Table 2.

S. Typhimurium genes of interest which were upregulated during colonization of the cecal lumen, compared to gene expression in broth culturesa

COGs classLocus tagGeneFunction or productChange in expression level (fold)P value
Not in COGsSTM1144csgAMajor curlin subunit precursor3.90.002
STM1601ugtLPutative exported protein2.90.02
STM1602sifBSecreted effector3.40.01
STM1384ttrCTetrathionate reductase complex subunit C2.30.03
STM0550fimYPutative regulatory protein3.10.01
STM1143csgBMinor curlin subunit precursor4.20.04
STM3758fidLPutative inner protein2.20.04
Amino acid transport and metabolismSTM0878potGPutrescine transporter5.60.03
STM2992argAN-α-acetylglutamate synthase4.60.03
STM4296adiCatabolic arginine decarboxylase4.40.047
STM1094pipDPathogenicity island-encoded protein D4.10.05
STM4105metF5,10-Methylenetetrahydrofolate reductase3.60.03
STM3965metE5-Methyltetrahydropteriryltriglutamate-homocystein S-methyltransferase2.20.04
STM3086speAArginine decarboxylase3.60.02
STM0887artJArginine transport system component2.40.02
STM2055pduUPolyhedral body protein3.70.05
STM2056pduVPropanediol utilization protein2.80.01
STM2469eutPPutative ethanolamine utilization protein3.50.0006
STM2468eutQPutative ethanolamine utilization protein3.00.007
STM0877potFPutrescine transporter2.50.05
STM0878potGPutrescine transporter5.60.03
Carbohydrate transport and metabolismSTM1928otsATrehalose-6-phosphate synthase4.30.03
STM4298melAα-Galactosidase3.20.04
STM3674lyxKl-Xylulose kinase2.00.047
STM3675sgbHPutative 3-hexulose-6-phosphate isomerase3.10.02
STM0018Putative exochitinase3.00.014
STM1560Putative α-amylase2.90.008
STM3254Putative fructose-1-phosphate kinase2.70.009
STM3671Putative transporter3.00.02
Energy production and conversionSTM0369prpCPutative citrate synthase6.00.004
STM1383ttrATetrathionate reductase complex subunit A4.60.03
STM2057pduWPropionate kinase3.40.02
General functionSTM0370prpD2-Methylcitrate dehydratase7.10.001
Inorganic ion transportSTM2862sitBPutative ATP-binding protein2.80.04
STM0206butFPutative periplasmic cobalamin-binding protein2.60.01
STM2863sitCPutative permease2.30.05
LipidSTM0371prpEPutative acetyl-CoA synthetase3.50.003
MotilitySTM0339stbBPutative fimbrial chaperone2.80.01
STM0195stfAPutative fimbrial subunit3.40.02
STM4593sthBPutative fimbrial usher protein2.60.05
STM0198stfEPutative minor fimbrial subunit3.10.02
STM0199stfFPutative minor fimbrial subunit3.70.03
STM0200stfGPutative minor fimbrial subunit3.50.02
ReplicationSTM2150stcCPutative outer membrane protein2.30.04
STM0395sbcCATP-dependent dsDNA exonuclease2.90.01
STM1992dcmDNA cytosine methylase3.40.01
STM2996recCExonuclease V subunit2.30.02
Secondary metabolites biosynthesis, transport and catabolismSTM2046pduKPolyhedral body protein4.10.03
STM2054pduTPolyhedral body protein2.60.04
STM2047pduLPropanediol utilization protein3.50.03
STM2465eutMPutative detox protein2.40.02
STM2464eutNPutative detox protein2.40.02
TranscriptionSTM3964metRmetE/metH regulator2.20.03
STM3756rmbAPutative cytoplsmic protein3.10.04
STM0552fimWPutative fimbrial protein3.00.02
TranslationSTM1909argSArginine tRNA synthetase2.00.04
Function unknownSTM1088pipBSecreted effector protein5.50.01
STM3764mgtCMg2+ transport protein2.50.05
STM0884Putative inner membrane protein4.80.04
  • a Genes selected as genes of interest showed a >2-fold increase in expression levels and a P value of <0.05.