Thermogenetic tools to monitor temperature-dependent gene expression in bacteria.

Free-living bacteria constantly monitor their ambient temperature. Drastic deviations elicit immediate protective responses known as cold shock or heat shock response. Many mammalian pathogens use temperature surveillance systems to recognize the successful invasion of a host by its body temperature, usually 37°C.

Multiple layers of control govern expression of the Escherichia coli ibpAB heat-shock operon.

The Escherichia coli ibpAB operon encodes two small heat-shock proteins, the inclusion-body-binding proteins IbpA and IbpB. Here, we report that expression of ibpAB is a complex process involving at least four different layers of control, namely transcriptional control, RNA processing, translation control and protein stability. As a typical member of the heat-shock regulon, transcription of the ibpAB operon is controlled by the alternative sigma factor σ(32) (RpoH).

The Escherichia coli ibpA thermometer is comprised of stable and unstable structural elements.

Translation of many small heat shock genes in alpha- and gamma-proteobacteria is controlled by the ROSE (Repression Of heat Shock gene Expression) element, a thermo-responsive RNA structure in the 5'-untranslated region. ROSE(ibpA) regulates translation of the Escherichia coli ibpA gene coding for an inclusion body-associated protein. We present first structural insights into a full-length ROSE element by examining the temperature-induced conformational changes of ROSE(ibpA) using detailed enzymatic and lead probing experiments between 20 and 50 degrees C.

Genome-wide bioinformatic prediction and experimental evaluation of potential RNA thermometers.

Only recently, the fundamental role of regulatory RNAs in prokaryotes and eukaryotes has been appreciated. We developed a pipeline from bioinformatic prediction to experimental validation of new RNA thermometers. Known RNA thermometers are located in the 5'-untranslated region of certain heat shock or virulence genes and control translation by temperature-dependent base pairing of the ribosome binding site.