Ge et al. BMC Genomics 2010, 11:456 http://www.biomedcentral.com/1471-2164/11/456 Table 1 The leading genes that were differentially expressed between the two cell lines Name ssaN ssaO ssaR ssaS ssaV sscA sse I sspH2 dnaE gyrA gyrB cyoC cyoD nuoJ nuoK nuoM nuoN glnG glnL glnA gltB gltD aceF fruA fruF pykF pstC Genbank AAL20339 AAL20340 AAL20343 AAL20344 AAL20338 AAL20323 AAL19985 AAL21143 AAL19195 AAL21173 AAL22694 AAL19396 AAL19395 AAL21221 AAL21220 AAL21218 AAL21217 AAL22844 AAL22845 AAL22846 AAL22199 AAL22200 AAL19117 AAL21108 AAL21110 AAL20302 AAL22714 Function and product Secretion system apparatus Secretion system apparatus Secretion system apparatus Secretion system apparatus Secretion system apparatus Secretion system apparatus Gifsy-2 prophage; putative type III secreted protein Leucine-rich repeat protein, induced by the SPI-2 regulator ssrA/B DNA polymerase III, alpha subunit DNA gyrase, subunit A, type II topoisomerase DNA gyrase, subunit B, type II topoisomerase Cytochrome o ubiquinol oxidase subunit III Cytochrome o ubiquinol oxidase subunit IV NADH dehydrogenase I chain J NADH dehydrogenase I chain K NADH dehydrogenase I chain M NADH dehydrogenase I chain N Response regulator in two-component regulatory system with GlnL (EBP family) Sensory kinase (phosphatase) in two-component regulatory system with GlnG Glutamine synthetase Glutamate synthase, large subunit Glutamate synthase, small subunit Pyruvate dehydrogenase, dihydrolipoyltransacetylase component Sugar specific PTS system, fructose-specific transport Phosphoenolpyruvate-dependent sugarphosphotransferase system, EIIA Pyruvate kinase I (formerly F), fructose stimulated ABC superfamily (membrane), high affinity phosphate Page 5 of 13 Fold changesa 3.97 2.23 4.09 3.25 2.56 2.93 4.67 3.89 2.68 2.09 2.39 3.52 3.50 2.19 2.42 2.39 2.27 2.88 2.41 2.53 2.21 2.18 2.66 3.05 2.67 3.33 0.48 a FDR (P-value < 0.05) was set up during microarray data analysis. antibacterial activity but serves as a precursor for more toxic substrates, such as hydrogen peroxide and hydro- xyl radicals [40]. Compared to those grown in HLA-A2 cells, Salmonella grown in HLA-B27 cells showed increased expression of SPI-2 genes including ssaN, ssaO, ssaR, ssaS, ssaV, sscA, sseI and sspH2 (Additional file 1: Supplemental Table S6-1). SPI-2 deficient mutants have impaired ability to grow in macrophages but are able to survive and are virulent within gp91phox knock- out mice [39]. Patients with X-linked gp91phox muta- tions (chronic granulomatous disease, CGD) or gp91phox knockout mice that are unable to produce ROS are extremely susceptible to bacterial infection, including those caused by salmonellae [41,42]. Taken together, these findings indicated that SPI-2 is required for survival in the presence of ROS. The up-regulation of SPI-2 genes in HLA-B27 cells contributed to the increased intracellular growth and replication of Salmonella. Intracellular growth of Salmonella SPI-2 mutants affected by HLA-B27 To verify the significance of SPI-2 genes in Salmonella replication in HLA-B27 cells, three genes most markedly up-regulated in HLA-B27 cells - ssaN, ssaR and sspH2 - were deleted; ssaN and ssaR belong to the SPI-2 secre- tion apparatus and sspH2 is an effector gene. The intra- cellular growth of the mutants was compared with that of wild-type S. Enteritidis PT4 KS8822/88. Mutation of ssaR dramatically impaired intracellular Salmonella growth in HLA-B27 cells, decreasing it 19-fold at the 8 h and 33-fold at the 24 h time points (Figure. 5A). It has previously been shown that ΔssaR mutants cannot grow intracellularly in murine macrophages or form the elongated Salmonella-induced filaments (Sifs) in epithe- lial cells [43] required for the formation of Salmonella- containing vacuoles (SCV) [44]. The formation and maintenance of SCV promotes the survival and prolif- eration of bacteria in macrophages [45] and the lack of