Rapid acid treatment of Escherichia coli: transcriptomic response and recovery

Kannan, Geetha; Wilks, Jessica C; Fitzgerald, Devon M; Jones, Brian D; BonDurant, Sandra S; Slonczewski, Joan L

doi:10.1186/1471-2180-8-37

BMC Microbiology

Table 1 Genes upregulated at least 2-fold after acid shift.^a

From: Rapid acid treatment of Escherichia coli: transcriptomic response and recovery

1 min	Log2 ratios	Maurer et al 2005^b	% Recovery	5 min	Log2 ratios	Maurer et al 2005^b	% Recovery	10 min	Log2 ratios	Maurer et al 2005^b	% Recovery
hisL	2.3		66	yagU	4.3	+	10	cadB	4.7		0
thrL	1.7		77	bdm	4.0		20	yagU	3.8	+	10
b2596	1.6		90	ymgB	3.8		44	glpD	3.7		0
raiA	1.5		46	glpD	3.5		0	glpK	3.5		0
YfiD	1.5	+	52	sra	3.1	+	0	hdeB	3.5	+	0
YifN	1.4		75	cadB	3.1		0	glpF	3.3		0
YifO	1.4		87	ymgA	3.0		38	hdeA	3.3	+	0
evgA	1.3		45	ymgC	2.6		52	sra	3.3	+	0
yhcN	1.3	+	23	yhcN	2.6	+	23	yahO	3.2		0
ymgB	1.3		44	yneI	2.6		57	bdm	3.2		20
uspD	1.2		44	gatB	2.5	+	0	cadA	3.2	+	0
ymgA	1.2		38	raiA	2.5		46	osmY	3.1		0
yagU	1.1	+	10	aceB	2.4		33	gatB	3.1	+	0
pmrD	1.1		68	b2596	2.4		90	lldR	3.1		0
ycgZ	1.0		39	uspD	2.4	+	44	gatC	3.0	+
				gltA	2.3	+	10	yjbJ	3.0		0
				lldR	2.3		0	lldD	2.9	+	0
				gadE	2.2		15	yhjX	2.8		0
				lldD	2.2	+	0	gatA	2.8	+	0
				osmY	2.2		0	lldP	2.8	+	0
				glpF	2.2		0	rcsA	2.7		0
				ycgZ	2.2		39	yjdL	2.6		0
				osmB	2.2		0	gatZ	2.6	+	0
				rcsA	2.1		0	tnaC	2.5		0
				hdeB	2.1	+	0	glpQ	2.5		0
				gatA	2.1	+	0	clpB	2.4	+	0
				aceA	2.1		8	gcvT	2.4		0
				ygaC	2.1		46	ivy	2.3		0
				ivy	2.0		0	osmB	2.3		0
				yfiD	2.0	+	52	glpT	2.3		0
				yahO	2.0		0	dppF	2.3		0
				gatZ	2.0		0	msyB	2.2		0
				elbA	2.0		59	talA	2.2		0
				yjbJ	1.9		0	yiaG	2.2		0
				lldP	1.9	+	0	gcvH	2.2		0
				hisL	1.9		66	sucD	2.2	+	0
				amn	1.9		27	ymgB	2.1		44
				yeiG	1.9	+	25	gltA	2.1	+	10
				hdeA	1.9	+	0	gatY	2.0		0
				glpK	1.9		0	ydiZ	2.0		0
				gatC	1.8			yeaD	2.0
				yhjX	1.8		0	yhcN	2.0	+	23
				crl	1.8		64	gadE	1.9		15
				hchA	1.8		27	ygaM	1.9		0
				gadW	1.8		17	aceA	1.9		8
				gltB	1.7			yhcO	1.9		0
				ilvC	1.7		65	dps	1.9	+	0
				arcB	1.7		50	ymgA	1.9		38
				evgA	1.7		45	ygdI	1.8	+	0
				uspA	1.6		60	gadB	1.8		0
				asd	1.6		33	bfr	1.7		0
				ghrB	1.6		24	gltB	1.7
				osmC	1.6		11	ygiW	1.7	+	0
				cfa	1.6	+	17	sthA	1.7	+	0
				nlpA	1.6	+	51	aceB	1.6		33
				ycgK	1.6		38	yphA	1.6		0
				intA	1.6		77	elaB	1.6		0
				dps	1.6	+	0	yjiT	1.6		0
				rhsA	1.6		30	srlD	1.6	+	0
				fimB	1.6		98	spy	1.6		0
				yieF	1.6	+	0	aldA	1.6	+	0
				fpr	1.6	+	47	yieF	1.6	+	0
				yiiS	1.6	+	23	acs	1.6		0
				yieE	1.5	+	33	manY	1.6		0
				gatY	1.5		0	hdeD	1.6		0
				yhcO	1.5		0	dppA	1.5		0
				yggE	1.5		0	gadA	1.5		0
				insI	1.5		47	yeaG	1.5		0
				clpS	1.5		62	yggE	1.5		0
				glgC	1.5		2	mglB	1.5		0
				ydiZ	1.5		0	yncC	1.5		0
				dtd	1.5		47	b1005	1.5		0
				marA	1.5	+	21	gadW	1.5		17
				sthA	1.4	+	0	ykgA	1.4	+	0
				argE	1.4		57	osmC	1.4		11
				clpB	1.4	+	0	glgC	1.4		2
				serC	1.4	+	57	ytfK	1.4		0
				msyB	1.4	+	0	sdhB	1.4	+	0
				tas	1.4	+	24	dhaM	1.4	+	0
				ygdI	1.4	+	0	yeiG	1.4	+	25
				rsd	1.4		67	manZ	1.4		0
				aroG	1.4		58	ygaU	1.4		0
