Table S1. Up-Regulated Genes in the Relgsu Mutant

Table S1. Up-regulated genes in the relGsu mutant.

Locus / Annotation / Function / Mean log2 ratio a / Fold change /
GSU0944 / cystathionine beta-lyase / Amino acid biosynthesis / 4.05 ± 0.45 / 16.56
GSU0945 / cystathionine beta-lyase / 3.53 ± 0.50 / 11.53
GSU1183 / O-acetyl-L-homoserine sulfhydrylase / 2.91 ± 0.36 / 7.53
GSU0535 / cysteine synthase A / 2.72 ± 1.09 / 6.60
GSU2462 / homoserine O-acetyltransferase / 2.16 ± 0.15 / 4.48
GSU3142 / phospho-2-dehydro-3-deoxyheptonate aldolase / 1.15 ± 0.33 / 2.22
GSU2572 / serine acetyltransferase / 1.10 ± 0.15 / 2.15
GSU2874 / N-acetyl-gamma-glutamyl-phosphate reductase / 1.08 ± 0.39 / 2.11
GSU1198 / D-3-phosphoglycerate dehydrogenase / 1.00 ± 0.11 / 1.99
GSU1705 / 3-methyl-2-oxobutanoate hydroxymethyltransferase / Biosynthesis of cofactors, prosthetic groups, and carriers / 1.40 ± 0.21 / 2.64
GSU1706 / pantoate--beta-alanine ligase / 1.07 ± 0.13 / 2.09
GSU0021 / quinolinate synthetase complex, subunit A / 1.03 ± 0.07 / 2.04
GSU1917 / undecaprenyl diphosphate synthase / 1.00 ± 0.24 / 2.00
GSU1936 / nicotinate-nucleotide pyrophosphorylase / 0.89 ± 0.17 / 1.85
GSU3453 / uroporphyrinogen decarboxylase / 0.84 ± 0.06 / 1.79
GSU0135 / delta-aminolevulinic acid dehydratase / 0.84 ± 0.07 / 1.79
GSU0652 / NAD+ synthetase / 0.82 ± 0.13 / 1.76
GSU2526 / membrane protein, putative / Cell envelope / 2.01 ± 0.35 / 4.04
GSU1853 / membrane protein, putative / 1.66 ± 0.27 / 3.17
GSU1336 / membrane protein, TerC family / 1.51 ± 0.30 / 2.85
GSU2940 / lipoprotein, putative / 1.46 ± 0.09 / 2.74
GSU3466 / membrane protein, putative / 1.44 ± 0.16 / 2.72
GSU1852 / membrane protein, putative / 1.27 ± 0.29 / 2.41
GSU1789 / glycosyl transferase, group 2 family protein / 1.25 ± 0.16 / 2.39
GSU1854 / UDP-glucose/GDP-mannose dehydrogenase family / 1.17 ± 0.24 / 2.24
GSU1851 / glycosyl transferase, group 1 family protein / 1.14 ± 0.21 / 2.20
GSU1896 / 3-deoxy-D-manno-octulosonate cytidylyltransferase / 1.06 ± 0.30 / 2.08
GSU2552 / lipoprotein, putative / 0.90 ± 0.14 / 1.87
GSU3386 / lipoprotein, putative / 0.89 ± 0.13 / 1.85
GSU2372 / methyl-accepting chemotaxis protein, putative / Cellular processes / 1.25 ± 0.21 / 2.38
GSU1810 / cell cycle protein MesJ, putative / 0.77 ± 0.10 / 1.71
GSU1717 / sulfate adenylyltransferase, subunit 2 / Central intermediary metabolism / 4.23 ± 0.36 / 18.80
GSU1716 / phosphoadenosine phosphosulfate reductase, putat. / 3.27 ± 0.23 / 9.65
GSU1875 / adenosylhomocysteinase / 0.86 ± 0.16 / 1.81
GSU0338 / NADH dehydrogenase I, A subunit / Energy metabolism / 1.57 ± 0.07 / 2.96
GSU1996 / cytochrome c family protein / 1.53 ± 0.13 / 2.88
