The lack of one regulatory player can SIS3 deregulate the whole flagellar biosynthetic cascade and alter motility in H. pylori. Since ablation of the HP0256 gene reduced motility, we investigated BMS907351 the effect of HP0256 mutation upon the expression of the flagellar regulon using global transcript analysis. Array analysis was performed in quadruplicate, including a dye-swap. Five genes were selected to confirm the reliability of our microarray data by qRT-PCR. Transcriptional level of hpn was unchanged in the HP0256 mutant and was therefore used a control for qRT-PCR. The fold changes thus established were in good agreement

with the array data (Figure 6). The difference observed in fold-changes of flgE transcription between array data and qRT-PCR is due to the microarray analysis method used for the study. This method tends to attenuate the dispersion of the fold-changes compared to the overall signal on the slide. Figure 6 Confirmation of transcriptional PR171 changes in selected flagellar genes in the HP0256 mutant using qRT-PCR. Fold changes and standard deviations were calculated using the era transcript abundance as reference. qRT-PCRs were performed on at least two biological replicates. A total of forty six genes had altered expression levels in the

HP0256 mutant. Nineteen genes were significantly up-regulated and twenty seven genes down-regulated in the HP0256 mutant compared to the wild-type strain (Table 1). Data for some biologically relevant genes, below the two-fold cut-off, are also included in Table 1. Among the differentially expressed genes, seventeen encode proteins associated with the membrane. Table 1 Gene list of significantly up- and down-regulated

genes in the HP0256 mutant based on the array experiment. TIGR orf no. Putative gene product (gene) Expression ratio p-value Down-regulated genes: Hp26695-0092 type II restriction enzyme M protein (hsdM) 0.15 0.02 HpJ99-1132 dimethyladenosine transferase 0.17 0.00 Hp26695-0093 Doxorubicin solubility dmso alpha-2-fucosyltransferase 0.22 0.01 Hp26695-0229 outer membrane protein (omp6) ( hopA ) 0.24 0.01 Hp26695-0492 flagellar sheath associated protein ( hpaA3 ) 0.26 0.00 Hp26695-1210 serine acetyltransferase (cysE) 0.26 0.00 Hp26695-1587 conserved hypothetical protein 0.27 0.00 Hp26695-1208 ulcer associated adenine specific DNA methyltransferase 0.27 0.00 Hp26695-0610 toxin-like outer membrane protein 0.32 0.03 Hp26695-1207 hypothetical protein 0.34 0.01 HpJ99-0055 putative 0.35 0.03 Hp26695-1211 hypothetical protein 0.37 0.00 Hp26695-0430 hypothetical protein 0.40 0.04 Hp26695-1492 conserved hypothetical nifU-like protein 0.41 0.01 Hp26695-0805 lipooligosaccharide 5G8 epitope biosynthesis-associated protein 0.42 0.02 Hp26695-1203a Preprotein translocase subunit SecE 0.43 0.01 Hp26695-1219 hypothetical protein 0.43 0.04 Hp26695-0711 hypothetical protein 0.45 0.01 Hp26695-1180 pyrimidine nucleoside transport protein (nupC) 0.46 0.