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Table 1 List of significantly up or downregulated P. aeruginosa genes that are discussed in this report

From: Toxicogenomic response of Pseudomonas aeruginosa to ortho-phenylphenol

Affymetrix ORF # Probe ID a20 minutes a60 minutes Description Symbol Functional class
   bFold change P value bFold change P value    
Group I: Upregulation (20 min) – Upregulation (60 min)
PA1964_at PA1964 2.029 0.0112 2.381 0.0112 probable ATP-binding component of ABC transporter   Transport of small molecules
PA2760_at PA2760 2.152 0.0416 2.94 0.0416 probable outer membrane protein precursor   Transport of small molecules
PA4687_hitA_at PA4687 2.219 0.00808 2.069 0.00808 ferric iron-binding periplasmic protein HitA hit A Transport of small molecules
PA2743_infC_at PA2743 2.044 0.000327 2.634 0.000327 translation initiation factor IF-3 inf C Translation, post-translational modification, degradation
PA2619_infA_at PA2619 2.14 0.000526 3.644 0.000526 translation initiation factor inf A Translation, post-translational modification, degradation
PA4266_fusA1_at PA4266 2.18 0.012 3.88 0.012 elongation factor G fus A1 Translation, post-translational modification, degradation
PA3655_tsf_at PA3655 2.197 0.017 5.495 0.017 elongation factor Ts tsf Translation, post-translational modification, degradation
PA4665_prfA_at PA4665 2.426 0.00398 2.774 0.00398 peptide chain release factor 1 prf A Translation, post-translational modification, degradation
PA4273_rplA_at PA4273 2.725 0.0349 6.018 0.0349 50S ribosomal protein L1 rpl A Translation, post-translational modification, degradation
PA3656_rpsB_at PA3656 2.543 0.00953 7.267 0.00953 30S ribosomal protein S2 rps B Translation, post-translational modification, degradation
PA4744_infB_at PA4744 2.783 0.0134 3.826 0.0134 translation initiation factor IF-2 inf B Translation, post-translational modification, degradation
PA4934_rpsR_at PA4934 2.894 0.000276 6.619 0.000276 30S ribosomal protein S18 rps R Translation, post-translational modification, degradation
PA4255_rpmC_at PA4255 2.927 0.00331 6.655 0.00331 50S ribosomal protein L29 rpm C Translation, post-translational modification, degradation
PA4528_pilD_at PA4528 2.144 0.014 2.65 0.014 type 4 prepilin peptidase PilD pil D Motility & Attachment
PA0408_pilG_at PA0408 2.294 0.0144 4.026 0.0144 twitching motility protein PilG pil G Chemotaxis
PA5041_pilP_at PA5041 2.169 0.00817 2.232 0.00817 type 4 fimbrial biogenesis protein PilP pil P Motility & Attachment
PA0410_pilI_at PA0024 2.188 0.0484 2.267 0.0484 twitching motility protein PilI pil I Motility & Attachment
PA5042_pilO_at PA5042 2.26 0.000345 2.056 0.000345 type 4 fimbrial biogenesis protein PilO pil O Motility & Attachment
PA4527_pilC_at PA4527 2.27 0.00205 2.678 0.00205 still frameshift type 4 fimbrial biogenesis protein PilC pil C Motility & Attachment
PA5043_pilN_at PA5043 2.34 0.000628 2.914 0.000628 type 4 fimbrial biogenesis protein PilN pil N Motility & Attachment
PA5044_pilM_at PA5044 2.893 0.00702 3.12 0.00702 type 4 fimbrial biogenesis protein PilM pil M Motility & Attachment
PA4688_hitB_at PA4688 2.282 0.0261 2.513 0.0261 iron (III)-transport system permease HitB hit B Membrane proteins
PA4747_secG_at PA4747 2.294 0.00628 3.795 0.00628 secretion protein SecG sec G Membrane proteins
PA4243_secY_at PA4243 2.914 9.26E-05 6.799 9.26E-05 secretion protein SecY sec Y Membrane proteins
