Table S2. Pseudomonas Aeruginosa Genes That Showed Significant Changes in Expression With

Table S2. Pseudomonas aeruginosa genes that showed significant changes in expression with different sources of sulfur for growth. The table includes all genes whose expression was significantly affected by sulfur source (p<0.05), and represents an analysis of the entire transcriptome dataset from both P. aeruginosa PAO1 and P. aeruginosa E601, and including experiments with single sulfur sources and combinations of sulfur sources (GEO accession no. GSE8408).

Gene Name / P-value / Synonyms / Description
PA0004_gyrB_at / 0.0418 / DNA gyrase subunit B
PA0024_hemF_at / 0.0414 / coproporphyrinogen III oxidase, aerobic
PA0026_at / 0.00059 / hypothetical protein
PA0027_at / 0.0425 / hypothetical protein
PA0028_at / 0.037 / hypothetical protein
PA0037_trpI_at / 0.0089 / transcriptional regulator TrpI
PA0049_at / 0.00754 / hypothetical protein
PA0064_at / 0.0184 / hypothetical protein
PA0066_at / 0.0324 / yrdA / conserved hypothetical protein
PA0070_at / 0.0247 / hypothetical protein
PA0119_at / 0.0185 / probable dicarboxylate transporter
PA0120_at / 0.0104 / probable transcriptional regulator
PA0126_at / 0.00244 / hypothetical protein
PA0129_gabP_at / 0.0112 / gamma-aminobutyrate permease
PA0130_at / 0.0378 / probable aldehyde dehydrogenase
PA0160_at / 0.00088 / hypothetical protein
PA0161_at / 0.0289 / hypothetical protein
PA0162_at / 0.0205 / opdC / probable porin
PA0169_at / 0.0166 / hypothetical protein
PA0170_at / 0.00279 / hypothetical protein
PA0171_at / 0.00699 / hypothetical protein
PA0183_atsA_at / 3.04E-05 / arylsulfatase
PA0184_at / 0.00109 / atsC / probable ATP-binding component of ABC transporter
PA0185_at / 0.000507 / atsB / probable permease of ABC transporter
PA0186_at / 4.18E-05 / atsR / probable binding protein component of ABC transporter
PA0187_at / 0.0138 / hypothetical protein
PA0192_at / 0.000948 / probable TonB-dependent receptor
PA0193_at / 7.78E-05 / hypothetical protein
PA0194_at / 6.13E-05 / hypothetical protein
PA0197_at / 0.000346 / hypothetical protein
PA0198_exbB1_at / 0.000356 / transport protein ExbB
PA0199_exbD1_at / 3.31E-05 / transport protein ExbD
PA0208_mdcA_at / 0.0423 / malonate decarboxylase alpha subunit
PA0213_at / 0.0371 / mdcG / hypothetical protein
PA0266_gabT_at / 0.00283 / 4-aminobutyrate aminotransferase
PA0280_cysA_at / 0.0122 / sulfate transport protein CysA
PA0281_cysW_at / 0.00654 / sulfate transport protein CysW
PA0282_cysT_at / 0.00476 / sulfate transport protein CysT
PA0283_sbp_at / 0.00464 / sulfate-binding protein precursor
PA0284_at / 0.000869 / hypothetical protein
PA0285_at / 0.0296 / conserved hypothetical protein
PA0286_at / 0.014 / probable fatty acid desaturase
PA0295_at / 0.0261 / probable periplasmic polyamine binding protein
PA0299_at / 0.0364 / probable aminotransferase
PA0300_potF2_at / 0.0182 / polyamine transport protein
PA0301_potF3_at / 0.0364 / polyamine transport protein
PA0303_potH_at / 0.0105 / polyamine transport protein PotH
PA0364_at / 0.00105 / probable oxidoreductase
PA0365_at / 0.0146 / hypothetical protein
PA0366_at / 0.013 / probable aldehyde dehydrogenase
PA0377_at / 0.0487 / hypothetical protein
PA0387_at / 0.0203 / yggV / conserved hypothetical protein
