Table 2.

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

COGs class	Locus tag	Gene	Function or product	Change in expression level (fold)	P value
Not in COGs	STM1144	csgA	Major curlin subunit precursor	3.9	0.002
	STM1601	ugtL	Putative exported protein	2.9	0.02
	STM1602	sifB	Secreted effector	3.4	0.01
	STM1384	ttrC	Tetrathionate reductase complex subunit C	2.3	0.03
	STM0550	fimY	Putative regulatory protein	3.1	0.01
	STM1143	csgB	Minor curlin subunit precursor	4.2	0.04
	STM3758	fidL	Putative inner protein	2.2	0.04
Amino acid transport and metabolism	STM0878	potG	Putrescine transporter	5.6	0.03
	STM2992	argA	N-α-acetylglutamate synthase	4.6	0.03
	STM4296	adi	Catabolic arginine decarboxylase	4.4	0.047
	STM1094	pipD	Pathogenicity island-encoded protein D	4.1	0.05
	STM4105	metF	5,10-Methylenetetrahydrofolate reductase	3.6	0.03
	STM3965	metE	5-Methyltetrahydropteriryltriglutamate-homocystein S-methyltransferase	2.2	0.04
	STM3086	speA	Arginine decarboxylase	3.6	0.02
	STM0887	artJ	Arginine transport system component	2.4	0.02
	STM2055	pduU	Polyhedral body protein	3.7	0.05
	STM2056	pduV	Propanediol utilization protein	2.8	0.01
	STM2469	eutP	Putative ethanolamine utilization protein	3.5	0.0006
	STM2468	eutQ	Putative ethanolamine utilization protein	3.0	0.007
	STM0877	potF	Putrescine transporter	2.5	0.05
	STM0878	potG	Putrescine transporter	5.6	0.03
Carbohydrate transport and metabolism	STM1928	otsA	Trehalose-6-phosphate synthase	4.3	0.03
	STM4298	melA	α-Galactosidase	3.2	0.04
	STM3674	lyxK	l-Xylulose kinase	2.0	0.047
	STM3675	sgbH	Putative 3-hexulose-6-phosphate isomerase	3.1	0.02
	STM0018		Putative exochitinase	3.0	0.014
	STM1560		Putative α-amylase	2.9	0.008
	STM3254		Putative fructose-1-phosphate kinase	2.7	0.009
	STM3671		Putative transporter	3.0	0.02
Energy production and conversion	STM0369	prpC	Putative citrate synthase	6.0	0.004
	STM1383	ttrA	Tetrathionate reductase complex subunit A	4.6	0.03
	STM2057	pduW	Propionate kinase	3.4	0.02
General function	STM0370	prpD	2-Methylcitrate dehydratase	7.1	0.001
Inorganic ion transport	STM2862	sitB	Putative ATP-binding protein	2.8	0.04
	STM0206	butF	Putative periplasmic cobalamin-binding protein	2.6	0.01
	STM2863	sitC	Putative permease	2.3	0.05
Lipid	STM0371	prpE	Putative acetyl-CoA synthetase	3.5	0.003
Motility	STM0339	stbB	Putative fimbrial chaperone	2.8	0.01
	STM0195	stfA	Putative fimbrial subunit	3.4	0.02
	STM4593	sthB	Putative fimbrial usher protein	2.6	0.05
	STM0198	stfE	Putative minor fimbrial subunit	3.1	0.02
	STM0199	stfF	Putative minor fimbrial subunit	3.7	0.03
	STM0200	stfG	Putative minor fimbrial subunit	3.5	0.02
Replication	STM2150	stcC	Putative outer membrane protein	2.3	0.04
	STM0395	sbcC	ATP-dependent dsDNA exonuclease	2.9	0.01
	STM1992	dcm	DNA cytosine methylase	3.4	0.01
	STM2996	recC	Exonuclease V subunit	2.3	0.02
Secondary metabolites biosynthesis, transport and catabolism	STM2046	pduK	Polyhedral body protein	4.1	0.03
	STM2054	pduT	Polyhedral body protein	2.6	0.04
	STM2047	pduL	Propanediol utilization protein	3.5	0.03
	STM2465	eutM	Putative detox protein	2.4	0.02
	STM2464	eutN	Putative detox protein	2.4	0.02
Transcription	STM3964	metR	metE/metH regulator	2.2	0.03
	STM3756	rmbA	Putative cytoplsmic protein	3.1	0.04
	STM0552	fimW	Putative fimbrial protein	3.0	0.02
Translation	STM1909	argS	Arginine tRNA synthetase	2.0	0.04
Function unknown	STM1088	pipB	Secreted effector protein	5.5	0.01
	STM3764	mgtC	Mg2+ transport protein	2.5	0.05
	STM0884		Putative inner membrane protein	4.8	0.04

^aGenes selected as genes of interest showed a >2-fold increase in expression levels and a P value of <0.05.