5 fold) in the fluoroquinolone-resistant strains. The altered genes with known functions that were affected in both strains as the results of fluoroquinolone resistance selection are grouped in Tables 1, 2, 3 according to the classification used by the Institute for Genomic Research (http://​www.​jcvi.​org/​). In addition, the microarray detected alterations of many genes, for which the function is not known, which are listed as hypothetical proteins in the GenBank. Some of these were upregulated manyfold in both resistant strains, especially in 13124R. The genes that were differentially affected in the resistant strains are shown in Table 1. Many of

these genes were generally upregulated in NCTRR and downregulated in 13124R. The common genes that were upregulated in one or both mutants are in Table 2 and those that were downregulated in both are in Table 3. Some genes involved in amino acid biosynthesis, protein ABT-263 molecular weight synthesis, fatty acid synthesis, and phospholipid metabolism were mostly upregulated in 13124R. Some genes for putative membrane proteins were upregulated in either one (Table 1) or both mutants (Table 2). The ATP synthase and potassium transporter genes were upregulated in both mutants (Table 2). Some of the genes involved in purine, pyrimidine,

nucleotide, and nucleoside transport and metabolism were selleckchem upregulated in both mutants and some were downregulated in both mutants (Tables 2 and 3). Several transcriptional regulators, transporters and kinases also were downregulated in one or both mutants (Tables 1 and 3). Resistance selection also affected the expression of

genes involved in virulence (phospholipase C, perfringolysin O, collagenase, hemolysin III and α-clostripain). Surprisingly, these genes were upregulated in strain NCTRR and downregulated in strain 13124R. Table 1 Microarray and qRT-PCR analysis of the genes that were differentially affected in the gatifloxacin resistant mutants, NCTR R and 13124 R Gene ID and name Function Microarray qRT-PCR     mt/wt mt/wt     NCTR ATCC 13124 NCTR ATCC 13124 Cell envelope CPE1089 CPF_1345 putative membrane protein 4.3 −2.1 7.3 −2.8 CPE0162 CPF_0155 (pfoR) putative membrane protein 2.6 −4.0 3.3 −3.5 CPE0251 CPF_0244 putative lipoprotein 5.0 −2.4 2.0 −3.5 CPE0278 CPF_0274 (sagA) Cell Penetrating Peptide sagA protein 1.1 −2.4 4.7 −2.6 CPE0714 CPF_0710 putative monogalactosyl-diacylglycerol synthase 2.4 −2.4 7.6 6.3 Cellular processes CPE0036 CPF_0042 (plc) phospholipase C 4.8 −6.8 1.9 −3.3 CPE0846 CPF_0840 (cloS1) α-clostripain 17.3 −15.6 8.3 −1143 CPE1474 CPF_1725 (hlyC) hemolysin III 3.2 −1.8 15.1 −2.6 CPE0163 CPF_0156 (pfoA) perfringolysin O 3.6 −71.4 6.4 −462 CPE0782 CPF_0784 (ahpC) alkyl hydroperoxide reductase-C subunit 10.3 −2.6 13.4 −12.6 CPE1092 CPF_1348 (pac) choloylglycine hydrolase family protein 1.7 −2.5 25.7 −1.7 Energy metabolism CPE0778 CPF_0780 oxidoreductase, FDA-binding 4.8 −2.8 85 2.6 CPE1299 CPF_1505 (eno) enolase 3.5 −1.6 11.9 −1.9 CPE2058 CPF_2315 (gadB) glutamate decarboxylase 31.9 −3.