title: 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 histone-like proteins to form a complex known as bacterial chromatin. The histone-like 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.
  
  
  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.
authors.affiliation: Department of Molecular and Cellular Biology, Laboratory of Molecular Microbiology, ICBM, Faculty of Medicine, University of Chile, Avda. Independencia, 1027, Santiago, Chile.
authors.forename: Oscar
authors.initials: O
authors.lastname: Almarza
authors.forename: Daniel
authors.initials: D
authors.lastname: Núñez
authors.forename: Hector
authors.initials: H
authors.lastname: Toledo
mesh_terms: D000143:Acids / Q000633:toxicity*; D001426:Bacterial Proteins / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D004247:DNA / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D020869:Gene Expression Profiling; D005798:Genes, Bacterial; D016480:Helicobacter pylori / Q000187:drug effects* / Q000502:physiology*; D006863:Hydrogen-Ion Concentration; D050505:Mutant Proteins / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D011485:Protein Binding; D013312:Stress, Physiological
chemical_list: D000143:Acids; D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D050505:Mutant Proteins; C040330:histone-like protein HU, bacteria; D004247:DNA
keywords: Acidic condition; DNA; DNA damage; protein; proteome