TABLE 1.

Genes significantly (adjusted P value of <0.05) induced 1.5-fold or greater upon exposure to MAJ

Category and ECs no.a	Geneb	Log2 expression ratio
		MAJ/MOPS	Exponential phase/stationary phasec
Amino acid biosynthesis
ECs0512	ylaD	1.01
ECs0646	ybdQ	1.06	−2.52
ECs0704	asnB	0.77	2.72
ECs2509	yeaU	4.51
ECs2638	O157	0.60
ECs2784	nac	3.69
ECs3696	lysR	0.64
ECs4791	glnL	1.94	1.78
ECs4867	metJ	1.07	−1.34
ECs4937	metH	0.73	1.71
Biosynthesis of cofactors, prosthetic groups, and carriers
ECs0475	ispA	1.03	1.60
ECs0632	entC	1.03
ECs2594	cheR	2.98	1.49
ECs5311	yjiA	0.89	−0.91
Cell envelope
ECs0100	lpxC	0.99
ECs1428	yceK	0.65	−2.08
ECs2001	hslJ	2.25	1.35
ECs2306	mdtJ	1.98	2.63
ECs2348	ydhA	0.87	1.04
ECs2515	yeaY	0.92	−1.40
ECs2690	rcsA	1.59	2.43
ECs2859	wcaF	1.45	1.15
ECs2914	O157	0.64
ECs3151	yfbB	1.11
ECs3669	ygdI	2.83
ECs3860	O157	0.93	0.85
ECs4321	dcrB	1.30	1.58
ECs4493	yibD	0.79	−1.54
ECs4666	O157	1.73	1.51
ECs4884	yijP	1.30	1.65
ECs5011	yjbG	1.32
ECs5098	adiY	1.34
ECs5188	ytfF	0.86	1.22
ECs5350	slt	0.90	0.82
Cellular processes
ECs2086	osmC	1.59
ECs3258	ddg	0.73	−1.37
ECs1351	terZ	1.16	2.28
ECs1652	O157	1.60
ECs1766	O157	0.72	2.36
ECs2086	osmC	1.59
ECs2365	sodB	0.70
ECs2511	yeaW	0.74
ECs2597	cheW	1.79	2.89
ECs2974	stx1A	0.63	0.89
ECs3910	mdaB	3.68
ECs4307	O157	1.18
ECs4367	uspA	0.79
ECs4399	treF	1.11	−1.99
ECs4626	ibpB	1.87
ECs4971	O157	0.93
ECs5233	yjgM	1.23	1.69
ECs5313	yjiY	0.76	−0.74
ECs5315	tsr	1.17
Central intermediary metabolism
ECs0899	ybiV	1.17	1.97
ECs1487	ndh	1.99	1.61
ECs2132	yneI	1.23
ECs2239	O157	1.36
ECs2511	yeaW	0.74
ECs3604	cysC	1.41
ECs3668	gcvA	0.88
ECs5086	phnE	0.85
DNA metabolism
ECs1477	holB	1.47	1.11
ECs2056	yncE	0.71
ECs2571	ruvA	0.85
ECs3556	recA	0.96	0.68
Energy metabolism
ECs0117	pdhR	2.02
ECs0512	ylaD	1.01
ECs1054	yccA	1.93	1.95
ECs1487	ndh	1.99	1.61
ECs1862	O157	1.54	1.34
ECs2002	ldhA	0.62	−0.97
ECs2056	yncE	0.71
ECs2078	fdnG	0.85
ECs2132	yneI	1.23
ECs2239	O157	1.36
ECs2511	yeaW	0.74
ECs2583	yecK	1.26
ECs3346	hyfD	0.92	−2.17
ECs3527	ygaE	0.84
ECs4217	nirD	1.30
ECs4355	O157	1.12	1.32
ECs4399	treF	1.11	−1.99
ECs4627	ibpA	1.66
ECs4819	fdoH	0.98
ECs4820	fdoG	1.02
ECs4867	metJ	1.07	−1.34
ECs4934	aceK	1.65
