TABLE 2.

P. aeruginosa genes differentially regulated during in vivo growth

ORFaGeneHomology or functionaFold regulationb
0149Probable sigma-70 factor7
0171Hypothetical protein−8
0200Hypothetical protein7
0280 cysA Sulfate transport protein−11
0281 cysW Sulfate transport protein−17
0282 cysT Sulfate transport protein−11
0283 sbp Sulfate-binding protein precursor−15
0284Hypothetical protein−17
0440* Probable oxidoreductase 7
0466Hypothetical protein−7
0509* nirN Probable c -type cytochrome 7
0510Probable uroporphyrin III c-methyltransferase13
0511* nirJ Heme d1 biosynthesis protein 7
0512Conserved hypothetical protein8
0513Probable transcriptional regulator8
0514* nirL Heme d1 biosynthesis protein 11
0515Probable transcriptional regulator9
0516* nirF Heme d1 biosynthesis protein 8
0517* nirC Probable c -type cytochrome precursor 11
0518* nirM Cytochrome c 551 precursor 12
0519* nirS Nitrate reductase precursor 15
0521Probable cytochrome c oxidase subunit6
0523* norC Nitric oxide reductase subunit C 32
0524* norB Nitric oxide reductase subunit B 68
0525* Probable denitrification protein 15
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
0782 putA Proline dehydrogenase 8
0865 hpd 4-Hydroxyphenylpyruvate dioxygenase 5
0872 phhA Phenylalanine-4-hydroxylase 31
0910Hypothetical protein−18
0911Hypothetical protein−6
0921Hypothetical protein−6
0984Colicin immunity protein7
1123Hypothetical protein5
1178 oprH Outer membrane protein H1 precursor−17
1179 phoP Two-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
1838 cysI Sulfite reductase−10
1871 lasA LasA 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
1999 Probable CoA transferase, subunit A 35
2000 Probable CoA transferase, subunit B 44
2001 atoB Acetyl-CoA acetyltransferase13
2003 bdhA 3-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
2247 bkdA1 2-Oxoisovalerate dehydrogenase (alpha subunit) 38
2248 BkdA2 2-Oxoisovalerate dehydrogenase (beta subunit) 14
2249 bkdB Branched-chain alpha-keto acid dehydrogenase (lipoamide component) 15
2250 lpdV Lipoamide dehydrogenase (−Val) 9
2466Probable TonB-dependent receptor5
2534Probable transcriptional regulator5
2567Hypothetical protein5
2648 nuoM NADH dehydrogenase I chain−5
2686 pfeR Two-component response regulator6
2687 pfeS Two-component sensor5
2753Hypothetical protein7
2807Hypothetical protein−19
2825Probable transcriptional regulator5
2826Probable glutathione peroxidase5
2929Hypothetical protein5
2931Probable transcriptional regulator19
2932 morB Morphinone reductase71
2933Probable MFS transporter31
2934Probable hydrolase16
2945Conserved hypothetical protein−6
3038Probable porin−6
3118 leuB 3-Isopropylmalate dehydrogenase −5
3120 leuD 3-Isopropylmalate dehydratase small subunit −6
3121 leuC 3-Isopropylmalate dehydratase large subunit −6
3126 ibpA Heat shock protein7
3188Probable permease of ABC sugar transporter−382
3189Probable permease of ABC sugar transporter−79
3195 gapA Glyceraldehyde-3-phosphate dehydrogenase−6
3249Probable transcriptional regulator5
3309Conserved hypothetical protein6
3313Hypothetical protein−5
3391* nosR Regulatory protein 54
3392* nosZ Nitrous oxide reductase precursor 25
3393* nosD NosD protein 11
3394* nosF NosF protein 16
3395* nosY NosY protein 8
3396* nosL NosL protein 8
3404Probable secretion protein7
3405 hasE Metalloprotease secretion protein32
3406 hasD Transport protein16
3415Probable dihydrolipoamide acetyltransferase9
3416Probable pyruvate dehydrogenase E1 component, beta chain36
3417Probable pyruvate dehydrogenase E1 component, alpha subunit7
3418 ldh Leucine dehydrogenase 8
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
3581 glpF Glycerol uptake facilitator protein9
3582 glpK Glycerol kinase6
3584 glpD Glycerol-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
3870 moaA1 Molybdopterin biosynthetic protein7
3871Probable peptidyl-prolyl cis-trans isomerase7
3872* narI Respiratory nitrate reductase gamma chain 9
3873* narJ Respiratory nitrate reductase delta chain 11
3874* narH Respiratory nitrate reductase beta chain 24
3875* narG Respiratory nitrate reductase alpha chain 19
3876* narK2 Nitrite extrusion protein 2 10
3877* narK1 Nitrite extrusion protein 1 6
3914 moeA1 Molybdenum cofactor biosynthetic protein7
3915 moaB1 Molybdopterin biosynthetic protein5
3922Conserved hypothetical protein−6
3931Conserved hypothetical protein−16
3933Probable choline transporter10
3935 tauD Taurine 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
4160 fepD Ferric 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
4442 cysN ATP sulfurylase GTP-binding subunit, APS kinase −22
4443 cysD ATP sulfurylase small subunit −10
4577Hypothetical protein5
4588 gdhA Glutamate 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
5100 hutU Urocanase 7
5102Hypothetical protein−8
5106Conserved hypothetical protein6
5170 arcD Arginine-ornithine antiporter 11
5171 arcA Arginine deiminase 9
5172 arcB Ornithine carbamoyltransferase, catabolic 10
5173 arcC Carbamate kinase 6
5302 dadX Catabolic alanine racemase 6
5303Conserved hypothetical protein9
5304 dadA d-Amino acid dehydrogenase, small subunit 9
5351Rubredoxin−5
5372 betA Choline dehydrogenase 12
5373 betB Betaine aldehyde dehydrogenase12
5374 betI Transcriptional regulator11
5427 adhA Alcohol dehydrogenase6
5446Hypothetical protein13
5475Hypothetical protein5
5481Hypothetical protein−7
5482Hypothetical protein−8
5499 np20 Transcriptional regulator 6
5500 znuC Zinc transport protein6
5532Hypothetical protein8
5534Hypothetical protein13
5535Conserved hypothetical protein15
5536Conserved hypothetical protein52
5538 amiA N-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.