Table 3.

S. Typhimurium genes of interest which were downregulated during colonization of the cecal lumen, compared with expression in broth culturesa

COGs classLocus tagGeneFunction or productChange in expression level (fold)P value
Not in COGsSTM2770fljAPhase 1 flagellin repressor2.50.03
STM2304pmrDPolymyxin resistance protein B6.020.005
Amino acid transport and metabolismSTMdsdAd-Serine deaminase6.650.0036
STM3244tdcBThreonine dehydratase4.90.01
STM3240tdcGl-Serine deaminase2.60.03
Carbohydrate transport and metabolismSTM2433crrGlucose-specific IIA component10.780.026
STM4231lamBMaltoporin precursor4.40.04
STM2190mglBGalactose transport protein5.60.001
STM0684nagBGlucosamine-6-phosphate deaminase2.50.05
STM0685nagEN-Acetylglucosamine-specific enzyme IIABC2.10.04
STM2431ptsHPhosphohistidinoprotein-hexose phosphotransferase9.000.014
Cell cycleSTM3569ftsXPutative cell division protein3.30.008
STN3570ftsEPutative cell division ATPase3.30.03
STM0960ftsKCell division protein3.50.02
Energy production and conversionSTM2320nuoJNADH dehydrogenase I chain J2.30.03
STM2321nuoINADH dehydrogenase I chain I2.40.03
STM2255napCPeriplasmic nitrate reductase3.00.02
STM0440cyoDCytochrome o ubiquinol oxidase subunit IV3.40.04
STM4340frdDFumarate reductase membrane anchor polypeptide3.60.05
STM2325nuoENADH dehydrogenase I chain E4.10.03
STM2324nuoFNADH dehydrogenase I chain F3.50.05
STM0441cyoCCytochrome o ubiquinol oxidase subunit III6.960.013
STM0740cydACytochrome d terminal oxidase polypeptide subunit I6.330.0062
General functionSTM4361hfqHost factor I10.080.0005
STM1751hnsDNA-binding protein HLP-II8.730.0033
Cell motilitySTM1959fliCFlagellin14.890.00055
STM1171flgNPutative FlgK/FlgL export chaperone7.790.007
STM1920cheWChemotaxis docking protein7.260.0027
STM1183flgKFlagellar hook-associated protein 12.30.02
STM4533tsrMethyl-accepting chemotaxis protein3.90.03
STM1915cheZChemotactic response protein4.00.02
STM2771fljBPhase 2 flagellin4.00.01
STM1921cheAChemotaxis sensory histidine protein kinase4.00.02
STM1174flgBFlagellar basal body rod protein4.20.05
STM3577tcpMethyl-accepting transmembrane citrate/phenol5.20.002
    chemoreceptor
Replication, recombination, and repairSTM1339himAIntegration host factor alpha subunit3.90.013
STM3185yqiEADP-ribose pyrophosphatase3.60.007
STM0484dnaXDNA polymerase III tau/gamma subunits3.10.01
STM4170hupADNA-binding protein HU-alpha6.360.00079
Signal transduction mechanismsSTM1916cheYChemotaxis regulator6.620.01
TranscriptionSTM0900Putative helicase12.50.002
STM2875hilDInvasion protein regulatory protein10.30.008
STM1172flgMAnti-FliA factor7.710.011
STM2867hilCInvasion regulatory protein5.890.014
STM3245tdcATranscriptional activator3.00.005
STM1956fliASigma 283.00.025
TranslationSTM3728rpmB50S ribosomal subunit protein L285.920.02
STM3440rplC50S ribosomal subunit protein L32.10.04
STM3437rplB50S ribosomal subunit protein L22.220.02
STM3425rplF50S ribosomal subunit protein L62.60.02
STM3414rplQ50S ribosomal subunit protein L173.30.01
STM3438rplW50S ribosomal subunit protein L232.90.01
STM3430rplN50S ribosomal subunit protein L143.20.008
STM3422rplP50S ribosomal subunit protein L163.30.01
STM4393rpsR30S ribosomal subunit protein S182.20.03
STM3441rpsJ30S ribosomal subunit protein S102.50.02
STM0981rpsA30S ribosomal subunit protein S13.20.03
STM3447rpsG30S ribosomal subunit protein S73.60.03
STM3448rpsL30S ribosomal subunit protein S123.70.045
STM3436rpsS30S ribosomal subunit protein S193.90.012
STM3419rpmJ50S ribosomal subunit protein X3.60.02
STM1335rpmI50S ribosomal subunit protein L353.90.01
TranslocationSTM3321yhbHPutative sigma N modulation factor16.110.0049
Function unknownSTM2390yfcZPutative cytoplasmic protein9.520.0051
STM3995yihDPutative cytoplasmic protein6.990.00041
STM2697Phage tail-like protein6.870.003
STM4088yiiUPutative cytoplasmic protein6.260.0017
  • a Genes selected as genes of interest showed a >2-fold change in expression levels and a P value of <0.05.