TABLE 1.

Top 50 genes upregulated in vivo during UTI

GeneFunctionFold changeaP value
rspA Repression of stationary-phase gene sigma-S6.0210.0059
sitA b Iron transport system SitA protein5.634<0.0001
c1903 Unknown5.5560.0018
rspB Repression of stationary-phase gene sigma-S5.532<0.0001
entE Enterobactin synthetase component E (enterochelin)5.4820.0032
chuW b Putative coproporphyrinogen III oxidase; hemin utilization5.4170.0016
yhjX Putative drug resistance protein YhjX5.4160.0312
iucA b Aerobactin protein IucA5.1660.0025
proV Glycine betaine/l-proline transport ATP-binding protein ProV5.1500.0025
entA Enterobactin system dehydrogenase5.1150.0113
entF Enterobactin synthetase component F5.0120.0134
uxuB d-mannonate oxidoreductase4.9820.0049
srlD Sorbitol-6-phosphate 2-dehydrogenase4.9120.0055
uxuA Mannonate dehydratase4.7400.0026
tyrA T protein4.6430.0002
fdnI Formate dehydrogenase, nitrate inducible4.6230.0066
deaD Cold-shock DEAD-box protein A4.6140.0024
nirD Nitrite reductase [NAD(P)H] small subunit4.6010.0022
yeaR Hypothetical protein YeaR4.5790.0018
lpxB Lipid-A-disaccharide synthase4.5700.0006
fimC Type 1 fimbriae; chaperone protein FimC precursor4.553<0.0001
c1905 b Hypothetical protein4.5520.0081
c5174 b Putative iron-regulated outer membrane virulence protein4.5390.0024
c1220 Phospho-2-dehydro-3-deoxyheptonate aldolase, Trp sensitive4.5290.0013
yhfI Hypothetical oxidoreductase YdfI4.5230.0065
iroN b Siderophore receptor IroN4.4910.0207
dut Deoxyuridine 5′-triphosphate nucleotidohydrolase4.4880.0163
chuS b Putative heme/hemoglobin transport protein; hemin utilization4.4730.0128
iroB b Putative glucosyltransferase; siderophore system4.4660.0056
iucD b Aerobactin protein IucD4.4330.0009
sitB b Iron transport system SitB protein4.4040.0020
yncE Hypothetical protein YncE precursor4.3410.0058
rplI 50S ribosomal protein L94.3180.0122
c4088 Hypothetical protein4.2710.0142
yoaG Hypothetical protein YoaG4.268<0.0001
c3610 b Putative receptor4.2420.0113
c0672 Conserved hypothetical protein4.2340.0030
c2203 Hypothetical protein4.2180.0001
kpsE b Capsule biosynthesis KpsE protein4.1270.0126
entC Isochorismate synthase EntC, enterobactin system4.1080.0011
srlE PTS system, glucitol/sorbitol-specific IIBC component4.0960.0002
rnpA Ribonuclease P protein component4.0940.0122
fimF Type 1 fimbriae; FimF protein precursor4.0840.0001
gidA Glucose inhibited division protein A4.0520.0021
marR Multiple antibiotic resistance protein MarR4.0380.0002
hmpA Flavohemoprotein (hemoglobin-like protein)3.9930.0148
glnP Glutamine transport system permease protein GlnP3.9920.0016
c4090 Hypothetical protein3.9660.0225
srlB PTS system, glucitol/sorbitol-specific IIA component3.9560.0012
chuT b Putative 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.