TABLE 1.

P. aeruginosa genes differentially regulated during growth in CF sputum

Function and ORFaGeneaCategory or classaFold regulationb
Amino acid biosynthesis
    PA0035trpATryptophan synthase alpha chain−7
    PA0036trpBTryptophan synthase beta chain−9
    PA0904lysCAspartate kinase alpha and beta chain−2.9
    PA1326ilvA2Threonine dehydratase, biosynthetic−9.1
    PA3118leuB3-Isopropylmalate dehydrogenase−4.3
    PA3120leuD3-Isopropylmalate dehydratase small subunit−7
    PA3121leuC3-Isopropylmalate dehydratase large subunit−7
    PA3525argGArgininosuccinate synthase−2.6
    PA3537argFOrnithine carbamoyltransferase, anabolic−3.7
    PA4588gdhAGlutamate dehydrogenasec−4.2
    PA4695ilvHAcetolactate synthase isozyme III small subunit−2.6
    PA4696ilvIAcetolactate synthase large subunit−2.7
    PA5035gltDGlutamate synthase small chainc−4.8
    PA5036gltBGlutamate synthase large chain precursorc−4.2
Amino acid transport and degradation
    PA0782putAProline dehydrogenase PutA4.3
    PA0865hpd4-Hydroxyphenylpyruvate dioxygenase66
    PA0866aroP2Aromatic amino acid transport protein AroP213
    PA0870phhCAromatic amino acid aminotransferase9
    PA0871phhBPterin-4-α-carbinolamine dehydratase5
    PA0872phhAPhenylalanine-4-hydroxylased32
    PA0897aruGArginine/ornithine succinyltransferase AII subunit3
    PA0898aruDSuccinylglutamate-5-semialdehyde dehydrogenase2.7
    PA2001atoBAcetyl coenzyme A acetyltransferase16
    PA2007maiAMaleylacetoacetate isomerase8
    PA2008fahAFumarylacetoacetase9
    PA2009hmgAHomogentisate 1,2-dioxygenase11
    PA2247bkdA12-Oxoisovalerate dehydrogenase, α subunit20
    PA2248bkdA22-Oxoisovalerate dehydrogenase, β subunit19
    PA2249bkdBBranched-chain α-keto acid dehydrogenase13
    PA2250lpdVLipoamide dehydrogenase-Val19
    PA3766Probable aromatic amino acid transporter2.8
    PA4470fumC1Fumarate hydratase6
    PA5302dadXCatabolic alanine racemase9
    PA5304dadAd-amino acid dehydrogenase, small subunit20
Glucose transport and metabolism
    PA2322Gluconate permease−5.5
    PA2323Probable glyceraldehyde-3-phosphate dehydrogenase−3.8
    PA31812-Keto-3-deoxy-6-phosphogluconate aldolase−3
    PA3186oprBGlucose/carbohydrate outer membrane porin OprB−2.7
    PA3195gapAGlyceraldehyde-3-phosphate dehydrogenase−3.2
Flagellar synthesis and chemotaxis
    PA1092fliCFlagellin type B−21
    PA2867Probable chemotaxis transducer−8
    PA4307pctCChemotactic transducer PctC−8
    PA4310pctBChemotactic transducer PctB−23
Pseudomonas quinolone signaling
    PA0996pqsAProbable coenzyme A ligase18
    PA0997pqsBHomologous to β-keto-acyl-acyl-carrier protein synthase17
    PA0998pqsCHomologous to β-keto-acyl-acyl-carrier protein synthase19
    PA0999pqsD3-Oxoacyl-(acyl carrier protein) synthase III17
    PA1000pqsEQuinolone signal response protein19
    PA1001phnAAnthranilate synthase component I22
    PA1002phnBAnthranilate synthase component II14
Other genes
    PA0034Probable two-component response regulator−7
    PA0435Hypothetical protein9
    PA0672hemOHeme oxygenase6
    PA0730Probable transferase−7
    PA0781Hypothetical protein36
    PA1093Hypothetical protein−20
    PA1300Probable σ70 factor, ECF subfamily6
    PA1325Conserved hypothetical protein−11
    PA1892Hypothetical protein−5
    PA1894Hypothetical protein−13
    PA1895Hypothetical protein−9
    PA1896Hypothetical protein−15
    PA1897Hypothetical protein−23
    PA1922Probable TonB-dependent receptor9
    PA1924Hypothetical protein22
    PA1925Hypothetical protein6
    PA1981Hypothetical protein−14
    PA1982exaAQuinoprotein alcohol dehydrogenase−18
    PA1983exaBCytochrome c550−16
    PA1999Probable coenzyme A transferase, subunit A28
    PA2000Probable coenzyme A transferase, subunit B22
    PA2006Probable MFS transporter7
    PA2027Hypothetical protein−25
    PA2194hcnBHydrogen cyanide synthase HcnB5
    PA2384Hypothetical protein12
    PA2385pvdQPvdQ15
    PA2386pvdAl-Ornithine-N5-oxygenase24
    PA2392pvdPPvdP9
    PA2393Probable dipeptidase precursor19
