TABLE 1.

Relative RNA levels for genes in DNA microarray comparisons of global gene expression in E. coli MG1655 grown on various media^a

Gene		Operon organization	Function	Avg relative mRNA levels obtained on LB medium with or without:
Designation	Name			Acetate	Propionate	NaCl
b0002	thrA	↓	Aspartokinase I, homoserine dehydrogenase I	1.18	2.04*	1.06
b0003	thrB	↓	Homoserine kinase	1.01	2.43	1.16
b0004	thrC	↓	Threonine synthase	1.07	2.03	0.99
b0030	yaaF	↓	ORF, hypothetical protein	0.35*	0.42*	0.93
b0064	araC	↓	Transcriptional regulator for ara operon	0.36*	0.49*	0.83*
b0124	gcd	↑	Glucose dehydrogenase	3.11*	3.36*	1.14
b0162	yaeG	↓	ORF, hypothetical protein	0.42*	0.72	1.00
b0259	yi52_1	↑	IS5 transposase	0.61*	0.50*	1.04
b0268	yagE	↓	Putative lyase/synthase	0.25*	0.33*	0.85
b0269	yagF	↓	Putative dehydratase
b0306	ykgE	↓	Putative dehydrogenase subunit	0.33	0.75	0.60
b0307	ykgF	↓	ORF, hypothetical protein	0.38*	0.76	0.25
b0308	ykgG	↓	Putative transporter	0.62*	0.78	0.80
b0311	betA	↑	Choline dehydrogenase, a flavoprotein	1.77*	2.10*	0.78
b0312	betB	↑	NAD+-dependent betaine aldehyde	1.84*	2.14*	0.94
b0313	betI	↑	Probably transcriptional repressor of bet genes	1.63*	2.07*	0.87
b0342	lacA	↑	Thiogalactoside acetyltransferase	0.88	0.93	0.91
b0343	lacY	↑	Galactoside permease (M protein)	0.58*	0.48	0.62*
b0344	lacZ	↑	β-d-Galactosidase	0.66	0.48*	0.75
b0522	purK	↑	Phosphoribosylaminoimidazole carboxylase, CO2-fixing subunit	2.11*	1.24	0.98
b0523	purE	↑	Phosphoribosylaminoimidazole carboxylase, catalytic subunit	1.90*	1.29	0.99
b0598	cstA	↓	Carbon starvation protein	0.34*	0.53*	0.75
b0679	nagE	↓	PTS, N-acetylglucosamine specific	0.44*	0.48*	0.95*
b0681	b0681	↓	ORF, hypothetical protein	0.39*	0.53*	0.91
b0682	b0682	↓	ORF, hypothetical protein	1.82
b0756	galM	↑	Galactose-1-epimerase (mutarotase)	0.79	0.91	1.02
b0757	galK	↑	Galactokinase	0.61*	0.83	0.83
b0758	galT	↑	Galactose-1-phosphate uridylytransferase	0.49*	0.69	0.67
b0759	galE	↑	UDP-galactose-4-epimerase	0.54*	0.77	0.78
b0797	rhlE	↓	Putative ATP-dependent RNA helicase	2.05*	2.27*	1.00
b0812	dps	↑	Global regulator, starvation conditions	2.14*	2.03	1.49*
b0869	b0869	↑	Putative dTDP-glucose enzyme	0.89	1.03	1.06*
b0870	b0870	↑	Putative arylsulfatase	1.07	1.01	1.32*
b0871	poxB	↑	Pyruvate oxidase	2.06*	2.99	1.42
b1015	putP	↓	Major sodium/proline symporter	0.33*	0.50*	0.77
b1070	flgN	↑	Protein of flagellar biosynthesis Fli A
b1071	flgM	↑	Anti-FliA (anti-sigma) factor; also known as RflB	2.33*	2.70*	0.95