PA0403_pyrR_at / 0.0263 / transcriptional regulator PyrR
PA0408_pilG_at / 0.0185 / twitching motility protein PilG
PA0409_pilH_at / 0.0202 / twitching motility protein PilH
PA0410_pilI_at / 0.0367 / twitching motility protein PilI
PA0411_pilJ_at / 0.0086 / twitching motility protein PilJ
PA0423_at / 0.0225 / yceI / conserved hypothetical protein
PA0425_mexA_at / 0.0289 / RND multidrug efflux membrane fusion protein MexA precursor
PA0426_mexB_at / 0.031 / RND multidrug efflux transporter MexB
PA0431_at / 0.0356 / hypothetical protein
PA0432_sahH_at / 0.0104 / ahcY / S-adenosyl-L-homocysteine hydrolase
PA0454_at / 0.0322 / yccS / conserved hypothetical protein
PA0458_at / 0.0252 / yieO / probable MFS transporter
PA0459_at / 0.0409 / clpC / probable ClpA/B protease ATP binding subunit
PA0473_at / 0.0266 / psfA / probable glutathione S-transferase
PA0501_bioF_at / 0.0201 / 8-amino-7-oxononanoate synthase
PA0502_at / 0.0157 / bioH / probable biotin biosynthesis protein bioH
PA0504_bioD_at / 0.00913 / dethiobiotin synthase
PA0509_nirN_at / 0.0262 / probable c-type cytochrome
PA0510_at / 0.0164 / nirE / probable uroporphyrin-III c-methyltransferase
PA0511_nirJ_at / 0.00859 / heme d1 biosynthesis protein NirJ
PA0512_at / 0.00134 / nirH / conserved hypothetical protein
PA0513_at / 0.00456 / nirG / probable transcriptional regulator
PA0514_nirL_at / 0.00602 / heme d1 biosynthesis protein NirL
PA0515_at / 0.0239 / nirD / probable transcriptional regulator
PA0516_nirF_at / 0.00942 / heme d1 biosynthesis protein NirF
PA0517_nirC_at / 0.0391 / probable c-type cytochrome precursor
PA0518_nirM_at / 0.0222 / cytochrome c-551 precursor
PA0519_nirS_at / 0.0362 / nitrite reductase precursor
PA0529_at / 0.0369 / conserved hypothetical protein
PA0542_at / 0.0127 / yqjC / conserved hypothetical protein
PA0547_at / 0.0236 / probable transcriptional regulator
PA0555_fda_at / 0.00781 / fbaA, cbbA, cfxB / fructose-1,6-bisphosphate aldolase
PA0561_at / 0.00615 / hypothetical protein
PA0570_at / 0.038 / hypothetical protein
PA0571_at / 0.0228 / hypothetical protein
PA0604_at / 0.0376 / probable binding protein component of ABC transporter
PA0606_at / 0.0255 / probable permease of ABC transporter
PA0610_prtN_at / 0.0301 / transcriptional regulator PrtN
PA0612_i_at / 0.000371 / hypothetical protein
PA0613_at / 0.00504 / hypothetical protein
PA0625_at / 0.00615 / hypothetical protein
PA0633_at / 0.00479 / hypothetical protein
PA0672_at / 0.00494 / pigA / hypothetical protein
PA0733_at / 0.00836 / rsuA / probable pseudouridylate synthase
PA0744_at / 0.0465 / probable enoyl-CoA hydratase/isomerase
PA0745_at / 0.0235 / probable enoyl-CoA hydratase/isomerase
PA0746_at / 0.0123 / probable acyl-CoA dehydrogenase
PA0753_at / 0.0157 / hypothetical protein
PA0756_at / 0.017 / probable two-component response regulator
PA0779_at / 0.00586 / probable ATP-dependent protease
PA0782_putA_at / 0.00163 / pruA; pruB / proline dehydrogenase PutA
PA0793_at / 0.00663 / hypothetical protein
PA0794_at / 0.0157 / probable aconitate hydratase
PA0795_prpC_at / 0.00168 / citrate synthase 2
PA0796_prpB_at / 0.00283 / bcpA / carboxyphosphonoenolpyruvate phosphonomutase
PA0801_at / 0.0325 / hypothetical protein
PA0802_i_at / 0.0166 / hypothetical protein
