The heat-shock response of Helicobacter pylori: genomic and molecular characterization of the master repressor HspR

The heat-shock response (HSR) induces the expression of heat-shock proteins, ensuring the bacterial cells to adapt to hostile environmental conditions during stress. In Helicobacter pylori, the regulation of the principal genes encoding the heat-shock proteins is under the transcriptional control of two repressor proteins named HspR and HrcA, with the former acting as the master regulator of the circuit. In order to further characterize the HspR regulon and deepen our understanding of HSR in H. pylori we used global transcriptome analysis in combination with Chromatin ImmunoPrecipitation of in vivo HspR genomic binding sites. These data showed that HspR is involved in the regulation of different cellular crucial functions directly controlling a limited set of target genes. Moreover, to provide further details on HspR-DNA interactions on its genomic targets we performed hydroxyl-radical footprinting experiments. This analysis revealed a peculiar periodic pattern of DNA protection. From a nucleotide sequence alignment of HspR binding sites, DNA sequences with similarities to the HAIR motif were identified. Through sitedirected mutagenesis we demonstrated in vitro that the HAIR-like motif is essential for the HspR binding to its own promoter region and that non-conserved nucleotides flanking the HAIR-like motif are necessary for the HspR complete binding on its operator sequence. An important role in resistance against environmental stresses is also played by the ATP-dependent caseinolytic proteases (Clp), a class of serine proteases involved in protein quality control as well as in degradation of regulatory proteins. In order to get more information about the role played by the Clp proteases in H. pylori and to directly identify their protein substrates, we implemented a strategy to express in vivo a proteolytic inactive form of ClpP, the catalytic subunit of this class of proteases, that will retain but not degrade substrates translocated into its proteolytic chamber.