GSU1351 / iron-sulfur cluster-binding protein / 1.37 ± 0.42 / 2.59
GSU0342 / NADH dehydrogenase I, E subunit / 1.35 ± 0.18 / 2.55
GSU0333 / ATP synthase F0, C subunit / 1.33 ± 0.51 / 2.52
GSU1628 / phosphoglycerate kinase/triosephosphate isomerase / 1.32 ± 0.68 / 2.49
GSU1629 / glyceraldehyde 3-phosphate dehydrogenase 1 / 1.18 ± 0.51 / 2.27
GSU3259 / cytochrome c family protein / 1.18 ± 0.27 / 2.26
GSU0110 / ATP synthase F1, delta subunit / 1.13 ± 0.08 / 2.19
GSU0343 / NADH dehydrogenase I, F subunit / 1.09 ± 0.07 / 2.13
GSU0109 / ATP synthase F0, B subunit / 1.08 ± 0.11 / 2.11
GSU0348 / NADH dehydrogenase I, K subunit / 1.00 ± 0.12 / 1.99
GSU0340 / NADH dehydrogenase I, C subunit / 0.98 ± 0.11 / 1.98
GSU0108 / ATP synthase F0, B' subunit, putative / 0.97 ± 0.10 / 1.96
GSU2645 / cytochrome c family protein / 0.95 ± 0.17 / 1.93
GSU2937 / cytochrome c family protein / 0.85 ± 0.08 / 1.81
GSU0142 / phosphatidylglycerophosphatase A / Fatty acid and phospholipid metabolism / 0.77 ± 0.07 / 1.70
GSU1363 / RNA-directed DNA polymerase / Mobile and extrachromosomal element functions / 1.41 ± 0.53 / 2.66
GSU1710 / integrative genetic element Gsu5, integrase / 1.13 ± 0.22 / 2.19
GSU1793 / trigger factor / Protein fate / 1.81 ± 0.14 / 3.50
GSU1627 / preprotein translocase, SecG subunit / 1.54 ± 0.16 / 2.91
GSU1792 / ATP-dependent Clp protease,proteolytic subnt, ClpP / 1.38 ± 0.07 / 2.61
GSU1267 / signal peptidase I / 1.26 ± 0.50 / 2.39
GSU2409 / heat shock protein, Hsp20 family / 1.20 ± 0.43 / 2.29
GSU3319 / peptidyl-prolyl cis-trans isomerase A / 1.17 ± 0.30 / 2.25
GSU1790 / ATP-dependent protease La / 1.06 ± 0.21 / 2.08
GSU2869 / preprotein translocase, SecE subunit, putative / 0.93 ± 0.12 / 1.90
GSU0689 / protein export membrane protein, SecD/SecF family, putative / 0.92 ± 0.07 / 1.89
GSU0707 / sugE protein / 0.84 ± 0.09 / 1.79
GSU0856 / peptidase, M48 family / 0.82 ± 0.13 / 1.76
GSU1752 / translation elongation factor P / Protein synthesis / 1.56 ± 0.27 / 2.95
GSU1750 / translation initiation factor IF-1 / 1.43 ± 0.30 / 2.69
GSU0662 / ribosoma protein L25 / 1.38 ± 0.33 / 2.61
GSU0663 / peptidyl-tRNA hydrolase / 1.35 ± 0.58 / 2.55
GSU1918 / ribosome recycling factor / 1.31 ± 0.16 / 2.48
GSU2839 / ribosomal protein L30 / 1.28 ± 0.43 / 2.43
GSU2870 / ribosomal protein L33 / 1.28 ± 0.13 / 2.42
GSU1659 / histidyl-tRNA synthetase / 1.27 ± 0.15 / 2.41
GSU2859 / translation elongation factor Tu / 1.23 ± 0.41 / 2.34
GSU0138 / peptide chain release factor 3 / 1.17 ± 0.28 / 2.25
GSU0465 / translation elongation factor P / 1.13 ± 0.11 / 2.19
GSU2045 / valyl-tRNA synthetase / 1.11 ± 0.05 / 2.16
GSU2849 / ribosomal protein L29 / 1.03 ± 0.33 / 2.05