b1072	flgA	↑	Flagellar biosynthesis, assembly of basal body	2.94*	3.19*	0.95
b1073	flgB	↓	Flagellar biosynthesis, cell-proximal portion	3.97*	5.12*	1.02
b1074	flgC	↓	Flagellar biosynthesis, cell-proximal portion	3.88*	5.61*	0.98
b1075	flgD	↓	Flagellar biosynthesis, initiation of hook	3.95*	5.67*	1.09
b1076	flgE	↓	Flagellar biosynthesis, hook protein	3.70*	6.10*	1.05
b1077	flgF	↓	Flagellar biosynthesis, cell-proximal portion	2.57*	3.73*	0.88
b1078	flgG	↓	Flagellar biosynthesis, cell-distal portion
b1079	flgH	↓	Flagellar biosynthesis, basal body outer portion	2.67*	3.79*	0.67
b1080	flgI	↓	Homolog of Salmonella P-ring of flagellum basal body	2.10	3.04*
b1081	flgJ	↓	Flagellar biosynthesis	2.56*	3.63*	0.83
b1082	flgK	↓	Flagellar biosynthesis, hook-filament junction	3.35*	4.53*	0.92
b1083	flgL	↓	Flagellar biosynthesis, hook-filament junction	2.80*	3.45*	1.12
b1156	ycfA	↑	ORF, hypothetical protein
b1157	b1157	↑	Putative fail fiber protein	0.60*	0.49*	0.90*
b1198	ycgC	↑	Putative PTS enzyme I	0.22*	0.67	1.10
b1199	b1199	↑	Putative dihydroxyacetone kinase (EC 2.7.1.2)	0.31*	0.62	1.27
b1200	b1200	↑	Putative dihydroxyacetone kinase (EC 2.7.1.2)	0.19*	0.51	0.95
b1243	oppA	↓	Oligopeptide transport, periplasmic binding	1.47*	2.19*	1.15*
b1244	oppB	↓	Oligopeptide transport, permease protein	1.54*	2.31*	1.06
b1245	oppC	↓	Oligopeptide transport permease protein	1.50*	2.18*	0.93
b1246	oppD	↓	ATP-binding protein	1.49*	2.07	0.90
b1329	b1329	↓	Putative transport periplasmic protein	0.46*	0.59*	0.91
b1370	yi52_5	↑	IS5 transposase	0.57*	0.47*	0.96
b1380	IdhA	↑	Fermentative d-lactate dehydrogenase, NAD	3.27*	1.78	1.80*
b1480	rpsV	↑	30S ribosomal subunit protein S22	2.57*	2.06	1.50
b1494	yddC	↑	Putative peptidase	0.46	0.26
b1495	yddB	↑	ORF, hypothetical protein	0.64	0.69	0.98
b1496	yddA	↑	Putative ATP-binding component of a transport system	0.68*	0.50*	0.85
b1530	marR	↓	Multiple antibiotic resistance protein, repressor	1.25*	2.08*	0.82
b1531	marA	↓	Multiple antibiotic resistance, transcription	1.16	2.16*	1.15*
b1532	marB	↓	Multiple antibiotic resistance protein	1.32	1.72*	0.95
b1621	malX	↓	PTS, maltose- and glucose-specific enzyme II	0.38*	0.57*	0.82*
b1622	malY	↓	Enzyme that may degrade or block biosynthesis	0.53*	0.66*	0.60
b1722	b1722	↑	ORF, hypothetical protein	2.32*	2.21	0.89
b1729	b1729	↓	Part of a kinase	0.96	2.28*	0.91
b1878	b1878	↑	Flagellar protein		3.33
b1879	flhA	↑	Flagellar biosynthesis, possible export of flagellar proteins	2.35*	2.52*	0.99
b1880	b1880	↑	Putative part of export apparatus for flagellar proteins	3.06*	3.56*	0.91
