Supplemental table 1: Summary of microarray experiments Arithmetic mean of mRNA fluorescence signals, expressed as a ratio against the control channel C A L B l e e M n v E a e r r l b T / n n e t m o o i i o m e t r s s a p n P s i m e i n r s e s s a c r s n s F i s p m a a R l e x D w r o d T E S C D S O SA0001 P49994 Chromosomal replication initiator protein dnaA 1.5 0.10 L 0 SA0002 P50029 DNA polymerase III, beta chain (EC 2.7.7.7) 1.3 0.09 L 0 Hypothetical protein SAV0003 (Hypothetical protein SA0003 Q99XG7 MW0003) 0.9 0.10 S 0 SA0004 P29232 DNA replication and repair protein recF 1.1 0.10 L 0 SA0005 Q99XG6 DNA gyrase subunit B (EC 5.99.1.3) 1 0.09 L 0 SA0006 Q99XG5 DNA gyrase subunit A (EC 5.99.1.3) 1.9 0.10 L 0 SA0007 Q99XG4 Hypothetical protein SAV0007 2.3 0.22 G 0 SA0008 Q99XG3 Histidine ammonia-lyase (EC 4.3.1.3) (Histidase) 3.5 0.31 E 0 Seryl-tRNA synthetase (EC 6.1.1.11) (Serine--tRNA ligase) SA0009 P99178 (SerRS) 1 0.15 J 0 SA0010 Q99XG1 Hypothetical protein SAV0010 0.7 0.11 E 7 SA0010.1 Q99XG0 Hypothetical protein SAV0011 0.5 0.02 S 0 SA0011 Q99XF9 Hypothetical protein SAV0012 0.7 0.13 E 0 SA0012 Q99XF8 Hypothetical protein SAV0013 0.6 0.13 S 7 SA0013 Q99XF7 Hypothetical protein SAV0014 0.9 0.10 T 2 SA0014 Q99XF6 50S ribosomal protein L9 2 0.11 J 0 SA0015 Q99XF5 Replicative DNA helicase 1.3 0.11 L 0 Adenylosuccinate synthetase (EC 6.3.4.4) (IMP--aspartate SA0016 Q99XF4 ligase) (AdSS) (AMPSase) 0.7 0.14 F 0 SA0017 Q99XF3 Response regulator 1.5 0.09 T 0 Histidine kinase YYCG (TWO-component sensor histidine SA0018 Q9XCM6 kinase) 0.7 0.14 T 2 SA0019 Q99XF2 Hypothetical protein SAV0020 0.9 0.10 S 1 SA0020 Q99XF1 Hypothetical protein SAV0021 0.7 0.14 S 1 Hypothetical protein SAV0022 (Hypothetical protein SA0021 Q99XF0 MW0022) 0.7 0.17 R 0 SA0022 Q99XE9 Hypothetical protein SA0022 0.6 0.12 F 1 SA0023 Q9WVW7 Hypothetical UPF0247 protein SAV0024/SA0023 0.6 0.13 S 0 ORF CN050 (Hypothetical protein SA0024) (Hypothetical SA0024 Q9XB68 protein SAV0025) 0.6 0.11 - 0 ORF CN049 (Hypothetical protein SA0025) (Hypothetical SA0025 Q9XB69 protein SAV0026) (Hypothetical protein MW0026) 0.6 0.42 - 0 Replication protein (Truncated replication protein for PUB110 SA0028 Q9XB70 plasmid) 1.2 0.13 - 0 SA0028.1 Q99XE8 Hypothetical protein SAV0030 0.5 0.02 - 0 SA0029 P22490 Plasmid recombination enzyme (Mobilization protein) 1 0.17 - 0 SA0030 Q99XE7 Hypothetical protein SAV0032 2.3 0.11 - 0 SA0031 Q99XE6 Hypothetical protein SAV0033 2.8 0.63 - 0 Bleomycin resistance protein (Bleomycin resistance SA0032 Q99XE5 protein(BRP)) 1.5 0.10 E 0 Aminoglycoside ADENYLTRANSFERASE AADD (Kanamycin SA0033 O87369 resistance protein) (Kanamycin nucleotidyltransferase) 2.8 0.11 - 0 SA0034 P19380 Transposase for insertion sequence-like element IS431MEC 0.4 0.13 L 0 SA0035 Q99XE4 SA0035 protein (Probable HMG-CoA synthase) 0.7 0.16 I 0 Hypothetical protein (GLYCEROPHOSPHORYLDIESTER phosphodiesterase) (SA0036 protein) (GLYCEROPHOSPHORYLDIESTER SA0036 Q9S3K5 PHOPHODIESTERASE) (MW0029 protein) 0.7 0.15 - 0 ORF CN038 (Hypothetical protein SA0037) (Hypothetical SA0037 O54520 protein SAV0040) (Hypothetical protein MW0030) 0.7 0.25 I 0 Penicillin-binding protein 2' (EPIDERMIDIS MECA PBP2) SA0038 