GSU1515 / threonyl-tRNA synthetase / 0.96 ± 0.05 / 1.94
GSU2876 / ribosomal protein L13 / 0.95 ± 0.20 / 1.94
GSU1920 / translation elongation factor Ts / 0.87 ± 0.11 / 1.83
GSU2875 / ribosomal protein S9 / 0.83 ± 0.08 / 1.77
GSU1921 / ribosomal protein S2 / 0.81 ± 0.17 / 1.75
GSU1919 / uridylate kinase / Purines, pyrimidines, nucleosides, and nucleotides / 1.63 ± 0.30 / 3.10
GSU1110 / nucleoside diphosphate kinase / 1.31 ± 0.10 / 2.47
GSU1271 / aspartate carbamoyltransferase / 1.23 ± 0.24 / 2.35
GSU1632 / adenylosuccinate lyase / 1.17 ± 0.31 / 2.25
GSU0661 / ribose-phosphate pyrophosphokinase / 1.08 ± 0.08 / 2.11
GSU0933 / uracil phosphoribosyltransferase / 0.80 ± 0.07 / 1.74
GSU0946 / sensory box/GGDEF family protein / Regulatory functions / 1.72 ± 0.33 / 3.29
GSU1626 / transcriptional regulator, GntR family / 1.67 ± 0.33 / 3.18
GSU0106 / soj protein / 1.30 ± 0.29 / 2.47
GSU1270 / pyrimidine operon regulatory protein PyrR / 1.22 ± 0.19 / 2.32
GSU0649 / ribonuclease HII / Transcription / 1.25 ± 0.29 / 2.38
GSU1277 / transcription elongation factor GreA / 1.24 ± 0.20 / 2.36
GSU0522 / ATP-dependent RNA helicase RhlB / 0.86 ± 0.13 / 1.82
GSU1347 / sulfate ABC transporter, permease protein / Transport and binding proteins / 3.61 ± 0.56 / 12.22
GSU1346 / sulfate ABC transporter, periplasmic sulfate-binding protein / 3.21 ± 0.41 / 9.22
GSU1348 / sulfate ABC transporter, permease protein / 2.61 ± 0.64 / 6.10
GSU1349 / sulfate ABC transporter, ATP-binding protein / 2.23 ± 0.48 / 4.69
GSU1855 / capsule polysaccharide export protein, putative / 1.54 ± 0.27 / 2.91
GSU3291 / V-type H(+)-translocating pyrophosphatase / 1.40 ± 0.24 / 2.64
GSU0389 / phosphate transporter, putative / 1.17 ± 0.33 / 2.24
GSU3401 / branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein, putative / 1.13 ± 0.29 / 2.19
GSU0169 / ABC transporter, ATP-binding protein / 1.10 ± 0.31 / 2.15
GSU1774 / cell division ABC transporter, permease protein FtsX, putative / 1.06 ± 0.26 / 2.09
GSU2055 / extracellular solute-binding protein, family 7 / 1.02 ± 0.33 / 2.03
GSU1644 / ABC transporter, ATP-binding protein / 0.98 ± 0.13 / 1.97
GSU1775 / cell division ATP-binding protein FtsE / 0.87 ± 0.11 / 1.83
GSU2485 / potassium transporter family protein / 0.70 ± 0.02 / 1.63
GSU2527 / nitrite/sulfite reductase domain protein / Unknown function / 3.23 ± 0.22 / 9.36
GSU1345 / Rrf2 family protein / 2.86 ± 0.34 / 7.28
GSU1718 / elongation factor Tu GTP binding domain protein / 2.02 ± 0.42 / 4.05
GSU0534 / Rrf2 family protein / 1.98 ± 0.43 / 3.94
GSU1350 / thiF family protein / 1.94 ± 0.37 / 3.83
GSU2525 / nitroreductase family protein / 1.45 ± 0.30 / 2.74