ECs5003	O157	1.06
ECs5055	nrfD	0.57	1.70
ECs5061	fdhF	1.06	−2.00
ECs5216	treC	1.02
Fatty acid and phospholipid metabolism
ECs0529	ybaC	0.57
ECs1255	rutD	1.67	1.46
ECs1682	fadR	0.97	0.96
ECs3693	aas	1.00	1.38
Mobile element functions
ECs1881	pspA	1.80
ECs1882	pspB	0.99
ECs3240	O157	1.07
ECs4535	O157	0.91
ECs4537	O157	0.93
ECs4960	O157	1.18	0.88
Protein fate
ECs0165	htrA	1.34
ECs0813	O157	0.63
ECs2056	yncE	0.71
ECs2539	htpX	1.80	1.39
ECs2882	mdtA	0.90
ECs4007	sohA	0.59
ECs4626	ibpB	1.87
ECs5122	yjeH	0.77
Protein synthesis
ECs3077	rplY	0.67	4.06
ECs3398	trmJ	0.65	1.76
ECs3460	yfiA	1.66
ECs3503	O157	0.62
ECs4968	O157	1.24	−1.19
ECs4969	O157	0.87
ECs4970	O157	0.77
ECs4977	O157	0.99	1.19
ECs4982	O157	1.03	−1.03
ECs5147	miaA	2.13	1.40
ECs5350	slt	0.90	0.82
Purines, pyrimidines, and nucleotides
ECs1476	tmk	1.52	1.30
ECs2559	purT	1.02
ECs3117	nrdA	1.37	1.64
ECs4947	O157	1.17
ECs5191	cpdB	0.76
Regulatory functions
ECs0504	glnK	4.88
ECs0507	ybaY	2.08
ECs0755	O157	1.12
ECs0902	ybiY	1.34
ECs0967	yljA	0.64
ECs1199	O157	0.67
ECs1250	O157	1.52
ECs1489	ycfQ	1.14
ECs1557	O157	0.58	0.68
ECs1682	fadR	0.97	0.96
ECs1880	pspF	0.75	−1.65
ECs2445	osmE	1.61	−1.27
ECs2706	yedV	1.08	1.19
ECs2783	cbl	1.95	1.36
ECs2784	nac	3.69
ECs2988	O157	0.65
ECs2993	O157	1.01
ECs3014	yehV	1.09	1.33
ECs3058	yeiC	1.79	1.61
ECs3136	yfaX	2.23	1.92
ECs3260	ypdA	1.05	−1.04
ECs3427	yfhH	0.90
ECs3668	gcvA	0.88
ECs3911	ygiN	1.83
ECs4310	rpoH	1.23
ECs4697	yieP	0.75	1.05
ECs4867	metJ	1.07	−1.34
ECs4890	oxyR	0.69	1.75
ECs5004	O157	1.18	−0.67
ECs5044	soxS	1.77	2.05
ECs5313	yjiY	0.76	−0.74
ECs5325	yjjQ	0.76
Transcription
ECs3248	evgA	0.89	−0.71
ECs4048	rbfA	1.30	0.87
ECs4060	greA	1.51
ECs4310	rpoH	1.23
ECs5220	yjgF	0.65	2.49
Transport and binding proteins
ECs0377	O157	0.63	−1.60
ECs0505	amtB	4.01
ECs0537	copA	0.80
ECs0624	fes	1.26
ECs0694	ybeJ	1.42
ECs0780	ybgR	2.04
ECs0887	glnQ	1.21	1.06
ECs0888	glnP	1.85
ECs0889	glnH	2.08
ECs1746	oppD	1.11	−2.23
ECs2087	ddpF	1.04	1.03
ECs2103	ydeN	0.79
ECs2302	ynfM	1.61
ECs2443	celB	0.69
ECs2510	yeaV	1.28
ECs2569	yebI	1.21
ECs3061	fruB	0.65
ECs3354	focB	2.21	2.38
ECs3540	proV	1.99
ECs3541	proW	1.57	1.62
ECs3543	ygaY	0.80
ECs3819	galP	1.41	2.38
