Table 1 Potential regulation targets of CyuR, suggested by motif scanning

From: CyuR is a dual regulator for L-cysteine dependent antimicrobial resistance in Escherichia coli

#	Gene	Locus tag	Gene function	Position	Z-score	CyuR predicted DNA-binding site	Log₂ Fold change
#	Gene	Locus tag	Gene function	Position	Z-score	CyuR predicted DNA-binding site	ΔcyuR^a	Cys^b
-	cyuR	b0447	DNA-binding transcriptional activator	−69	5.84	GAATAAATTGTcGtgATTTcaCC	n.a.	-
1	yaiV	b0375	Putative DNA-binding transcriptional factor	−75	5.41	GAAgAAATacTgGtAATTTAaTC	-	4.5
2	etp	b0982	Phosphotyrosine-protein phosphatase	−199	4.88	GGcaAAATcGCcAatATTTATCa	-	1.5
3	ycfT	b1115	Inner membrane protein (biofilm-related)	−143	4.8	GGcTAAATTGCcAtgtTTTATCa	-	7.9
4	lapA	b1279	Lipopolysaccharide assembly protein A	−50	4.69	GGtaAgtTgaCcAtAATTTATTC	-	1.4
5	puuD	b1298	Putrescine utilization	−42	4.84	GcAgtAATgGCgAtAATTTAgTC	−2.1	2.4
6	pspF	b1303	Psp membrane-stress response, σ54-enhancer binding protein	−179	4.88	GAAaAAATacCcAtAATgTtgTC	-	-
7	pspA	b1304	Psp membrane-stress response	−10	4.88	GAcaAcATTaTgGgtATTTtTTC	-	−2.9
8	dbpA	b1343	RNA helicase	−10	4.71	GAATAgATTGTgACcgcTTtTTC	-	-
9	ydcP	b1435	23S rRNA 5-hydroxycytidine C2501 synthase	−40	4.95	GctaAAATaGCcGCcATTTtTCa	-	-
10	yoaF	b1793	Lipoprotein	−160	4.92	GGgTAAATgcTgAttATTTAaTC	-	-
11	dgcP	b1794	Diguanylate cyclase	−45	4.92	GAtTAAATaaTcAgcATTTAcCC	-	−1.4
12	zwf	b1852	Glucose-6-P dehydrogenase	−233	4.61	GAtaAAAaaGTTGttATTTtTTt	-	−2.8
13	yebK	b1853	DNA-binding transcriptional repressor	−127	4.61	aAAaAAATaaCAACttTTTtaTC	-	-
14	fruB	b2169	Fructose-specific PTS	−192	4.58	GGAaAAATgGCAAaAAaTTgTgC	1.1	-
15	setB	b2170	Sugar export transporter	−198	4.58	GcAcAAtTTtTTGCcATTTtTCC	1.4	1.4
16	yfaL	b2233	Putative autotransporter adhesin	−277	4.79	GGcgAAATgGTTGtttTcTATTC	-	2.4
17	raiA	b2597	Ribosome-associated inhibitor A	−89	4.89	GAcaAAATTaTgAgAtTTTcaTC	2.2	−4.0
18	araE	b2841	Arabinose symporter	−5	4.7	GAAaAAATgGTTACtATcaATaC	-	1.6
19	yhiJ	b3488	DUF4049 protein	−49	4.97	GAtaAAATgtTAACtATgTATTC	-	3.4
20	aldB	b3588	Aldehyde dehydrogenase	−199	5.61	GAAgAAATTGTgGCgATTTATCg	1.2	-
21	pfkA	b3916	6-Phosphofructokinase	−148	4.77	GtATAAAaTaCcGCcATTTggCC	2.2	−3.7
22	argC	b3958	Arginine biosynthesis	−182	4.76	cGATAAATgGCgGtAATTTgTTt	-	−1.9
23	malE	b4034	Maltose ABC transporter	−178	4.93	GcAaAAATcGTgGCgATTTtaTg	1.4	1.8
24	malK	b4035	Maltose ABC transporter	−209	4.93	cAtaAAATcGCcACgATTTtTgC	2.7	3.9
25	prfC	b4375	Peptide chain release factor 3	−71	5.53	GGtaAAATaGCcGCAATTTtTCg	−1.1	−1.0

^aFold changes in gene expression when cyuR was deleted in E. coli MG1655¹⁰.
^bFold changes in gene expression by supplementing 5 mM Cys in E. coli W. Both studies were performed by using the same M9 medium. ‘-’ indicates a gene was not differentially expressed. ‘n.a.’ indicates not applicable. The underlined genes are potential regulation targets with strong evidence with the gene expression changes.

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Table 1 Potential regulation targets of CyuR, suggested by motif scanning

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