The DNA-Binding Protein HU has a Regulatory Role in the Acid Stress Response Mechanism in Helicobacter pylori

Abstract

Background: Bacterial genomes are compacted by association with histonelike proteins to form a complex known as bacterial chromatin. The histonelike protein HU is capable of binding and bending the DNA molecule, a function related to compaction, protection, and regulation of gene expression. In Helicobacter pylori, HU is the only histone-like protein described so far. Proteomic analysis from our laboratory showed that this protein is overexpressed under acidic stress. Materials and Methods: We used a purified recombinant wild-type protein and two mutant proteins with the amino acid substitutions K3A/S27D and K62R/V63N/P64A to characterize the function of the N-terminal domain and the flexible arm of HU. Results: In vitro assays for DNA protection, bending, and compaction were performed. We also designed a H. pylori hup::cat mutant strain to study the role of HU in the acid stress response. HUwt protein binds DNA and promotes its bending and compaction. Compared with the wild-type protein, both mutant proteins have less affinity for DNA and an impaired bending and compaction ability. By using qRT-PCR, we confirmed overexpression of two genes related to acid stress response (ureA and speA). Such overexpression was abolished in the hup::cat strain, which shows an acid-sensitive phenotype. Conclusions: Altogether, we have shown that HUwt–DNA complex formation is favored under acidic pH and that the complex protects DNA from endonucleolytic cleavage and oxidative stress damage. We also showed that the amino-terminal domain of HU is relevant to DNA–protein complex formation and that the flexible arm of HU is involved in the bending and compaction activities of HU.