ECs4013	O157	0.65
ECs4250	feoA	1.30
ECs4352	O157	1.07	−0.84
ECs4422	dppC	0.65	0.75
ECs4450	xylG	0.68
ECs4646	tnaB	1.09
ECs4839	cpxP	3.12
ECs5086	phnE	0.85
ECs5093	proP	1.76	1.25
ECs5316	yjiZ	1.32	0.94
Viral functions
ECs0278	O157	0.59
ECs0507	ybaY	2.08
ECs0902	ybiY	1.34
ECs0967	yljA	0.64
ECs1110	O157	0.60
ECs1758	O157	1.50	−0.94
ECs3058	yeiC	1.79	1.61
ECs3503	O157	0.62
ECs3911	ygiN	1.83
ECs4588	ler	1.17	2.17
ECs4968	O157	1.24	−1.19
ECs4969	O157	0.87
ECs4970	O157	0.77
ECs4977	O157	0.99	1.19
ECs4982	O157	1.03	−1.03
Hypothetical or unknown function
ECs0069	yabI	1.07
ECs0191	yaeO	1.18	−1.18
ECs0202	yaeD	1.15	1.66
ECs0203	yafB	3.25
ECs0214	O157	0.70	−1.50
ECs0233	O157	0.88
ECs0239	O157	0.74	−0.87
ECs0247	ykfE	2.23	1.75
ECs0252	yafQ	0.80
ECs0253	dinJ	1.42	−1.38
ECs0266	yafA	0.74
ECs0272	O157	0.62
ECs0429	yaiY	2.49	1.74
ECs0445	rdgC	1.17	2.00
ECs0478	thiJ	0.68	1.69
ECs0514	ybaJ	1.14
ECs0552	ybbK	1.27
ECs0561	ybbD	1.27
ECs0629	fepD	1.10	−0.58
ECs0646	ybdQ	1.06	−2.52
ECs0661	crcA	2.45
ECs0728	ybfA	2.23	−2.16
ECs0781	ybgS	3.38
ECs0896	ybiS	0.87	1.84
ECs0963	ybjX	1.07	1.60
ECs1068	O157	1.29	−0.95
ECs1091	pchA	2.07	−1.79
ECs1180	O157	1.32
ECs1181	O157	1.17	−0.87
ECs1182	O157	1.27	−1.25
ECs1183	O157	1.45	1.17
ECs1184	O157	1.14
ECs1197	O157	1.52	−1.15
ECs1198	O157	1.10	−1.33
ECs1243	O157	0.89
ECs1246	O157	0.80	−0.86
ECs1293	O157	0.61
ECs1318	O157	1.16	−1.23
ECs1342	O157	0.66
ECs1350	O157	0.57
ECs1397	O157	0.90
ECs1438	yceP	1.76	−1.80
ECs1441	yceB	1.49
ECs1488	ycfJ	4.02	2.83
ECs1490	ycfR	4.88
ECs1576	O157	0.69	−1.18
ECs1588	O157	0.77
ECs1593	O157	1.34	−0.82
ECs1612	O157	0.70
ECs1654	O157	0.99
ECs1655	O157	0.72	−1.60
ECs1691	ycgR	1.36	1.79
ECs1760	O157	0.76
ECs1763	O157	0.59
ECs1771	O157	0.90	−0.98
ECs1775	O157	1.92	−1.36
ECs1823	O157	0.69	0.97
ECs1824	nleG	1.30	1.09
ECs1829	yciE	0.89	−2.67
ECs1830	yciF	1.67	−2.54
ECs1831	yciG	1.89	−3.55
ECs1845	O157	1.01
ECs2000	ydbK	0.95	−1.76
ECs2019	O157	1.04	2.23
ECs2020	ydcF	1.90	1.80
ECs2085	bdm	4.28
ECs2144	ydeH	2.03	1.43
ECs2182	pchB	1.75	−1.65
ECs2196	O157	1.21	−1.01
ECs2200	O157	1.03
ECs2265	O157	1.03
ECs2278	O157	0.96	−0.65
ECs2279	O157	1.46	−1.53
ECs2280	O157	1.37	−1.09
ECs2281	O157	0.79	−1.17
