Convergence of molecular, modeling, and systems approaches for an understanding of the Escherichia coli heat shock response

Abstract

The heat shock response (HSR) is a homeostatic response that maintains the proper protein-folding environment in the cell. This response is universal, and many of its components are well conserved from bacteria to humans. In this review, we focus on the regulation of one of the most well-characterized HSRs, that of Escherichia coli. We show that even for this simple model organism, we still do not fully understand the central component of heat shock regulation, a chaperone-mediated negative feedback loop. In addition, we review other components that contribute to the regulation of the HSR in E. coli and discuss how these additional components contribute to regulation. Finally, we discuss recent genomic experiments that reveal additional functional aspects of the HSR.

FIG. 1.

Activation and repression of the HSR during temperature upshift and downshift. (A) Activation of the HSR during a temperature shift from 30 to 42°C reveals three distinct phases: induction, adaptation, and steady state. (B) Repression of the HSR during a temperature shift from 42° to 30°C. The relative σ³² activities measured by HSP synthesis are shown by the solid lines; relative σ³² levels measured by Western blotting analysis are shown by the dotted lines.

FIG. 2.

Wiring diagram of σ³² regulation. There are three primary modes of regulation as follows: (i) excess free DnaK/J and GroEL/S chaperones directly bind to and inactivate σ³²; (ii) the FtsH protease degrades σ³², with chaperones participating in this process; and (iii) temperature directly controls the rate of σ³² translation. Misfolded proteins titrate chaperones from these regulatory roles, allowing active σ³² to increase the synthesis of chaperones and proteases during conditions where they are needed.

FIG. 3.

The domain structure of σ³². A schematic map reveals the domain structure and conserved regions of σ³². Note that domains are divided into subdomains as follows: domain 2 is comprised of subdomains 1.2 to 2.4 and encompasses amino acids 16 to 126, domain 3 is comprised of subdomains 3.1 and 3.2 and encompasses amino acids 127 to 177, and domain 4 is comprised of subdomains 4.1 and 4.2 and encompasses amino acids 213 to 280. The RpoH box is comprised of amino acids 132 to 141. Regions that bind RNA polymerase and promoter DNA are shown below the schematic; features specific to σ³² are indicated above the schematic. “Activity/stability mutants” marks the position of mutations in σ³² that affect the stability and/or activity of σ³².

FIG. 4.

Modeling the HSR. (A) A simple open-loop design containing only a feed-forward element that senses temperature. (B) A closed-loop design with feed-forward and inactivation loops. (C) A full model containing feed-forward, inactivation, and degradation loops. (Reprinted from reference with permission of the publisher. Copyright 2005 National Academy of Sciences, U.S.A.)

FIG. 5.

Functions of the HSR. The induction of σ³² and protein products of the target heat shock (hs) genes are shown in a model of the E. coli cell, illustrating the compartmentalization of the response. (A) The σ³² regulon protects many cytoplasmic molecules and processes, including transcription factors. The environmental cues that regulate the transcription factors are indicated next to the curved brace. (B) The σ³² regulon also protects cytoplasmic membranes and inner membrane proteins. Note that the overexpression of many inner membrane proteins also induces the σ³² response.