PA4276_secE_at PA4276 2.274 2.07E-05 4.198 2.07E-05 secretion protein SecE sec E Protein secretion/export apparatus
PA2968_fabD_at PA2968 2.137 0.0131 3.506 0.0131 malonyl-CoA-[acyl-carrier-protein] transacylase fab D Fatty acid and phospholipid metabolism
PA1609_fabB_at PA1609 2.373 0.0147 2.855 0.0147 beta-ketoacyl-ACP synthase I fab B Fatty acid and phospholipid metabolism
PA2967_fabG_at PA2967 2.387 0.00109 3.416 0.00109 3-oxoacyl-[acyl-carrier-protein] reductase fab G Fatty acid and phospholipid metabolism
PA1610_fabA_at PA1610 2.864 0.00295 4.071 0.00295 beta-hydroxydecanoyl-ACP dehydrase fab A Fatty acid and phospholipid metabolism
PA3645_fabZ_at PA3645 2.854 2.25E-05 4.671 2.25E-05 (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase fab Z Cell wall/LPS/capsule
PA5556_atpA_at PA5556 2.202 0.00136 3.907 0.00136 ATP synthase alpha chain atp A Energy metabolism
PA5491_at PA5491 2.354 0.0049 2.854 0.0049 probable cytochrome   Energy metabolism
PA5561_atpI_at PA5561 2.558 0.0015 2.542 0.0015 ATP synthase protein I atp I Energy metabolism
PA3818_at PA4263 2.746 0.00537 5.447 0.00537 extragenic suppressor protein SuhB Suh B Adaptation, protection
PA4743_rbfA_at PA4743 2.824 0.0177 4.063 0.0177 ribosome-binding factor A rbf A Adaptation, protection
PA5117_typA_at PA5117 3.136 0.000343 5.723 0.000343 regulatory protein TypA Typ A Adaptation, protection
Group II: Upregulation (20 min) – No change (60 min)
PA0524_norB_at PA0524 3.869 0.0456    nitric-oxide reductase subunit B nor B Energy metabolism
PA3479_rhlA_at PA3479 2.376 0.0364    rhamnosyltransferase chain A rhl A Secreted Factors (toxins, enzymes, alginate)
PA0177_at PA0177 2.683 0.00294    probable purine-binding chemotaxis protein   Adaptation, protection
Group III: Downregulation (20 min) – No change (60 min)
PA2193_hcnA_at PA2193 -2.268 0.0324    hydrogen cyanide synthase HcnA hcn A Central intermediary metabolism
PA2194_hcnB_at PA2194 -2.762 0.018    hydrogen cyanide synthase HcnB hcn B Central intermediary metabolism
PA2195_hcnC_at PA2195 -2.183 0.0437    hydrogen cyanide synthase HcnC hcn C Central intermediary metabolism
PA4385_groEL_at PA4385 -2.16 0.00513    GroEL protein gro EL Chaperones & heat shock proteins
PA4542_clpB_at PA4542 -2.77 0.00253    ClpB protein clp B Translation, post-translational modification, degradation
Group IV: No change(20 min) – Upregulation(60 min)
PA4272_rplJ_at PA4272    5.918 0.00886 50S ribosomal protein L10 rpl J Translation, post-translational modification, degradation
PA4271_rplL_at PA4271    5.898 0.00319 50S ribosomal protein L17/L12 rpl L Translation, post-translational modification, degradation
PA2740_pheS_at PA2740    3.323 0.000548 phenylalanyl-tRNA synthetase, alpha-subunit phe S Translation, post-translational modification, degradation
PA4240_rpsK_at PA4240    3.283 0.0292 30S ribosomal protein S11 rps K Translation, post-translational modification, degradation
PA4267_rpsG_at PA4267    3.104 0.0138 30S ribosomal protein S7 rps G Translation, post-translational modification, degradation
PA2739_pheT_at PA2739    2.142 0.0375 phenylalanyl-tRNA synthetase, beta subunit phe T Translation, post-translational modification, degradation
PA3987_leuS_at PA3987    2.632 0.0216 leucyl-tRNA synthetase leu S Amino acid biosynthesis and metabolism
PA0009_glyQ_at PA0009    2.568 0.000361 glycyl-tRNA synthetase alpha chain gly Q Amino acid biosynthesis and metabolism