PA0803_at / 0.0345 / hypothetical protein
PA0835_pta_at / 0.0244 / phosphate acetyltransferase
PA0836_at / 0.021 / ackA tdcD / probable acetate kinase
PA0851_at / 0.015 / hypothetical protein
PA0852_cpbD_at / 0.00246 / chitin-binding protein CbpD precursor
PA0853_at / 0.0422 / probable oxidoreductase
PA0854_fumC2_at / 0.0251 / fumarate hydratase
PA0865_hpd_at / 0.000522 / 4-hydroxyphenylpyruvate dioxygenase
PA0866_aroP2_at / 0.0245 / aromatic amino acid transport protein AroP2
PA0870_phhC_at / 0.0436 / tyrB aspC / aromatic amino acid aminotransferase
PA0871_phhB_at / 0.0312 / pterin-4-alpha-carbinolamine dehydratase
PA0872_phhA_at / 0.0332 / phenylalanine-4-hydroxylase
PA0930_at / 0.0471 / pirS / two-component sensor
PA0931_at / 0.0161 / pirA / siderophore receptor protein
PA0958_oprD_at / 0.0361 / outer membrane porin protein OprD precursor
PA0979_s_at / 0.0228 / conserved hypothetical protein
PA1015_at / 0.0307 / probable transcriptional regulator
PA1029_at / 0.00537 / hypothetical protein
PA1048_at / 0.0352 / probable outer membrane protein
PA1053_at / 0.0314 / slyB / conserved hypothetical protein
PA1070_braG_at / 0.0264 / branched-chain amino acid transport protein BraG
PA1071_braF_at / 0.0186 / branched-chain amino acid transport protein BraF
PA1072_braE_at / 0.00689 / branched-chain amino acid transport protein BraE
PA1073_braD_at / 0.00565 / branched-chain amino acid transport protein BraD
PA1074_braC_at / 0.0036 / branched-chain amino acid transport protein BraC
PA1119_at / 9.01E-06 / probable outer membrane lipoprotein
PA1123_at / 0.00513 / hypothetical protein
PA1127_at / 7.14E-05 / gsp69 / probable oxidoreductase
PA1168_at / 0.00863 / hypothetical protein
PA1173_napB_at / 0.0486 / cytochrome c-type protein NapB precursor
PA1177_napE_at / 0.0404 / periplasmic nitrate reductase protein NapE
PA1196_at / 0.0186 / probable transcriptional regulator
PA1197_at / 0.0203 / hypothetical protein
PA1216_at / 0.0437 / hypothetical protein
PA1224_at / 0.0342 / probable NAD(P)H dehydrogenase
PA1227_at / 0.0354 / hypothetical protein
PA1245_at / 0.0424 / aprX / hypothetical protein
PA1249_aprA_at / 0.0202 / alkaline metalloproteinase precursor
PA1250_aprI_at / 0.000988 / alkaline proteinase inhibitor AprI
PA1288_at / 0.000619 / fadL; ompP1 / probable outer membrane protein
PA1317_cyoA_at / 0.000654 / cytochrome o ubiquinol oxidase subunit II
PA1318_cyoB_at / 0.0304 / cytochrome o ubiquinol oxidase subunit I
PA1319_cyoC_at / 0.0105 / cytochrome o ubiquinol oxidase subunit III
PA1320_cyoD_at / 0.019 / cytochrome o ubiquinol oxidase subunit IV
PA1321_cyoE_at / 0.0237 / cytochrome o ubiquinol oxidase protein CyoE
PA1342_at / 0.00415 / probable binding protein component of ABC transporter
PA1344_at / 0.0318 / yvaG / probable short-chain dehydrogenase
PA1354_at / 0.0227 / hypothetical protein
PA1358_at / 0.0432 / hypothetical protein
PA1428_at / 0.0431 / yjaB / conserved hypothetical protein
PA1430_lasR_at / 0.0371 / transcriptional regulator LasR
PA1441_at / 0.0297 / hypothetical protein
PA1447_fliQ_at / 0.0331 / flagellar biosynthetic protein FliQ
PA1471_at / 0.0499 / hypothetical protein
PA1475_ccmA_at / 0.0498 / cycV, helA / heme exporter protein CcmA
PA1476_ccmB_at / 0.0204 / cyt10; cycW; helB / heme exporter protein CcmB