b1881	cheZ	↑	Chemotactic response, CheY protein	2.21	2.70*	0.94
b1882	cheY	↑	Chemotaxis regulator, transmits chemoreceptor		3.54
b1883	cheB	↑	Response regulator for chemotaxis (cheA)		1.80
b1884	cheR	↑	Response regulator for chemotaxis, protein	2.91*	2.79
b1885	tap	↑	Methyl-accepting chemotaxis protein IV	6.82	7.81
b1886	tar	↑	Methyl-accepting chemotaxis protein II	2.84*	2.31*	1.12*
b1891	flhC	↑	Regulator of flagellar biosynthesis	1.61*	2.04*	1.08
b1892	flhD	↑	Regulator of flagellar biosynthesis	1.54*	1.92*	0.94
b1896	otsA	↑	Trehalose-6-phosphate synthase	2.23*	2.13	1.31
b1897	otsB	↑	Trehalose-6-phosphate phophatase	2.38*	2.14	1.40
b1917	b1917	↑	Putative ATP-binding component of a transport system	1.27	1.46
b1918	yecC	↑	Putative transport system permease protein		1.25	0.80
b1919	b1919	↑	Putative 1-aminocyclopropane-1-carboxylate	1.30	1.57*	0.73
b1920	fliY	↑	Putative periplasmic binding protein	1.92*	2.10*	1.09
b1921	fliZ	↑	ORF, hypothetical protein	3.38*	3.80*	1.09*
b1922	fliA	↑	Flagellar biosynthesis, alternative sigma factor	4.82*	5.86*	1.26*
b1923	fliC	↑	Flagellar biosynthesis, flagellin, filament	21.46	10.39	1.03
b1924	fliD	↓	Flagellar biosynthesis, filament capping protein	5.87*	5.48*
b1925	fliS	↓	Flagellar biosynthesis, repressor of class 3a	2.89*	2.76*	0.91
b1926	fliT	↓	Flagellar biosynthesis, repressor of class 3a	1.09	1.21	0.82
b1936	b1936	↓	ORF, hypotheticla protein	2.50*	2.93*	1.05
b1937	fliE	↑	Flagellar biosynthesis, basal body component	4.07*	4.75*	1.23
b1938	fliF	↓	Flagellar biosynthesis, basal body	2.01*	2.90*	0.91
b1939	fliG	↓	Flagellar biosynthesis, component of motor	2.96*	3.75*	1.10
b1940	fliH	↓	Flagellar biosynthesis, export of flagellar proteins?	2.28*	2.92*	0.91
b1941	fliI	↓	Flagellum-specific ATP synthase	3.36*	3.94*	0.76
b1942	fliJ	↓	Flagellar fliJ protein	3.00*	3.74*	0.71
b1943	fliK	↓	Flagellar hook-length control protein	3.12*	4.76*	0.78
b1944	fliL	↓	Flagellar biosynthesis	2.27*	3.25*	0.85
b1945	fliM	↓	Flagellar biosynthesis, component of motor	1.96*	2.61*	0.78
b1946	fliN	↓	Flagellar biosynthesis, component of motor
b1947	fliO	↓	Flagellar biosynthesis	2.25*	3.05*	0.77
b1948	fliP	↓	Flagellar biosynthesis	2.26*	2.79*	0.66
b1949	fliQ	↓	Flagellar biosynthesis	2.61*	3.22*
b1950	fliR	↓	Flagellar biosynthesis	3.73	4.05*
b1976	b1976	↓	ORF, hypothetical protein	0.49*	0.56	1.25
b1994	yi52_6	↑	IS5 transposase	0.69*	0.50*	1.09
b2146	b2146	↓	Putative oxidoreductase	0.27	0.69*
b2147	yeiA	↓	Putative oxidoreductase	0.47*	0.87	0.67