PA3525_argG_at PA3525    2.45 0.0411 argininosuccinate synthase arg G Amino acid biosynthesis and metabolism
PA3167_serC_at PA3167    2.345 0.0396 3-phosphoserine aminotransferase ser C Amino acid biosynthesis and metabolism
PA0904_lysC_at PA0904    2.337 0.00528 aspartate kinase alpha and beta chain lys C Amino acid biosynthesis and metabolism
PA5263_argH_at PA5263    2.29 0.00853 argininosuccinate lyase arg H Amino acid biosynthesis and metabolism
PA4007_proA_at PA4007    2.282 0.0231 gamma-glutamyl phosphate reductase pro A Amino acid biosynthesis and metabolism
PA5277_lysA_at PA5277    2.247 0.0334 diaminopimelate decarboxylase lys A Amino acid biosynthesis and metabolism
PA5143_hisB_at PA5143    2.246 0.00461 imidazoleglycerol-phosphate dehydratase his B Amino acid biosynthesis and metabolism
PA5039_aroK_at PA5039    2.234 0.013 shikimate kinase aro K Amino acid biosynthesis and metabolism
PA0018_fmt_at PA0018    2.222 0.0137 methionyl-tRNA formyltransferase fmt Amino acid biosynthesis and metabolism
PA5067_hisE_at PA5067    2.212 0.00214 phosphoribosyl-ATP pyrophosphohydrolase his E Amino acid biosynthesis and metabolism
PA3482_metG_at PA3482    2.043 0.0312 methionyl-tRNA synthetase met G Amino acid biosynthesis and metabolism
PA5119_glnA_at PA5119    2.038 0.0442 glutamine synthetase gln A Amino acid biosynthesis and metabolism
PA4439_trpS_at PA4439    2.002 0.0155 tryptophanyl-tRNA synthetase trp S Amino acid biosynthesis and metabolism
PA0903_alaS_at PA0903    2.099 0.0102 alanyl-tRNA synthetase ala S Transcription, RNA processing and degradation
PA4602_glyA3_at PA4602    3.347 2.83E-05 serine hydroxymethyltransferase gly A3 Amino acid biosynthesis and metabolism
PA0971_tolA_at PA0971    2.249 0.000381 TolA protein tol A Transport of small molecules
PA5479_gltP_at PA5479    2.413 0.00978 proton-glutamate symporter glt P Membrane proteins
PA3821_secD_at PA3821    3.516 0.00324 secretion protein SecD sec D Membrane proteins
PA3820_secF_at PA3820    2.206 0.0411 secretion protein sec F Protein secretion sec F Protein secretion/export apparatus
PA5070_tatC_at PA5070    2.312 0.0209 transport protein TatC tat C Membrane proteins
PA0973_oprL_at PA0973    2.281 0.00672 Peptidoglycan associated lipoprotein OprL precursor opr L Membrane proteins
PA0280_cysA_at PA0280    2.018 0.0139 sulfate transport protein CysA cys A Transport of small molecules
PA5217_at PA5217    2.141 0.00709 probable binding protein component of ABC iron transporter   Transport of small molecules
PA0295_at PA0295    2.643 0.0147 probable periplasmic polyamine binding protein   Transport of small molecules
PA4461_at PA4461    2.24 0.00116 probable ATP-binding component of ABC transporter   Transport of small molecules
PA5503_at PA5503    2.229 0.000446 probable ATP-binding component of ABC transporter   Transport of small molecules
PA4450_murA_at PA4450    2.855 0.00044 UDP-N-acetylglucosamine 1-carboxyvinyltransferase mur A Cell wall/LPS/capsule
PA3644_lpxA_at PA3644    2.83 0.00038 UDP-N-acetylglucosamine acyltransferase lpx A Cell wall/LPS/capsule
PA5276_lppL_i_at PA5276    2.786 0.0149 Lipopeptide LppL precursor lpp L Cell wall/LPS/capsule
PA3643_lpxB_at PA3643    2.561 0.0247 lipid A-disaccharide synthase lpx B Cell wall/LPS/capsule
PA5012_waaF_at PA5012    2.092 0.00978 heptosyltransferase II waa F Cell wall/LPS/capsule
