Characterization of the low-pH responses of Helicobacter pylori using genomic DNA arrays

Helicobacter pylori is unique among bacterial pathogens in its ability to i n the acidic environment of the human stomach. To identify H. pylori genes responsive to low pH, the authors assembled a high-density array of PCR-amp lified random genomic DNA. Hybridization of radiolabelled cDNA probes, prep ared using total RNA from bacteria exposed to buffer at either pH 4(.)0 or pH 7(.)0, allowed both qualitative and quantitative information on differen tial gene expression to be obtained. A previously described low-pH-induced gene, cagA, was identified together with several novel genes that may have relevance to the survival and persistence of H. pylori in the gastric envir onment. These include genes encoding enzymes involved in LPS and phospholip id synthesis and secF, encoding a component of the protein export machinery . A hypothetical protein unique to H. pylori (HP0681) was also found to be acid induced. Genes down-regulated at pH 4(.)0 include those encoding a sug ar nucleotide biosynthesis protein, a flagellar protein and an outer-membra ne protein. Differential gene expression was confirmed by total RNA slot-bl ot hybridization.