b2148	mgIC	↑	Methyl-galactoside transport and galactose taxis	0.29*	0.48	0.60*
b2149	mgIA	↑	ATP-binding component of methyl-galactoside	0.28*	0.48	0.62*
b2150	mgIB	↑	Galactose-binding transport protein, receptor for galactose taxis	0.22*	0.43	0.70*
b2151	galS	↑	mgl repressor, galactose operon inducer	0.30*	0.45*	0.83
b2192	yi52_8	↑	IS5 transposase	0.64*	0.50*	1.01
b2210	yojH	↑	ORF, hypothetical protein	2.11*	2.93*	1.02
b2239	glpQ	↑	Glycerophosphodiester phosphodiesterase	0.59*	0.75	1.39
b2240	glpT	↑	sn-Glycerol-3-phosphate permease	0.49*	0.68	1.39
b2241	glpA	↓	sn-Glycerol-3-phosphate dehydrogenase	0.32*	0.51	0.66*
b2242	glpB	↓	sn-Glycerol-3-phosphate dehydrogenase	0.37*	0.56	0.78
b2243	glpC	↓	sn-Glycerol-3-phosphate dehydrogenase	0.39*	0.65	0.67*
b2341	b2341	↑	Putative enzyme	0.45*	0.60*	0.85*
b2342	b2342	↑	Putative acyltransferase	0.38*	0.63*	0.76*
b2364	dsdC	↑	d-Serine dehydratase (deaminase)	0.40*	0.60*	1.01
b2365	dsdX	↓	Transport system permease (serine?)	1.00
b2366	dsdA	↓	d-Serine dehydratase (deaminase)	0.21*	0.85	0.90
b2388	glk	↑	Glucokinase	0.42*	0.48*	1.48
b2428	b2428	↓	Putative regulator	0.59*	0.66	0.74
b2429	b2429	↓	Putative PTS enzyme II	0.35*	0.40*	0.50
b2430	b2430	↓	Putative β-lactamase	0.48*	0.54*	0.70*
b2535	csiE	↓	ORF, hypothetical protein	0.38*	0.55	0.69
b2537	hcaR	↑	Transcriptional activator of hca cluster	0.38*	0.53*	0.82
b2595	b2595	↓	ORF, hypothetical protein	1.38	1.27	1.55*
b2596	b2596	↓	ORF, hypothetical protein	0.43*	0.67	1.02
b2597	yfiA	↓	Putative yhbH sigma 54 modulator	0.69	0.69	1.78*
b2677	proV	↓	ATP-binding component of transport system	1.56*	2.25	1.85*
b2678	proW	↓	High-affinity transport system for glycine	1.55*	2.24*	1.74*
b2679	proX	↓	High-affinity transport system for glycine	1.85*	2.78*	1.85*
b2680	b2680	↓	ORF, hypothetical protein	1.65*	2.33*	1.20
b2681	b2681	↓	Putative transport protein	0.97	1.54*	0.87
b2702	srlA1	↓	PTS, glucitol/sorbitol-specific IIC component	0.14*	0.38*	0.93
b2703	srlA2	↓	PTS, glucitol/sorbitol-specific IIB component	0.15*	0.42*	0.91
b2704	srlB	↓	PTS, glucitol/sorbitol-specific enzyme	0.18*	0.50*	0.95
b2705	srlD	↓	Glucitol (sorbitol)-6-phosphate dehydrogenase	0.30*	0.72	1.14*
b2706	gutM	↓	Glucitol operon activator	0.25*	0.54	0.68*
b2707	srlR	↓	Regulator for gut (srl), glucitol operon	0.43*	0.62*	0.84*
b2708	gutQ	↓	ORF, hypothetical protein	0.77	0.77*	0.82
b2797	sdaB	↓	l-Serine dehydratase (deaminase)	0.43	0.27*	0.71*
b2798	exo	↓	5′-3′ Exonuclease	0.77	0.66*	0.94
b2801	fucP	↓	Fucose permease	0.51*	0.65	0.82
b2802	fucI	↓	l-Fucose isomerase	0.66	0.67	0.83
