TABLE 2.

P. aeruginosa genes differentially regulated during in vivo growth

ORFaGeneHomology or functionaFold regulationb
0149Probable sigma-70 factor7
0171Hypothetical protein−8
0200Hypothetical protein7
0280cysASulfate transport protein−11
0281cysWSulfate transport protein−17
0282cysTSulfate transport protein−11
0283sbpSulfate-binding protein precursor−15
0284Hypothetical protein−17
0440*Probable oxidoreductase7
0466Hypothetical protein−7
0509*nirNProbable c-type cytochrome7
0510Probable uroporphyrin III c-methyltransferase13
0511*nirJHeme d1 biosynthesis protein7
0512Conserved hypothetical protein8
0513Probable transcriptional regulator8
0514*nirLHeme d1 biosynthesis protein11
0515Probable transcriptional regulator9
0516*nirFHeme d1 biosynthesis protein8
0517*nirCProbable c-type cytochrome precursor11
0518*nirMCytochrome c551 precursor12
0519*nirSNitrate reductase precursor15
0521Probable cytochrome c oxidase subunit6
0523*norCNitric oxide reductase subunit C32
0524*norBNitric oxide reductase subunit B68
0525*Probable denitrification protein15
0587Conserved hypothetical protein5
0613Hypothetical protein−5
0614Hypothetical protein−5
0617Probable bacteriophage protein−10
0621Conserved hypothetical protein−5
0622Probable bacteriophage protein−8
0627Conserved hypothetical protein−5
0629Conserved hypothetical protein−7
0631Hypothetical protein−6
0632Hypothetical protein−7
0633Hypothetical protein−8
0635Hypothetical protein−11
0636Hypothetical protein−8
0639Conserved hypothetical protein−9
0641Probable bacteriophage protein−19
0674Hypothetical protein25
0675Probable sigma-70 factor5
0713Hypothetical protein26
0714Hypothetical protein24
0781Hypothetical protein18
0782putAProline dehydrogenase8
0865hpd4-Hydroxyphenylpyruvate dioxygenase5
0872phhAPhenylalanine-4-hydroxylase31
0910Hypothetical protein−18
0911Hypothetical protein−6
0921Hypothetical protein−6
0984Colicin immunity protein7
1123Hypothetical protein5
1178oprHOuter membrane protein H1 precursor−17
1179phoPTwo-component response regulator−5
1195Hypothetical protein6
1196Probable transcriptional regulator5
1382Probable type II secretion system protein12
1414Hypothetical protein5
1516Hypothetical protein5
1537Probable short-chain dehydrogenase6
1540Conserved hypothetical protein7
1541Probable drug efflux transporter8
1552Probable cytochrome c−12
1553Probable cytochrome c oxidase subunit−13
1554Probable cytochrome oxidase subunit−5
1673Hypothetical protein5
1742Probable amidotransferase7
1746Hypothetical protein9
1837Hypothetical protein−13
1838cysISulfite reductase−10
1871lasALasA protease precursor6
1887Hypothetical protein11
1888Hypothetical protein10
1892Hypothetical protein−9
1894Hypothetical protein−9
1895Hypothetical protein−10
1896Hypothetical protein−9
1897Hypothetical protein−35
1911Probable transmembrane sensor6
1912Probable sigma-70 factor7
1922Probable TonB-dependent receptor11
1924Hypothetical protein9
1925Hypothetical protein8
1999Probable CoA transferase, subunit A35
2000Probable CoA transferase, subunit B44
2001atoBAcetyl-CoA acetyltransferase13
2003bdhA3-Hydroxybutyrate dehydrogenase6
2004Conserved hypothetical protein8
2016Probable transcriptional regulator5
2114Probable MFS transporter−7
2202Probable amino acid permease−7
2204Probable binding protein component of ABC transporter−10
2223Hypothetical protein6
2247bkdA12-Oxoisovalerate dehydrogenase (alpha subunit)38
2248BkdA22-Oxoisovalerate dehydrogenase (beta subunit)14
2249bkdBBranched-chain alpha-keto acid dehydrogenase (lipoamide component)15
2250lpdVLipoamide dehydrogenase (−Val)9
2466Probable TonB-dependent receptor5
2534Probable transcriptional regulator5
2567Hypothetical protein5
2648nuoMNADH dehydrogenase I chain−5
2686pfeRTwo-component response regulator6
2687pfeSTwo-component sensor5
2753Hypothetical protein7
2807Hypothetical protein−19
2825Probable transcriptional regulator5
2826Probable glutathione peroxidase5
2929Hypothetical protein5
2931Probable transcriptional regulator19
2932morBMorphinone reductase71
2933Probable MFS transporter31
2934Probable hydrolase16
2945Conserved hypothetical protein−6
3038Probable porin−6
3118leuB3-Isopropylmalate dehydrogenase−5
3120leuD3-Isopropylmalate dehydratase small subunit−6
3121leuC3-Isopropylmalate dehydratase large subunit−6
3126ibpAHeat shock protein7
3188Probable permease of ABC sugar transporter−382
3189Probable permease of ABC sugar transporter−79
3195gapAGlyceraldehyde-3-phosphate dehydrogenase−6
3249Probable transcriptional regulator5
3309Conserved hypothetical protein6