    PA2394pvdNPvdN15
    PA2395pvdOPvdO15
    PA2396pvdFPyoverdine synthetase F14
    PA2397pvdEPyoverdine biosynthesis protein PvdE12
    PA2399pvdDPyoverdine synthetase D10
    PA2400pvdJPvdJ28
    PA2401pvdJPvdJ17
    PA2402Probable nonribosomal peptide synthetase15
    PA2405Hypothetical protein5
    PA2411Probable thioesterase80
    PA2412Conserved hypothetical protein32
    PA2413Probable class III aminotransferase21
    PA2424pvdLPvdL16
    PA2425pvdGPvdG12
    PA2426pvdSσ factor PvdS10
    PA2427Hypothetical protein8
    PA2451Hypothetical protein6
    PA2452Hypothetical protein46
    PA2807Hypothetical protein−28
    PA2862lipALactonizing lipase precursor−7
    PA2911Probable TonB-dependent receptor6
    PA2912Probable ATP-binding component of ABC transporter5
    PA3281Hypothetical protein16
    PA3282Hypothetical protein10
    PA3283Conserved hypothetical protein23
    PA3284Hypothetical protein48
    PA3407hasApHeme acquisition protein HasAp13
    PA3444Conserved hypothetical protein−8
    PA3526Probable outer membrane protein precursor−8
    PA3598Conserved hypothetical protein6
    PA3600Conserved hypothetical protein171
    PA3601Conserved hypothetical protein80
    PA3662Hypothetical protein−6
    PA3749Probable MFS transporter−10
    PA3757Probable transcriptional regulator5
    PA3758Probable N-acetylglucosamine-6-phosphate deacetylase6
    PA3759Probable aminotransferase6
    PA3789Hypothetical protein12
    PA3790oprCOuter membrane porin OprC14
    PA3922Conserved hypothetical protein−5
    PA3936Probable permease of ABC taurine transporter−8
    PA3938Probable periplasmic taurine-binding protein precursor−5
    PA4063Hypothetical protein23
    PA4064Probable ATP-binding component of ABC transporter18
    PA4065Hypothetical protein10
    PA4066Hypothetical protein8
    PA4131Probable iron-sulfur protein7
    PA4170Hypothetical protein36
    PA4171Probable protease8
    PA4218Probable transporter23
    PA4219Hypothetical protein66
    PA4220Hypothetical protein104
    PA4221fptAFe(III)-pyochelin outer membrane receptor precursor44
    PA4222Probable ATP-binding component of ABC transporter88
    PA4223Probable ATP-binding component of ABC transporter41
    PA4224pchGPyochelin biosynthetic protein PchG96
    PA4225pchFPyochelin synthetase59
    PA4226pchEDihydroaeruginoic acid synthetase75
    PA4228pchDPyochelin biosynthesis protein PchD81
    PA4229pchCPyochelin biosynthetic protein PchC80
    PA4230pchBSalicylate biosynthesis protein PchB139
    PA4231pchASalicylate biosynthesis isochorismate synthase121
    PA4471Hypothetical protein5
    PA4498Probable metallopeptidase5
    PA4514Probable outer membrane receptor for iron transport−10
    PA4570Hypothetical protein5
    PA4633Probable chemotaxis transducer−5
    PA4770lldPl-Lactate permease35
    PA4771lldDl-Lactate dehydrogenase9
    PA4772Probable ferredoxin9
    PA4811fdnHNitrate-inducible formate dehydrogenase, β subunit6
    PA4834Hypothetical protein80
    PA4835Hypothetical protein45
    PA4836Hypothetical protein57
    PA4837Probable outer membrane protein precursor43
    PA4838Hypothetical protein8
    PA4929Hypothetical protein−6
    PA5303Conserved hypothetical protein21
    PA5532Hypothetical protein8
    PA5534Hypothetical protein42
    PA5535Conserved hypothetical protein43
    PA5536Conserved hypothetical protein74
    PA5538amiAN-acetylmuramoyl-l-alanine amidase38
    PA5539Hypothetical protein27
    PA5540Hypothetical protein28
    PA5541Probable dihydroorotase40
    tRNA-ArgNoncoding RNA gene16
  • a From P. aeruginosa genome website, http://www.pseudomonas.com.

  • b Regulation (n-fold) of genes differentially expressed during P. aeruginosa growth in 10% CF sputum compared to growth in glucose; a positive number indicates an up-regulation of the gene during growth in sputum.

  • c Involved in synthesis of glutamate and degradation of glutamate and glutamine.

  • d Involved in synthesis of tyrosine and degradation of phenylalanine.