Q54113 (Penicillin binding protein 2 PRIME) 0.4 0.13 M 1 SA0039 P26597 Methicillin resistance mecR1 protein 1 0.11 T 4 SA0040 P26598 Methicillin resistance regulatory protein mecI 3.4 0.10 K 0 SA0041 Q99XE2 XylR protein 0.6 1.42 K 0 SA0042 Q99XE1 Hypothetical protein SAV0045 1.1 0.60 P 0 SA0043 Q99XE0 Hypothetical protein SAV0046 0.7 0.22 P 0 ORF N052 (Hypothetical protein SA0044) (Hypothetical SA0044 Q9XB85 protein SAV0047) 1.2 0.11 P 0 ORF CN031 (Hypothetical protein SA0045) (Hypothetical SA0045 Q9XB86 protein SAV0048) 1 0.18 S 0 ORF CN030 (Hypothetical protein SA0046) (Hypothetical SA0046 Q9XB87 protein SAV0049) 0.3 0.14 R 6 ORF N044 (TRUNCATED(RADC) protein) (Hypothetical SA0053 Q9XB90 protein truncated-RADC) 0.8 0.29 L 0 SA0054 Q99XD7 Hypothetical protein SAV0058 1.5 0.16 S 0 ORF N042 (Hypothetical protein SA0055) (Hypothetical SA0055 Q9KX76 protein SAV0059) 0.5 0.22 - 0 SA0056 Q9KX77 ORF N041 (Hypothetical protein SA0056) 1.1 0.16 - 0 Site-specific recombinase (Cassette chromosome SA0057 Q9XB94 recombinase B) 0.7 0.13 L 0 Site-specific recombinase (Cassette chromosome SA0058 Q9XB96 recombinase A) 1.4 0.26 L 0 ORF N031 (Hypothetical protein SA0059) (Hypothetical SA0059 Q9KX82 protein SAV0063) 0.6 0.20 - 0 ORF N030 (Hypothetical protein SA0060) (Hypothetical SA0060 Q9KX83 protein SAV0064) 1.4 0.17 - 0 ORF N029 (Hypothetical protein SA0061) (Hypothetical SA0061 Q9KX84 protein SAV0065) 2.9 0.11 - 0 SA0062 Q99XD6 Transposase-Staphylococcus aureus IS150 (Fragment) 1.2 0.19 L 0 SA0063 Q99XD5 Transposase 1 0.17 - 0 SA0064 P83125 Hypothetical protein SAV0068 0.9 0.76 - 0 Conserved hypotehtical protein (Hypothetical protein SA0065 Q99XD4 SAV0069) 0.3 0.24 S 6 KDP operon transcriptional regulatory protein KDPE SA0066 Q9XBA2 (KDPE(SCCMEC) protein) (Hypothetical protein KDPE) 0.7 0.12 T 0 SA0067 Q99QS9 KdpD(SCCmec) protein (Hypothetical protein kdpD) 1.2 0.14 T 4 Potassium-transporting ATPase A chain (EC 3.6.3.12) (Potassium-translocating ATPase A chain) (ATP phosphohydrolase [potassium-transporting] A chain) SA0068 Q9XBA7 (Potassium binding and translocating subunit A) 3 0.28 - 12 Potassium-transporting ATPase B chain 1 (EC 3.6.3.12) (Potassium-translocating ATPase B chain 1) (ATP phosphohydrolase [potassium-transporting] B chain 1) SA0070 Q9XBA9 (Potassium binding and translocating subunit B 1) 4 0.59 P 7 SA0071 Q99QS7 KdpC(SCCmec) protein 1 0.20 P 0 SA0072 Q99XD3 Hypothetical protein SAV0075 6 0.34 - 0 SA0073 Q99XD2 Hypothetical protein SAV0076 1.5 0.14 - 0 SA0073.1 Q99XD1 Hypothetical protein SAV0077 0.9 0.02 - 0 SA0074 Q99XD0 Hypothetical protein SAV0078 2.6 0.12 - 0 SA0075 Q99XC9 Hypothetical protein SAV0079 2.2 0.12 - 1 ORF N007 (Hypothetical protein SA0076) (Hypothetical SA0076 Q9KX89 protein SAV0080) 2.5 0.15 - 0 ORF CN005 (SA0077 protein) (Hypothetical protein SA0077 Q9XBB4 SAV0081) 2 0.11 R 0 SA0078 Q99XC8 Hypothetical protein SAV0082 1.5 0.11 - 0 ORF N002 (Hypothetical protein SA0080) (Hypothetical SA0080 Q9XBB8 protein SAV0084) 1.1 0.14 R 7 ORF N001 (Hypothetical protein SA0081) (Hypothetical SA0081 Q9XBC0 protein SAV0085) 0.8 0.17 S 0 SA0082 Q99XC6 Hypothetical protein SA0082 0.3 0.17 S 0 Hypothetical protein SAV0087 (Hypothetical protein SA0083 Q99XC5 MW0057) 0.5 0.16 R 0 SA0084 Q99XC4 Hypothetical protein SAV0088 (MW0058 protein) 1.5 0.11 R 0 SA0085 Q99XC3 Probable tRNA-dihydrouridine synthase (EC 1.