PA1493_cysP_at / 0.0375 / sulfate-binding protein of ABC transporter
PA1513_at / 0.0208 / hypothetical protein
PA1514_at / 0.00458 / ybbT / conserved hypothetical protein
PA1522_at / 0.00826 / hypothetical protein
PA1524_xdhA_at / 0.0265 / xanthine dehydrogenase
PA1531_at / 0.0151 / hypothetical protein
PA1542_at / 0.0182 / hypothetical protein
PA1545_at / 0.0385 / hypothetical protein
PA1579_at / 0.017 / hypothetical protein
PA1590_braB_at / 0.0298 / branched chain amino acid transporter
PA1592_i_at / 0.0403 / hypothetical protein
PA1596_htpG_at / 0.00339 / heat shock protein HtpG
PA1597_at / 0.0175 / hypothetical protein
PA1601_at / 0.0306 / probable aldehyde dehydrogenase
PA1625_at / 0.0103 / conserved hypothetical protein
PA1647_at / 0.0262 / probable sulfate transporter
PA1651_at / 0.0217 / probable transporter
PA1653_at / 0.0359 / probable transcriptional regulator
PA1654_at / 0.00109 / probable aminotransferase
PA1655_at / 0.0475 / probable glutathione S-transferase
PA1657_at / 0.00527 / conserved hypothetical protein
PA1658_at / 0.00899 / conserved hypothetical protein
PA1659_at / 0.0161 / hypothetical protein
PA1660_at / 0.016 / hypothetical protein
PA1661_at / 0.0233 / hypothetical protein
PA1662_at / 0.0175 / probable ClpA/B-type protease
PA1663_at / 0.0168 / probable transcriptional regulator
PA1664_at / 0.00726 / hypothetical protein
PA1667_at / 0.0104 / hypothetical protein
PA1668_at / 0.0202 / hypothetical protein
PA1669_at / 0.0375 / hypothetical protein
PA1670_stp1_at / 0.0136 / serine/threonine phosphoprotein phosphatase Stp1
PA1671_stk1_at / 0.00268 / serine-threonine kinase Stk1
PA1672_at / 0.0475 / hypothetical protein
PA1680_at / 0.0463 / hypothetical protein
PA1684_at / 0.021 / probable oxidase
PA1707_pcrH_at / 0.043 / regulatory protein PcrH
PA1708_popB_at / 0.037 / pepB / translocator protein PopB
PA1709_popD_at / 0.0483 / pepD / translocator protein PopD
PA1711_at / 0.0298 / hypothetical protein
PA1712_exsB_at / 0.00889 / exoenzyme S synthesis protein B
PA1723_pscJ_at / 0.0156 / type III export protein PscJ
PA1742_at / 0.0307 / probable amidotransferase
PA1747_at / 0.00211 / hypothetical protein
PA1751_at / 0.029 / hypothetical protein
PA1755_at / 0.000687 / hypothetical protein
PA1759_at / 0.0439 / probable transcriptional regulator
PA1760_at / 0.00149 / probable transcriptional regulator
PA1761_at / 0.0439 / hypothetical protein
PA1766_at / 0.0351 / hypothetical protein
PA1775_at / 0.0369 / cmpX / conserved hypothetical protein
PA1778_cobA_at / 0.0419 / uroporphyrin-III C-methyltransferase
PA1789_at / 0.0215 / hypothetical protein
PA1828_at / 0.0489 / probable short-chain dehydrogenase
PA1829_at / 0.0407 / hypothetical protein
PA1830_at / 0.0459 / hypothetical protein
PA1832_at / 0.00205 / sohB / probable protease
PA1842_at / 0.00611 / hypothetical protein
PA1869_at / 0.00395 / probable acyl carrier protein
PA1878_at / 0.0187 / hypothetical protein
PA1901_s_at / 0.000354 / phzC2 / phenazine biosynthesis protein PhzC
PA1902_s_at / 0.0008 / phzD2 / phenazine biosynthesis protein PhzD
PA1903_s_at / 0.000898 / phzE2 / phenazine biosynthesis protein PhzE
PA1904_s_at / 0.000952 / phzF2 / probable phenazine biosynthesis protein