b2803	fucK	↓	l-Fuculokinase			0.30
b2804	fucU	↓	Protein of fucose operon	0.81	1.01	1.14*
b2805	fucR	↓	Positive regulator of the fuc operon	0.42*	0.48*	1.18*
b2844	b2844	↑	Putative acyltransferase	0.41*	0.55*	0.83
b2869	b2869	↑	Putative transcriptional regulator	0.41	0.49*	1.25
b2924	yggB	↑	Component of MscS	2.15*	1.56*	1.59*
b2973	b2973	↑	ORF, hypothetical protein	0.32*	0.25*	0.86
b2974	b2974	↑	Putative endoglucanase	0.27*	0.23	0.92
b3072	air	↑	Aerotaxis sensor receptor, flavoprotein	1.65*	2.08*	0.99
b3076	ebgA	↓	Evolved β-d-galactosidase, alpha subunit	0.39*	0.55	0.52
b3077	ebgC	↓	Evolved β-d-galactosidase, beta subunit
b3093	exuT	↓	Transport of hexuronates	0.32*	0.48*	0.58
b3112	tdcG	↑	l-Serine deaminase 3	0.80	0.86*
b3113	tdcF	↑	ORF, hypothetical protein	0.71*	1.01	0.86
b3114	tdcE	↑	2-Ketobutyrate formate lyase	0.74*	0.77	0.83*
b3115	tdcD	↑	Propionate kinase/acetate kinase C
b3116	tdcC	↑	Anaerobically inducible l-threonine, l-serine	0.26*	0.47*	0.80
b3117	tdcB	↑	Threonine dehydratase, catabolic	0.31	0.07*	0.38
b3118	tdcA	↑	Transcriptional activator of tdc operon	0.49*	0.37	1.02
b3218	yi52_10	↑	IS5 transposase	0.61*	0.50*	1.04
b3221	yhcH	↑	ORF, hypothetical protein	0.27*	0.47	0.86
b3222	nanK	↑	ManNAc kinase	0.22*	0.29	0.78*
b3223	nanE	↑	ManNAc epimerase	0.21*	0.32	0.81*
b3224	nanT	↑	Sialic acid transporter	0.15*	0.26	0.67*
b3225	nanA	↑	N-Acetylneuraminate lyase (aldolase)	0.13*	0.29	0.76*
b3418	malT	↓	Positive regulator of mal regulon	0.42*	0.62*	1.11*
b3509	hdeB	↑	ORF, hypothetical protein	4.26*	2.30*	1.21*
b3510	hdeA	↑	ORF, hypothetical protein	6.16*	3.82*	1.35
b3525	yhjH	↑	ORF, hypothetical protein	2.17*	2.42*	0.92
b3528	dctA	↑	Uptake of C4-dicarboxylic acids	0.38*	0.63	0.65*
b3603	IldP	↓	l-Lactate permease	0.34*	0.46	0.51*
b3686	hslS	↑	Heat shock protein	1.23	2.06*	1.12*
b3708	tnaA	↓	Tryptophanase	0.16*	0.31	1.41
b3709	tnaB	↓	Low-affinity tryptophan permease	0.10*	0.26	0.89
b3748	rbsD	↓	d-Ribose high-affinity transport system	0.49*	0.73*	0.97
b3749	rbsA	↓	ATP-binding component of d-ribose high-affinity transport system	0.41	0.62	0.75
b3750	rbsC	↓	d-Ribose high-affinity transport system	0.51*	0.80	0.65*
b3751	rbsB	↓	Periplasmic d-ribose binding protein	0.62*	0.98	1.26*
b3752	rbsK	↓	Ribokinase	0.61*	0.89	0.98
b3845	fadA	↑	Thiolase I, 3-ketoacyl-CoA thiolase, acetyl-CoA	0.67*	1.10	0.83
b3846	fadB	↑	Four-enzyme protein, 3-hydroxyacyl-CoA	0.39*	0.71	0.81*
b3872	b3872	↓	Putative transcriptional regulator	0.54*	0.67*	0.89*
b3873	yihM	↓	ORF, hypothetical protein	0.38*	0.48*	1.25*
