternative sigma factor, sigma(32). To determine its role, we used genome-wide expression analysis and promoter validation to identify genes directly regulated by sigma(32) and screened ORF overexpression libraries to identify sigma(32) inducers. We triple the number of genes validated to be transcribed by sigma(32). and provide new insights into the cellular role of this response. Our work indicates that the response is propagated as the regulon encodes numerous global transcriptional regulators, reveals that sigma(70) holoenzyme initiates from 12% of sigma(32) promoters, which has important implications for global transcriptional wiring, and identifies a new role for the response in protein homeostasis, that of protecting complex proteins. Finally, this study suggests that the response protects the cell membrane and responds to its status: Fully 25% of sigma(32) regulon members reside in the membrane and alter its functionality; moreover, a disproportionate fraction of overexpressed proteins that induce the response are membrane localized. The intimate connection of the response to the membrane rationalizes why a major regulator of the response resides in that cellular compartment.