Acid-induced gene expression in Helicobacter pylori: Study in genomic scale by microarray

To understand the RNA expression in response to acid stress of Helicobacter pylori in genomic scale, a microarray membrane containing 1,534 open readi ng frames (ORFs) from strain 26695 was used. Total RNAs of H. pylori under growth conditions of pH 7.2 and 5.5 were extracted, reverse transcribed int o cDNA, and labeled with biotin. Each microarray membrane was hybridized wi th cDNA probe from the same strain under two different pH conditions and de veloped by a catalyzed reporter deposition method. Gene expression of all O RFs was measured by densitometry, Among the 1,534 ORFs, 53 ORFs were highly expressed (greater than or equal to 30% of rRNA control in densitometry ra tios). There were 445 ORFs which were stably expressed (<30% of rRNA in den sitometry) under both pH conditions without significant variation. A total of 80 ORFs had significantly increased expression levels at low pH, while e xpressions of 4 ORFs were suppressed under acidic condition. The remaining 952 ORFs were not detectable under either pH condition. These data were hig hly reproducible and comparable to those obtained by the RNA slot blot meth od. Our results suggest that microarray can be used in monitoring prokaryot ic gene expression in genomic scale.