b3907	rhaT	↑	Rhamnose transport	0.14*	0.46	0.84
b3926	glpK	↑	Glycerol kinase	0.49*	0.67	0.80
b3927	glpF	↑	Facilitated diffusion of glycerol	0.41*	0.57	0.72
b4014	aceB	↓	Malate synthase A	1.59	3.31*	1.35*
b4015	aceA	↓	Isocitrate lyase	1.57*	2.67*	1.46*
b4016	aceK	↓	Isocitrate dehydrogenase kinase/phosphatase	1.50*	2.39	1.45
b4032	malG	↑	Part of maltose permease, inner membrane	0.03	0.09	1.32
b4033	malF	↑	Part of maltose permease, periplasmic	0.18	0.21	0.79
b4034	malE	↑	Periplasmic maltose-binding protein, substrate	0.46*	0.58*	1.18
b4055	yjbP	↓	Diadenosine tetraphosphatase	0.40*	0.50*	1.09
b4118	melR	↑	Regulator of melibiose operon	0.47*	0.73*	0.69
b4139	aspA	↑	Aspartate ammonia lyase (aspartase)	0.37*	0.45*	1.38
b4188	yjfN	↑	ORF, hypothetical protein	0.39*	0.50	0.67
b4189	yjfO	↑	ORF, hypothetical protein	0.28*	0.40*	0.88
b4239	treC	↑	Trehalase-6-phosphate hydrolase	0.31*	0.38	0.77*
b4240	treB	↑	PTS enzyme II, trehalose specific	0.23	0.25*	0.98
b4312	fimB	↓	Recombinase involved in phase variation	1.32	2.42	1.38*
b4313	fimE	↓	Recombinase involved in phase variation
b4314	fimA	↓	Major type 1 subunit fimbrin (pilin)	2.00	2.06*	1.02
b4315	fimI	↓	Fimbrial protein	4.04*	5.23*	0.94
b4316	fimC	↓	Periplasmic chaperone, required for type 1 fimbriae	3.91*	4.32*	0.71
b4317	fimD	↓	Outer membrane protein, export and assembly	0.86	1.30	0.82
b4318	fimF	↓	Fimbrial morphology	1.88*	2.32*	0.76
b4319	fimG	↓	Fimbrial morphology	3.04*	3.01*	0.75
b4320	fimH	↓	Minor fimbrial subunit, d-mannose specific	2.19*	2.35*	0.78
b4322	uxuA	↓	Mannonate hydrolase	0.29*	0.43*	0.86
b4323	uxuB	↓	d-Mannonate oxidoreductase	0.74	0.75	0.99
b4353	yjiX	↑	ORF, hypothetical protein	0.45*	0.53*	0.89
b4354	yjiY	↑	Putative carbon starvation protein	0.44*	0.46	0.90
b4357	yjjM	↑	ORF, hypothetical protein	0.32	0.48*
b4372	holD	↓	DNA polymerase III, psi subunit	1.44*	1.53	0.83
b4373	rimI	↓	Acyltransferase for 30S ribosomal subunit	1.13	1.32	0.83
b4374	yjjG	↓	Putative phosphatase	1.26*	1.41	0.97
b4375	prfC	↓	Peptide chain release factor RF-3	1.22	1.49	0.88
b4376	osmY	↓	Hyperosmotically inducible periplasmic protein	3.52*	3.02*	1.69*

^aMedia tested were LB, LB-20 mM sodium acetate, LB-20 mM sodium propionate, and LB-20 mM NaCl. Asterisks indicate significant RNA level differences (P value, <0.05; Student's t test) that exceeded 2-fold or were below 0.5-fold. For operons, RNA levels for all genes are given. At least three independent cultivations and DNA microarray experiments were performed. ORF, open reading frame.