ECs2283	O157	0.67	−1.48
ECs2289	ynfB	1.05	1.22
ECs2292	ynfD	1.07
ECs2303	asr	3.55
ECs2392	ydiH	0.92
ECs2449	spy	2.80
ECs2505	yoaG	0.84
ECs2506	yeaR	0.96
ECs2536	mgrB	1.09	1.35
ECs2544	yebT	0.87	1.31
ECs2558	yebG	1.16
ECs2581	yecP	1.06
ECs2614	yecH	0.84
ECs2622	O157	0.74
ECs2623	O157	0.68
ECs2692	yodD	1.09	−4.09
ECs2714	espJ	0.75
ECs2737	pchC	2.13	−1.53
ECs2758	O157	0.94
ECs2759	O157	0.59
ECs2987	O157	0.77
ECs3105	yojN	0.75	1.86
ECs3264	frc	0.80
ECs3267	fryB	1.35
ECs3270	ypeC	2.85	1.50
ECs3355	perM	1.21
ECs3358	hda	1.14	−1.61
ECs3426	yfhB	1.10	−1.82
ECs3441	yfiC	1.40	1.54
ECs3485	espM2	0.84
ECs3526	ygaU	1.00	−1.20
ECs3529	ygaP	0.99	−1.48
ECs3531	ygaW	0.95
ECs3643	chpR	0.62	0.67
ECs3692	ygeD	1.78	1.25
ECs3779	pepP	0.75
ECs3780	ygfB	0.72	1.33
ECs3887	yghA	0.64
ECs3906	ygiW	0.82	−0.61
ECs3953	yqjI	1.81
ECs3983	yqjF	2.07
ECs4034	yhbO	1.11
ECs4158	yhdN	1.35	1.04
ECs4204	yheT	1.37
ECs4256	yhgI	0.76
ECs4294	yhhA	1.33
ECs4335	O157	0.97	1.18
ECs4357	O157	0.63	−1.19
ECs4361	yhiJ	0.63	−1.11
ECs4384	chuX	1.32
ECs4453	bax	0.71	1.89
ECs4554	espB	1.06
ECs4571	sepZ	1.07
ECs4584	O157	0.57	1.38
ECs4585	O157	0.95	1.14
ECs4599	yicN	0.82	0.73
ECs4608	O157	1.18
ECs4610	O157	1.17	1.14
ECs4642	espL3	0.85
ECs4836	yiiM	1.36
ECs4958	O157	0.61	−1.30
ECs4959	O157	1.22	−1.00
ECs4981	O157	0.80	−0.91
ECs5013	yjbA	0.68	−1.03
ECs5028	yjbJ	3.16
ECs5042	yjcB	0.82	1.49
ECs5043	yjcC	1.18	2.20
ECs5110	yjdK	1.81
ECs5126	yjeJ	1.09	2.63
ECs5187	ytfE	0.73	1.69
ECs5189	ytfH	0.85	−2.18
ECs5190	ytfG	0.89	−1.71
ECs5255	O157	0.58	−1.24
ECs5312	yjiX	0.84	−0.64
ECs5326	bglJ	0.79
ECs5327	fhuF	0.63
ECs5334	osmY	2.23
ECs5338	yjjI	0.78	−0.63

^aECs numbers that are underlined were previously found to be upregulated under acid stress in E. coli K-12 (2, 43, 53, 78, 83). ECs numbers that are bolded were previously found to be upregulated under osmotic stress in E. coli K-12 (86, 87). ECs numbers that are italicized were previously found to be upregulated in stationary phase in MOPS minimal medium in E. coli O157:H7 (7).

^b“O157” indicates O157-specific genes.

^cExpression ratios are reported only for ORFs with a significant (adjusted P value of <0.05) growth phase effect.