GSU1753 / lysyl-tRNA synthetase-related protein / 1.20 ± 0.32 / 2.30
GSU1631 / metallo-beta-lactamase family protein / 1.14 ± 0.28 / 2.20
GSU1580 / ErfK/YbiS/YcfS/YnhG family protein / 1.10 ± 0.33 / 2.14
GSU1788 / NHL repeat domain protein / 1.09 ± 0.20 / 2.13
GSU2571 / Rrf2 family protein / 1.08 ± 0.09 / 2.12
GSU1266 / GTP-binding protein LepA / 1.04 ± 0.31 / 2.05
GSU3157 / hydrolase, alpha/beta fold family / 0.93 ± 0.10 / 1.91
GSU1794 / HAM1 protein / 0.90 ± 0.09 / 1.87
GSU1486 / MttB family protein / 0.89 ± 0.09 / 1.86
GSU3013 / GTP-binding protein / 0.89 ± 0.10 / 1.86
GSU0107 / parB-like domain protein / 0.87 ± 0.08 / 1.83
GSU1870 / GGDEF domain protein / 0.85 ± 0.06 / 1.81
GSU0117 / aminotransferase, classes I and II / 0.85 ± 0.11 / 1.80
GSU2183 / fic family protein / 0.71 ± 0.02 / 1.63
GSU0536 / conserved hypothetical protein TIGR00268 / Hypothetical proteins / 3.19 ± 0.38 / 9.16
GSU1184 / hypothetical protein / 2.15 ± 0.34 / 4.44
GSU3467 / conserved hypothetical protein TIGR00278 / 1.45 ± 0.18 / 2.73
GSU1598 / hypothetical protein / 1.29 ± 0.33 / 2.45
GSU0384 / hypothetical protein / 1.29 ± 0.18 / 2.44
GSU1771 / hypothetical protein / 1.28 ± 0.17 / 2.43
GSU2970 / hypothetical protein / 1.20 ± 0.13 / 2.30
GSU1152 / hypothetical protein / 1.19 ± 0.20 / 2.28
GSU2626 / hypothetical protein / 1.16 ± 0.10 / 2.23
GSU0388 / hypothetical protein / 1.02 ± 0.11 / 2.03
GSU0640 / hypothetical protein / 1.00 ± 0.13 / 2.00
GSU3106 / hypothetical protein / 0.91 ± 0.06 / 1.88
GSU0170 / hypothetical protein / 0.81 ± 0.08 / 1.75
GSU1074 / conserved hypothetical protein TIGR01033 / 0.75 ± 0.03 / 1.68
GSU1719 / hypothetical protein / 1.74 ± 0.22 / 3.34
GSU3141 / hypothetical protein / 1.50 ± 0.20 / 2.83
GSU1850 / hypothetical protein / 1.38 ± 0.36 / 2.60
GSU1849 / hypothetical protein / 1.26 ± 0.19 / 2.40
GSU2407 / hypothetical protein / 1.24 ± 0.47 / 2.37
GSU1751 / hypothetical protein / 1.17 ± 0.28 / 2.25
GSU0362 / hypothetical protein / 1.14 ± 0.22 / 2.20
GSU0964 / hypothetical protein / 1.13 ± 0.27 / 2.19
GSU0966 / hypothetical protein / 1.07 ± 0.19 / 2.10
GSU0336 / hypothetical protein / 1.05 ± 0.12 / 2.07
GSU2301 / hypothetical protein / 1.01 ± 0.16 / 2.02
GSU0965 / hypothetical protein / 0.94 ± 0.13 / 1.91
GSU1362 / hypothetical protein / 0.90 ± 0.11 / 1.87
GSU2298 / hypothetical protein / 0.89 ± 0.06 / 1.86
GSU3403 / hypothetical protein / 0.87 ± 0.08 / 1.82
GSU1472 / hypothetical protein / 0.86 ± 0.14 / 1.81
GSU2374 / hypothetical protein / 0.73 ± 0.06 / 1.66

a Mean log2 ratios represent the average of eight replicates; four technical replicates performed on two biological replicates.

Table S2. Down-regulated genes in the relGsu mutant.

