TABLE 4.

Top 50 genes upregulated during in vitro growth in human urine

GeneFunctionFold changeaP valueAlso upregulated in vivob
yeiC Hypothetical sugar kinase YeiC6.6460.0022+
rbsD High affinity ribose transport protein4.9870.0021
artJ Arginine-binding periplasmic protein 2 precursor4.7300.0195+
c0336 PTS system, mannitol (cryptic)-specific IIA component4.7210.0032
ompF Outer membrane protein F precursor4.6860.0048
iucD Aerobactin protein IucD4.5870.0047+
c0335 Hypothetical protein4.5130.0032+
nanA N-acetylneuraminate lyase subunit4.2250.0374+
leuC 3-Isopropylmalate dehydratase large subunit4.1800.0219
iroB Siderophore glucosyltransferase4.1440.0138+
leuB 3-Isopropylmalate dehydrogenase4.1410.0232
dppA Periplasmic dipeptide transport protein precursor4.1240.0131+
c0088 Hypothetical protein4.0300.0377
uxuA Mannonate dehydratase3.9670.0170+
c0334 Putative integral membrane protein3.8890.0079
ilvC Ketol-acid reductoisomerase3.8870.0343
yncE Hypothetical protein YncE precursor3.8490.0225+
ybiW Putative formate acetyltransferase 33.7280.0491
yeaR Hypothetical protein YeaR3.7090.0202+
argC N-acetyl-gamma-glutamyl-phosphate reductase3.6820.0267
ilvE Branched-chain amino acid aminotransferase3.5940.0274+
narK Nitrite extrusion protein 13.5680.0422
ybeJ Glutamate/aspartate periplasmic binding protein precursor3.3700.0262+
argB Acetylglutamate kinase3.3630.0320
ygbJ Hypothetical oxidoreductase YgbJ3.2630.0257
nanT Putative sialic acid transporter3.1940.0241
fdnH Formate dehydrogenase-N beta subunit3.1550.0427+
galE UDP-glucose 4-epimerase3.0390.0235
narG Respiratory nitrate reductase 1 alpha chain3.0140.0287
leuL Leu operon leader peptide3.0030.0167
fdnI Formate dehydrogenase-N gamma subunit2.9530.0207+
mglA Galactoside transport ATP-binding protein2.9250.0226
galK Galactokinase2.8950.0455
hmpA Flavohemoprotein (hemoglobin-like protein)2.8430.0302+
iutA Aerobactin protein IutA2.7960.0349+
serA d-3-phosphoglycerate dehydrogenase2.7930.0444
ytfE Hypothetical protein YtfE2.7530.0395+
c3835 Hypothetical protein2.5820.0401
livG High-affinity branched-chain amino acid transport ATP-binding protein2.4790.0493
ilvH Acetolactate synthase isozyme III small subunit2.4430.0166
uxaC Uronate isomerase2.4360.0392
livJ Leu/lle/Val-binding protein precursor2.4160.0291
hisJ Histidine-binding periplasmic protein precursor2.3850.0117
yjiY Hypothetical protein YjiY2.2780.0479
mchB Microcin H47 secretion protein2.2280.0462
asnB Asparagine synthetase B (glutamine hydrolyzing)2.2040.0395
cyoD Cytochrome o ubiquinol oxidase protein2.1840.0458
narI Respiratory nitrate reductase 1 gamma chain2.1760.0278
cyoE Protoheme IX farnesyltransferase2.1760.0370+
argE Acetylornithine 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.