TABLE 4.

Top 50 genes upregulated during in vitro growth in human urine

GeneFunctionFold changeaP valueAlso upregulated in vivob
yeiCHypothetical sugar kinase YeiC6.6460.0022+
rbsDHigh affinity ribose transport protein4.9870.0021
artJArginine-binding periplasmic protein 2 precursor4.7300.0195+
c0336PTS system, mannitol (cryptic)-specific IIA component4.7210.0032
ompFOuter membrane protein F precursor4.6860.0048
iucDAerobactin protein IucD4.5870.0047+
c0335Hypothetical protein4.5130.0032+
nanAN-acetylneuraminate lyase subunit4.2250.0374+
leuC3-Isopropylmalate dehydratase large subunit4.1800.0219
iroBSiderophore glucosyltransferase4.1440.0138+
leuB3-Isopropylmalate dehydrogenase4.1410.0232
dppAPeriplasmic dipeptide transport protein precursor4.1240.0131+
c0088Hypothetical protein4.0300.0377
uxuAMannonate dehydratase3.9670.0170+
c0334Putative integral membrane protein3.8890.0079
ilvCKetol-acid reductoisomerase3.8870.0343
yncEHypothetical protein YncE precursor3.8490.0225+
ybiWPutative formate acetyltransferase 33.7280.0491
yeaRHypothetical protein YeaR3.7090.0202+
argCN-acetyl-gamma-glutamyl-phosphate reductase3.6820.0267
ilvEBranched-chain amino acid aminotransferase3.5940.0274+
narKNitrite extrusion protein 13.5680.0422
ybeJGlutamate/aspartate periplasmic binding protein precursor3.3700.0262+
argBAcetylglutamate kinase3.3630.0320
ygbJHypothetical oxidoreductase YgbJ3.2630.0257
nanTPutative sialic acid transporter3.1940.0241
fdnHFormate dehydrogenase-N beta subunit3.1550.0427+
galEUDP-glucose 4-epimerase3.0390.0235
narGRespiratory nitrate reductase 1 alpha chain3.0140.0287
leuLLeu operon leader peptide3.0030.0167
fdnIFormate dehydrogenase-N gamma subunit2.9530.0207+
mglAGalactoside transport ATP-binding protein2.9250.0226
galKGalactokinase2.8950.0455
hmpAFlavohemoprotein (hemoglobin-like protein)2.8430.0302+
iutAAerobactin protein IutA2.7960.0349+
serAd-3-phosphoglycerate dehydrogenase2.7930.0444
ytfEHypothetical protein YtfE2.7530.0395+
c3835Hypothetical protein2.5820.0401
livGHigh-affinity branched-chain amino acid transport ATP-binding protein2.4790.0493
ilvHAcetolactate synthase isozyme III small subunit2.4430.0166
uxaCUronate isomerase2.4360.0392
livJLeu/lle/Val-binding protein precursor2.4160.0291
hisJHistidine-binding periplasmic protein precursor2.3850.0117
yjiYHypothetical protein YjiY2.2780.0479
mchBMicrocin H47 secretion protein2.2280.0462
asnBAsparagine synthetase B (glutamine hydrolyzing)2.2040.0395
cyoDCytochrome o ubiquinol oxidase protein2.1840.0458
narIRespiratory nitrate reductase 1 gamma chain2.1760.0278
cyoEProtoheme IX farnesyltransferase2.1760.0370+
argEAcetylornithine deacetylase2.0880.0199
  • a Fold change refers to growth in human urine relative to growth in LB.

  • b A plus sign indicates this gene was also upregulated during growth in vivo relative to growth in LB.