PA3337_rfaD_at PA3337    3.397 0.0498 ADP-L-glycero-D-mannoheptose 6-epimerase rfa D Cell wall/LPS/capsule
PA5129_grx_at PA5129    3.855 0.0334 glutaredoxin grx Energy metabolism
PA5555_atpG_at PA5555    3.527 0.0287 ATP synthase gamma chain atp G Energy metabolism
PA5554_atpD_at PA5554    3.011 0.00384 ATP synthase beta chain atp D Energy metabolism
PA3621_fdxA_at PA3621    3.01 0.0042 ferredoxin I fdx A Energy metabolism
PA5559_atpE_at PA5559    2.734 0.0205 atp synthase C chain atp E Energy metabolism
PA5560_atpB_at PA5560    2.433 0.0148 ATP synthase A chain atp B Energy metabolism
PA2995_nqrE_at PA2995    2.216 0.00617 Na+-translocating NADH:quinone oxidoreductase subunit Nqr5 nqr E Energy metabolism
PA5553_atpC_at PA5553    2.175 0.00502 ATP synthase epsilon chain atp C Energy metabolism
PA0362_fdx1_at PA0362    2.125 0.000346 ferredoxin [4Fe-4S] fdx 1 Energy metabolism
PA3527_pyrC_at PA3527    2.218 0.0211 dihydroorotase pyr C Nucleotide biosynthesis and metabolism
PA5331_pyrE_at PA5331    2.156 0.0166 orotate phosphoribosyltransferase pyr E Nucleotide biosynthesis and metabolism
PA3654_pyrH_at PA3654    2.434 0.0212 uridylate kinase pyr H Nucleotide biosynthesis and metabolism
PA3763_purL_at PA3763    2.279 0.00792 phosphoribosylformylglycinamidine synthase pur L Nucleotide biosynthesis and metabolism
Group V: No change(20 min) – Downregulation(60 min)
PA1174_napA_at PA1174    -3.425 0.0251 periplasmic nitrate reductase protein NapA nap A Energy metabolism
PA1175_napD_at PA1175    -2.949 0.0134 NapD protein of periplasmic nitrate reductase nap D Energy metabolism
PA1176_napF_at PA1176    -2.949 0.024 ferredoxin protein NapF nap F Energy metabolism
PA1173_napB_at PA1173    -3.077 0.00344 cytochrome c-type protein NapB precursor nap B Energy metabolism
PA2248_bkdA2_at PA2248    -5.076 0.0072 2-oxoisovalerate dehydrogenase (beta subunit) bkd A2 Amino acid biosynthesis and metabolism
PA2247_bkdA1_at PA2247    -9.434 0.00376 2-oxoisovalerate dehydrogenase (alpha subunit) bkd A1 Amino acid biosynthesis and metabolism
PA2250_lpdV_at PA2250    -3.497 0.00576 lipoamide dehydrogenase-Val lpd V Amino acid biosynthesis and metabolism
Group VI: Downregulation (20 min) – Downregulation (60 min)
PA3049_rmf_at PA3049 -6.25 0.000723 -25.907 0.000723 ribosome modulation factor rmf Translation, post-translational modification, degradation
PA3622_rpoS_at PA3622 -2.653 0.00961 -2.967 0.00961 sigma factor RpoS rpo S Transcriptional regulators
PA4762_grpE_at PA4762 -2.915 0.00501 -0.479 0.00501 heat shock protein GrpE grp E DNA replication, recombination, modification and repair
PA5054_hslU_at PA5054 -3.226 0.000316 -0.428 0.000316 heat shock protein HslU hsl U Chaperones & heat shock proteins
PA5053_hslV_at PA5053 -2.597 0.00113 -0.352 0.00113 heat shock protein HslV hsl V Chaperones & heat shock proteins
PA1596_htpG_at PA1596 -2.695 0.00706 -0.434 0.00706 heat shock protein HtpG htp G Chaperones & heat shock proteins
  1. Genes are categorized by their transcription patterns and related functions. The microarray results are the mean of four replicates of each gene.
  2. aThe microarray results are the mean of four replicates of each gene.
  3. bThe fold change is a positive number when the expression level in the experiment increased compared to the control and is a negative number when the expression level in the experiment decreased.