Locus / Annotation / Function / Mean log2 ratio a / Fold Change /
GSU1124 / phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine lig. / Biosynthesis of cofactors, prosthetic groups, and carriers / -0.90 / ± / 0.12 / -1.86
GSU1764 / deoxyxylulose-5-phosphate synthase / -0.90 / ± / 0.12 / -1.86
GSU3194 / thiamine monophosphate kinase / -1.04 / ± / 0.19 / -2.06
GSU3462 / lipoprotein, putative / Cell envelope / -0.82 / ± / 0.07 / -1.76
GSU2305 / peptidoglycan-associated lipoprotein / -0.85 / ± / 0.12 / -1.80
GSU2323 / membrane protein, putative / -0.99 / ± / 0.05 / -1.98
GSU2633 / lipoprotein, putative / -1.26 / ± / 0.33 / -2.39
GSU1817 / outer membrane lipoprotein, Slp family / -1.27 / ± / 0.27 / -2.41
GSU0073 / outer membrane protein, putative / -1.35 / ± / 0.34 / -2.55
GSU3063 / cell division protein FtsZ / Cellular processes / -0.74 / ± / 0.03 / -1.68
GSU0726 / chemotaxis protein CheD, putative / -1.01 / ± / 0.21 / -2.01
GSU0583 / methyl-accepting chemotaxis protein / -1.03 / ± / 0.27 / -2.04
GSU1013 / chemotaxis MotB protein, putative / -1.07 / ± / 0.26 / -2.10
GSU1118 / universal stress protein family / -1.29 / ± / 0.24 / -2.44
GSU2236 / GTP pyrophosphokinase / -1.69 / ± / 0.36 / -3.23
GSU0918 / S-adenosylmethionine synthetase family / Central intermediary metabolism / -0.94 / ± / 0.27 / -1.92
GSU0067 / carbonic anhydrase / -1.43 / ± / 0.44 / -2.70
GSU1613 / A/G-specific adenine glycosylase / DNA metabolism / -0.89 / ± / 0.06 / -1.85
GSU3132 / DNA-binding protein HU / -1.18 / ± / 0.27 / -2.27
GSU3439 / NADH dehydrogenase I, G subunit / Energy metabolism / -0.75 / ± / 0.06 / -1.68
GSU1496 / pilin domain protein / -1.56 / ± / 0.21 / -2.96
GSU1612 / phosphoglycerate mutase / -0.84 / ± / 0.11 / -1.79
GSU0220 / cytochrome c oxidase, subunit III / -0.89 / ± / 0.10 / -1.85
GSU0069 / oxidoreductase, Fe-S cluster-binding subunit / -0.96 / ± / 0.23 / -1.94
GSU1649 / cytochrome b/b6 / -1.02 / ± / 0.24 / -2.03
GSU0784 / nickel-dependent hydrogenase, membrane protein / -1.03 / ± / 0.15 / -2.04
GSU2813 / cytochrome c551 peroxidase / -1.05 / ± / 0.16 / -2.07
GSU2883 / cytochrome c family protein / -1.05 / ± / 0.22 / -2.07
GSU2882 / cytochrome c family protein / -1.08 / ± / 0.37 / -2.11
GSU2449 / 2-oxoglutarate dehydrogenase, E1 component / -1.08 / ± / 0.37 / -2.12
GSU0068 / cytochrome c family protein / -1.09 / ± / 0.29 / -2.12
GSU0070 / oxidoreductase, membrane subunit / -1.10 / ± / 0.35 / -2.14
GSU3257 / glycogen synthase / -1.10 / ± / 0.06 / -2.15
GSU1648 / cytochrome c family protein / -1.13 / ± / 0.29 / -2.18
GSU2732 / cytochrome c family protein / -1.13 / ± / 0.26 / -2.19
GSU2811 / cytochrome c Hsc / -1.15 / ± / 0.11 / -2.22
GSU0510 / Fe(III) reductase, beta subunit / -1.16 / ± / 0.29 / -2.23
GSU2504 / cytochrome c family protein / -1.18 / ± / 0.09 / -2.27
GSU3187 / ferredoxin family protein / -1.36 / ± / 0.12 / -2.56