Regulon and promoter analysis of theE. coliheat-shock factor, σ32, reveals a multifaceted cellular response to heat stress

Abstract

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 σ factor, σ³². To determine its role, we used genome-wide expression analysis and promoter validation to identify genes directly regulated by σ³² and screened ORF overexpression libraries to identify σ³² inducers. We triple the number of genes validated to be transcribed by σ³² 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 σ⁷⁰ holoenzyme initiates from 12% of σ³² 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 σ³² 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.