PA1905_s_at / 0.000365 / phzG2 / probable pyridoxamine 5'-phosphate oxidase
PA1913_at / 0.0316 / hypothetical protein
PA1948_rbsC_at / 0.0248 / membrane protein component of ABC ribose transporter
PA1967_at / 0.0112 / hypothetical protein
PA1984_s_at / 0.00112 / exaC1 / probable aldehyde dehydrogenase
PA1990_at / 0.0474 / probable peptidase
PA1992_at / 0.0116 / probable two-component sensor
PA1993_at / 0.0439 / yhhS / probable MFS transporter
PA1999_at / 0.000362 / scoA atoD pcaI / probable CoA transferase, subunit A
PA2000_at / 0.00018 / scoB atoA / probable CoA transferase, subunit B
PA2001_atoB_at / 0.027 / acetyl-CoA acetyltransferase
PA2006_at / 0.000573 / probable MFS transporter
PA2007_maiA_i_at / 0.00516 / maleylacetoacetate isomerase
PA2008_fahA_at / 0.00489 / fumarylacetoacetase
PA2009_hmgA_at / 0.0062 / homogentisate 1,2-dioxygenase
PA2011_at / 0.0022 / mvaB / hydroxymethylglutaryl-CoA lyase
PA2012_at / 0.00119 / accA / probable acyl-CoA carboxylase alpha chain
PA2013_at / 0.00284 / menB / probable enoyl-CoA hydratase/isomerase
PA2014_at / 0.0109 / probable acyl-CoA carboxyltransferase beta chain
PA2015_at / 0.0398 / probable acyl-CoA dehydrogenase
PA2030_at / 0.0181 / hypothetical protein
PA2031_i_at / 0.00191 / hypothetical protein
PA2037_at / 0.0442 / hypothetical protein
PA2043_at / 0.0261 / hypothetical protein
PA2048_at / 0.00471 / hypothetical protein
PA2049_at / 0.0117 / hypothetical protein
PA2050_at / 9.25E-05 / probable sigma-70 factor, ECF subfamily
PA2051_at / 0.000432 / probable transmembrane sensor
PA2057_at / 0.0486 / hypothetical protein
PA2062_at / 0.00372 / probable pyridoxal-phosphate dependent enzyme
PA2063_at / 0.00564 / hypothetical protein
PA2070_at / 0.0397 / hypothetical protein
PA2079_at / 0.0176 / probable amino acid permease
PA2080_at / 0.00993 / hypothetical protein
PA2083_at / 0.00654 / probable ring-hydroxylating dioxygenase subunit
PA2084_at / 0.00577 / asnB; yucB / probable asparagine synthetase
PA2085_at / 0.00807 / probable ring-hydroxylating dioxygenase small subunit
PA2086_at / 0.000406 / probable epoxide hydrolase
PA2087_at / 0.000897 / hypothetical protein
PA2088_at / 0.000285 / hypothetical protein
PA2089_at / 0.00161 / hypothetical protein
PA2090_at / 0.000259 / hypothetical protein
PA2091_at / 0.000354 / hypothetical protein
PA2092_at / 0.000543 / probable MFS transporter
PA2093_at / 5.96E-05 / probable sigma-70 factor, ECF subfamily
PA2094_at / 0.0147 / probable transmembrane sensor
PA2095_at / 0.00165 / hypothetical protein
PA2096_at / 0.0224 / probable transcriptional regulator
PA2109_at / 0.0368 / hypothetical protein
PA2110_at / 0.00045 / hypothetical protein
PA2111_at / 0.000566 / hypothetical protein
PA2112_at / 0.00106 / conserved hypothetical protein
PA2113_at / 0.00149 / opdO / probable porin
PA2114_at / 0.00762 / probable MFS transporter
PA2126_at / 0.0244 / conserved hypothetical protein
PA2127_at / 0.0194 / conserved hypothetical protein
PA2128_at / 0.0464 / probable fimbrial protein (precursor)
PA2185_at / 0.0281 / hypothetical protein
PA2193_hcnA_at / 0.0266 / hydrogen cyanide synthase HcnA
PA2194_hcnB_at / 0.0204 / hydrogen cyanide synthase HcnB
PA2195_hcnC_at / 0.0235 / hydrogen cyanide synthase HcnC
PA2202_at / 0.00278 / probable amino acid permease