-.-.-) 0.9 0.12 J 0 SA0086 Q99XC2 Hypothetical protein SAV0090 1.7 0.11 - 2 SA0088 Q99XC0 Hypothetical protein SAV0092 0.6 0.12 - 5 SA0089 Q99XB9 Hypothetical protein SAV0093 0.6 0.13 L 0 SA0090 Q99XB8 Hypothetical protein SAV0094 0.4 0.18 - 4 SA0091 Q99XB7 1-phosphatidylinositol phosphodiesterase precurosr 0.5 0.16 - 0 SA0092 Q99XB6 Hypothetical protein SAV0096 0.2 0.36 - 1 SA0094 Q99XB4 Hypothetical protein SAV0098 0.3 0.23 - 1 SA0095 Q99XB3 Hypothetical protein SAV0099 0.5 0.32 - 1 SA0096 Q99XB2 Hypothetical protein SAV0100 0.2 0.16 - 1 SA0097 Q99XB1 Hypothetical protein SAV0101 1 0.15 K 0 SA0098 Q99XB0 Hypothetical protein SAV0102 0.7 0.10 R 0 Blt-like protein (SA0099 protein) (Hypothetical protein SA0099 Q9F0Z2 SAV0103) 0.2 0.14 G 14 Hypothetical protein SAV0104 (Hypothetical protein SA0100 Q99XA9 MW0080) 1.3 0.09 P 9 SA0101 Q99XA8 Hypothetical protein SAV0105 5.5 0.10 - 0 SA0102 protein (67 kDa myosin-crossreactive streptococcal SA0102 Q99XA7 antigen homologue) 0.6 0.79 S 0 SA0103 Q99XA6 Hypothetical protein SAV0107 0.4 0.13 G 10 SA0104 Q99XA5 Hypothetical protein SAV0108 0.3 0.10 K 0 SA0105 Q99XA4 Hypothetical protein SAV0109 1 0.10 - 4 SA0106 Q99XA3 LctP protein (L-lactate permease homologue) 1.1 0.13 C 13 Immunoglobulin G binding protein A precursor (IgG binding SA0107 Q99XA2 protein A) (Staphylococcal protein A) 1.5 0.20 - 1 Hyothetical protein (SarH1 protein) (Staphylococcal SA0108 Q9KWJ2 accessory regulator A homologue) 2.4 0.74 K 0 SA0110 Q99XA0 Lipoprotein 0.6 0.22 P 9 SA0111 O87491 Lipoprotein SIRA 0.8 0.10 P 0 SA0112 Q99X99 Hypothetical protein SA0112 0.5 0.38 E 0 SA0113 protein (Hypothetical protein SAV0117) (EC SA0113 Q99X98 4.3.1.12) 0.2 0.23 E 0 SA0114 Q99X97 Hypothetical protein SAV0118 0.3 0.39 Q 0 SA0115 Q99X96 Hypothetical protein SAV0119 (MW0092 protein) 0.4 0.28 G 10 SA0116 Q99X95 Hypothetical protein SAV0120 0.3 0.17 Q 0 SA0117 Q99X94 Hypothetical protein SAV0121 0.3 0.22 Q 0 SA0118 Q99X93 Hypothetical protein SAV0122 (MW0095 protein) 0.3 0.13 G 0 SA0119 protein (Hypothetical protein SAV0123) (EC SA0119 Q99X92 4.1.1.20) 0.3 0.20 E 0 SA0120 Q99X91 Hypothetical protein SA0120 (Hypothetical protein MW0097) 0.4 0.74 K 0 SA0121 Q99X90 Hypothetical protein SAV0125 0.4 0.22 - 3 Acetoin(diacetyl) reductase (EC 1.1.1.5) (Acetoin SA0122 Q99X89 dehydrogenase) (AR) (Meso-2,3-butanediol dehydrogenase) 2 0.19 Q 0 SA0122.1 Q99X88 Hypothetical protein SAV0127 0.4 0.02 - 0 SA0123 Q99X87 Hypothetical protein SAV0128 (MW0102 protein) 0.2 0.21 M 0 SA0124 Q99X86 Hypothetical protein SAV0129 0.2 0.18 M 1 SA0126 Q99X84 Hypothetical protein SAV0131 0.4 0.21 - 11 SA0127 Q99X83 Hypothetical protein SAV0132 0.5 0.19 R 13 SA0128 Q99X82 Superoxide dismutase [Mn/Fe] 2 (EC 1.15.1.1) 1 0.19 P 0 SA0129 Q99X81 Hypothetical protein SAV0134 0.6 0.10 - 1 SA0130 Q99X80 Hypothetical protein SAV0135 0.9 0.16 K 0 SA0131 Q99X79 Purine nucleoside phosphorylase 0.6 0.38 F 0 SA0133 Q99X78 Hypothetical protein SAV0137 1.1 0.09 F 13 Phosphopentomutase (EC 5.4.2.7) SA0134 Q99X76 (Phosphodeoxyribomutase)