TABLE 1.

Top 50 genes upregulated in vivo during UTI

GeneFunctionFold changeaP value
rspARepression of stationary-phase gene sigma-S6.0210.0059
sitAbIron transport system SitA protein5.634<0.0001
c1903Unknown5.5560.0018
rspBRepression of stationary-phase gene sigma-S5.532<0.0001
entEEnterobactin synthetase component E (enterochelin)5.4820.0032
chuWbPutative coproporphyrinogen III oxidase; hemin utilization5.4170.0016
yhjXPutative drug resistance protein YhjX5.4160.0312
iucAbAerobactin protein IucA5.1660.0025
proVGlycine betaine/l-proline transport ATP-binding protein ProV5.1500.0025
entAEnterobactin system dehydrogenase5.1150.0113
entFEnterobactin synthetase component F5.0120.0134
uxuBd-mannonate oxidoreductase4.9820.0049
srlDSorbitol-6-phosphate 2-dehydrogenase4.9120.0055
uxuAMannonate dehydratase4.7400.0026
tyrAT protein4.6430.0002
fdnIFormate dehydrogenase, nitrate inducible4.6230.0066
deaDCold-shock DEAD-box protein A4.6140.0024
nirDNitrite reductase [NAD(P)H] small subunit4.6010.0022
yeaRHypothetical protein YeaR4.5790.0018
lpxBLipid-A-disaccharide synthase4.5700.0006
fimCType 1 fimbriae; chaperone protein FimC precursor4.553<0.0001
c1905bHypothetical protein4.5520.0081
c5174bPutative iron-regulated outer membrane virulence protein4.5390.0024
c1220Phospho-2-dehydro-3-deoxyheptonate aldolase, Trp sensitive4.5290.0013
yhfIHypothetical oxidoreductase YdfI4.5230.0065
iroNbSiderophore receptor IroN4.4910.0207
dutDeoxyuridine 5′-triphosphate nucleotidohydrolase4.4880.0163
chuSbPutative heme/hemoglobin transport protein; hemin utilization4.4730.0128
iroBbPutative glucosyltransferase; siderophore system4.4660.0056
iucDbAerobactin protein IucD4.4330.0009
sitBbIron transport system SitB protein4.4040.0020
yncEHypothetical protein YncE precursor4.3410.0058
rplI50S ribosomal protein L94.3180.0122
c4088Hypothetical protein4.2710.0142
yoaGHypothetical protein YoaG4.268<0.0001
c3610bPutative receptor4.2420.0113
c0672Conserved hypothetical protein4.2340.0030
c2203Hypothetical protein4.2180.0001
kpsEbCapsule biosynthesis KpsE protein4.1270.0126
entCIsochorismate synthase EntC, enterobactin system4.1080.0011
srlEPTS system, glucitol/sorbitol-specific IIBC component4.0960.0002
rnpARibonuclease P protein component4.0940.0122
fimFType 1 fimbriae; FimF protein precursor4.0840.0001
gidAGlucose inhibited division protein A4.0520.0021
marRMultiple antibiotic resistance protein MarR4.0380.0002
hmpAFlavohemoprotein (hemoglobin-like protein)3.9930.0148
glnPGlutamine transport system permease protein GlnP3.9920.0016
c4090Hypothetical protein3.9660.0225
srlBPTS system, glucitol/sorbitol-specific IIA component3.9560.0012
chuTbPutative periplasmic binding protein; hemin utilization3.9560.0270
  • a Fold change refers to growth in vivo relative to growth in LB.

  • b This gene was not present in E. coli K-12.