3313Hypothetical protein−5
3391*nosRRegulatory protein54
3392*nosZNitrous oxide reductase precursor25
3393*nosDNosD protein11
3394*nosFNosF protein16
3395*nosYNosY protein8
3396*nosLNosL protein8
3404Probable secretion protein7
3405hasEMetalloprotease secretion protein32
3406hasDTransport protein16
3415Probable dihydrolipoamide acetyltransferase9
3416Probable pyruvate dehydrogenase E1 component, beta chain36
3417Probable pyruvate dehydrogenase E1 component, alpha subunit7
3418ldhLeucine dehydrogenase8
3441Probable molybdopterin-binding protein−12
3442Probable ATP-binding component of ABC transporter−21
3443Probable permease of ABC transporter−43
3444Conserved hypothetical protein−161
3445Conserved hypothetical protein−62
3446Conserved hypothetical protein−19
3450Probable antioxidant protein−8
3516Probable lyase−5
3581glpFGlycerol uptake facilitator protein9
3582glpKGlycerol kinase6
3584glpDGlycerol-3-phosphate dehydrogenase44
3598Conserved hypothetical protein7
3600Conserved hypothetical protein139
3601Conserved hypothetical protein83
3719Hypothetical protein21
3720Hypothetical protein30
3721Probable transcriptional regulator5
3837Probable permease of ABC transporter−5
3862Hypothetical protein6
3870moaA1Molybdopterin biosynthetic protein7
3871Probable peptidyl-prolyl cis-trans isomerase7
3872*narIRespiratory nitrate reductase gamma chain9
3873*narJRespiratory nitrate reductase delta chain11
3874*narHRespiratory nitrate reductase beta chain24
3875*narGRespiratory nitrate reductase alpha chain19
3876*narK2Nitrite extrusion protein 210
3877*narK1Nitrite extrusion protein 16
3914moeA1Molybdenum cofactor biosynthetic protein7
3915moaB1Molybdopterin biosynthetic protein5
3922Conserved hypothetical protein−6
3931Conserved hypothetical protein−16
3933Probable choline transporter10
3935tauDTaurine dioxygenase−16
3936Probable permease of ABC taurine transporter−35
3937Probable ATP-binding component of ABC taurine transporter−25
3938Probable periplasmic taurine-binding protein precursor−21
4063Hypothetical protein15
4064Probable ATP-binding component of ABC transporter7
4065Hypothetical protein5
4156Probable TonB-dependent receptor10
4160fepDFerric enterobactin transport protein5
4167Probable oxidoreductase13
4168Probable TonB-dependent receptor17
4181Hypothetical protein16
4182Hypothetical protein10
4197Probable two-component sensor10
4288Probable transcriptional regulator8
4333Probable fumarase−5
4364Hypothetical protein113
4365Probable transporter54
4442cysNATP sulfurylase GTP-binding subunit, APS kinase−22
4443cysDATP sulfurylase small subunit−10
4577Hypothetical protein5
4588gdhAGlutamate dehydrogenase−6
4610Hypothetical protein9
4621Probable oxidoreductase5
4657Hypothetical protein5
4738Conserved hypothetical protein−6
4739Conserved hypothetical protein−9
4834Hypothetical protein18
4835Hypothetical protein16
4836Hypothetical protein32
4837Probable outer membrane protein38
4838Hypothetical protein7
5024Conserved hypothetical protein−13
5027Hypothetical protein5
5088Hypothetical protein7
5100hutUUrocanase7
5102Hypothetical protein−8
5106Conserved hypothetical protein6
5170arcDArginine-ornithine antiporter11
5171arcAArginine deiminase9
5172arcBOrnithine carbamoyltransferase, catabolic10
5173arcCCarbamate kinase6
5302dadXCatabolic alanine racemase6
5303Conserved hypothetical protein9
5304dadAd-Amino acid dehydrogenase, small subunit9
5351Rubredoxin−5
5372betACholine dehydrogenase12
5373betBBetaine aldehyde dehydrogenase12
5374betITranscriptional regulator11
5427adhAAlcohol dehydrogenase6
5446Hypothetical protein13
5475Hypothetical protein5
5481Hypothetical protein−7
5482Hypothetical protein−8
5499np20Transcriptional regulator6
5500znuCZinc transport protein6
5532Hypothetical protein8
5534Hypothetical protein13
5535Conserved hypothetical protein15
5536Conserved hypothetical protein52
5538amiAN-Acetylmuramoyl-l-alanine amidase28
5539Hypothetical protein8
5540Hypothetical protein17
5541Probable dihydroorotase11
  • a From the P. aeruginosa genome website, www.pseudomonas.com. Genes involved in anaerobic metabolism (*), transport and metabolism of amino acids (†), or identified previously using IVET (‡) are listed in bold.

  • b Fold change in P. aeruginosa mRNA level when grown in vivo in the DMC compared to that in bacteria grown in glucose minimal medium in vitro. Positive numbers represent induction, and negative numbers indicate repression in the DMC. All genes listed were also >5- fold regulated when DMC-grown and succinate-grown P. aeruginosa cultures were compared.