				bcsE	1.4	+	37	ykgE	1.4		0
				yciI	1.4		74	sdhC	1.4	+	0
				gcvR	1.4		81	dadA	1.4
				nrdH	1.3		78	amn	1.4		27
				bcsF	1.3		31	yodC	1.4	+	0
				ygdR	1.3		22	manX	1.4		0
				acnB	1.3	+	15	udp	1.4	+	0
				appY	1.3		36	fumA	1.4	+	0
				ypeC	1.3		36	glgS	1.4		0
				yrdA	1.3		29	ycgZ	1.3		39
				hdfR	1.3		73	cfa	1.3	+	17
				yjdJ	1.3		4	ybjP	1.3		0
				thrL	1.3		77	raiA	1.3		46
				umC	1.3		5	oppB	1.3
				yncC	1.3		0	yehE	1.3		0
				yjiT	1.3		0	uspD	1.3	+	44
				gcvT	1.3		0	mqo	1.3	+	0
				ugpB	1.3		25	oppA	1.3
				ygbE	1.3	+	1	sdhA	1.3	+	0
				hdfR	1.3		65	hdhA	1.3		0
				hdhA	1.3		0	hchA	1.3		27
				yjgK	1.3	+	41	yhhA	1.3		0
				cadA	1.2	+		dppD	1.3		0
				rpoS	1.2			poxB	1.3		0
				oppB	1.2			srlE	1.3	+	0
				dadA	1.2			yjdI	1.2		0
				oppA	1.2			ygbE	1.2	+	1
				ybjP	1.2		0	ghrB	1.2		24
				sbmC	1.2		47	yjdJ	1.2		4
				malP	1.2		55	ymgC	1.2		52
				msrA	1.2		50	mglA	1.2		0
				bcp	1.2		72	fumC	1.2		5
				arcA	1.2		47	wrbA	1.2		0
				mqo	1.2	+	0	ykgF	1.2		0
				ycbB	1.2		42	yqjD	1.2		0
				yjdL	1.2		0	cdd	1.2	+	0
				yhhA	1.2		0	yiiS	1.2	+	23
				malQ	1.2		58	yqjC	1.2		0
				nadE	1.2	+	39	groL	1.2	+	0
				aldA	1.2	+	0	ygaF	1.2		0
				cyaA	1.2	+	73	otsB	1.2		0
				dkgA	1.2		9	marA	1.1	+	21
				marR	1.2	+	28	htpG	1.1	+	0
				glgS	1.2		0	acnB	1.1	+	15
				yeaR	1.2		11	srlA	1.1	+	0
				gdhA	1.2		54	ybeL	1.1		0
				ykgA	1.2	+	0	ygaC	1.1		46
				yfaO	1.2		34	asd	1.1		33
				soxS	1.2		85	dkgA	1.1		9
				ygiN	1.2		63	rhsA	1.1		30
				fucK_	1.2		65	ydiH	1.1	+	0
				yodA	1.2		79	dhaK	1.1	+	0
				sucD	1.2	+	0	yneI	1.1		57
				argT	1.2		58	sdhD	1.1	+	0
				ygaM	1.2		0	dhaL	1.1		0
				rhsD	1.2		108	yhdN	1.1		6
				fxsA	1.1			yeaQ	1.1	+	0
				yqhD	1.1			uspB	1.1		0
				yihY	1.1			yeaR	1.1		11
				yhdN	1.1		6	gltD	1.1	+	0
				gloB	1.1		46	tas	1.0	+	24
				hdeD	1.1		0	ygdR	1.0		22
				sdhA	1.1	+	0	sodC	1.0		0
				yiaG	1.1		0	yieE	1.0	+	33
				zntR	1.1		23	galP	1.0		0
				yjeI	1.1		84	fliY	1.0	+	0
				ldhA	1.1		37	nemA	1.0
				yqhD	1.1		18
				srlD	1.1	+	0
				yihY	1.1		18
				yeaC	1.1	+	19
				gcvH	1.1		0
				talA	1.1		0
				yphA	1.1		0
				ybaQ	1.1		96
				nrdI	1.1		80
				ygiW	1.1	+	0
				yfjU	1.1		11
				elaB	1.1		0
				yjdC	1.1		16
				yfbU	1.1		46
				bcsG	1.1		34
				sdhC	1.1	+	0
				yohN	1.1	+	11
				bolA	1.1		65
				yjdI	1.1		0
				sdhB	1.1	+	0
				ydiV	1.1		62
				mcrB	1.1		15
				yggG	1.1		18
				dppA	1.1		0
				mcrC	1.1		12
				nemA	1.0
				yeaD	1.0
				ygaU	1.0		0
				yjbQ	1.0	+	55
				yfbQ	1.0	+	52
				yihD	1.0		65
				ybeL	1.0		0
				phoP	1.0		44
				nlpD	1.0		20
				gadB	1.0		0
				uspB	1.0		0
				rpoN	1.0		56
				yfjH	1.0		38
				yaiB	1.0		8
				spy	1.0		0
				betI	1.0		138
				lrp	1.0		44
				ybhGt	1.0		74
				gadX	1.0		23
				ygiT	1.0		101
				kch	1.0		47
				ygdH	1.0		37

^a Values shown represent the log₂ ratio of expression indices compared to those at time zero. Expression ratios of 2-fold or greater are shown. Percent recovery is defined under Results; a blank cell indicates recovery could not be defined.
^b Ref [11]

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