Identification of stress-responsive transcription factors with protein-bound Escherichia coli genomic DNA libraries

Li, Xianqiang; Jiang, Xin; Xu, Meiying; Fang, Yun; Wang, Yan; Sun, Guoping; Guo, Jun

doi:10.1186/s13568-020-01133-0

AMB Express

Table 2 List of clones containing with -35 and -10 conservative sequences or TF binding sequences

From: Identification of stress-responsive transcription factors with protein-bound Escherichia coli genomic DNA libraries

Gene names	Clone ID	Library	Encoded function	Insert length (bp)	TFBS
aor	141	TC	Aldehyde ferredoxin oxidoreductase	279	Sigma70
araH	28	GA	l-arabinose ABC transporter permease	167	Sigma70, DnaA
arcB	47	AC	Sensor histidine kinase	258	Sigma 70, Ihf
argB	80	AC	Acetylglutamate kinase	225	Sigma70, ArgR2, Ihf
arsB	65, 85, 108, 114	AG, CA CT, TT	Arsenite/antimonite:H(+) antiporter	320	Sigma70
bglH	72	AT	Carbohydrate-specific outer membrane porin	244	Sigma70, PurR
bsl78	107	CT	DNA (cytosine-5-)-methyltransferase	218	Sigma 70
cas1e	18	GG	Type I-E CRISPR-associated protein	186	Sigma70, RpoS17
casA	37	GG	CRISPR system Cascade subunit	158	Sigma70, RpoS17
chbC	73	AT	N,N’-diacetylchitobiose-specific PTS enzyme IIC	158	Fur, RpoD17
chbG	70, 91	AT	Chitin disaccharide deacetylase	157	Sigma70
clk_1237	177	TA	ADP-ribosylglycohydrolase family protein	124	Sigma70
ctk	93	CA	DUF4297 domain-containing protein	135	Sigma70, RpoD15, metJ
ctpA3	144	TC	Carboxyl-terminal-processing peptidase 3, chloroplastic	158	Sigma70
cydD	145	TC	Cysteine/glutathione ABC transporter permease/ATP-binding protein	167	Sigma70
dgc	122	TT	Diguanylate cyclases	105	Sigma70, RpoD17
dtpD	137	TC	Dipeptide permease	213	Sigma70, LexA
eamA	74	AT	Cysteine/O-acetylserine exporter EamA	184	Sigma70
ecm18	150	TG	Class I SAM-dependent methyltransferase	270	Sigma70, Crp, SoxS
ef2563	35	GG	Selenium-dependent molybdenum hydroxylase system protein	133	Sigma70
egc82	33	GG	d-hexose-6-phosphate mutarotase	139	Sigma70
elbB	138	TC	Isoprenoid biosynthesis glyoxalase	328	Sigma70, Irp,RpoH2, LexA, ArcA, argR, GlpR:
f0f1	171	TA	ATP synthase subunit delta	134	Sigma70
fimZ	165	TA	Fimbriae biosynthesis transcriptional regulator	96	Sigma70, PurR, LexA1, LexA2, PurR
frdA	117	TT	Fumarate reductase flavoprotein subunit	357	Sigma70
frsA	1, 81	GA, AC	Esterase	193	Sigma70
ftr1	3, 4, 11, 12, 13, 14, 15, 21, 27, 57, 62, 95, 97, 110, 111, 112, 126, 154	GA, GC, GT, AC, AG, CG, CT, TC, TG	Iron permease	145	Sigma70, RpoD16, MetJ
gaf	6, 24	GA, TC	GAF domain-containing protein	262	Ihf
gltT	86	CA	Cation:dicarboxylase symporter familytransporter	263	Sigma70, RpoD17, OmpR
gshB	59	AG	Glutathione synthase	208	Sigma70, Fis
hcaE	30	GA	3-Phenylpropionate/cinnamic acid dioxygenase subunit alpha	140	Sigma70, DnaA
hemK	147	TC	Peptide chain release factor N(5)-glutamate	366	Sigma70
hflC	63	AG	Protease modulator	320	Sigma 70
hipA	42	AA	Type II toxin-antitoxin system serine/threonine protein kinase toxin	230	Sigma70, RpoD17
hjr	22	GG	Holliday junction resolvase	432	RpoD17
hsdR	157	TG	Type I restriction-modification system endonuclease	278	Sigma70
IcsA	153	TG	Outer membrane protein IcsA autotransporter precursor	196	Sigma70, RpoD17, SoxS
IIA	55	AC	PTS mannitol transporter subunit	154	Sigma70, Ihf. ArgR2, RpoD17
kch	53	AC	Voltage-gated potassium channel	160	Sigma70, MetJ, RpoH2
kdo	170	TA	3-Deoxy-manno-octulosonate cytidylyltransferase	119	Sigma70, LexA, RpoD18, PurR
kup	155	TG	Low affinity potassium transporte	154	Sigma70
lpfC	136, 178	TC, TA	Fimbrial biogenesis outer membrane usher protein	155	Sigma70
maaFP003_1916	31	GA	Si-specific NAD(P) (+) transhydrogenase	381	Sigma70
maeB	94, 116	CA, TT	NADP-dependent oxaloacetate-decarboxylating malate dehydrogenase	121	Sigma, RpoD17, ArgR
mcrB	39	GG	5-Methylcytosine-specific restriction enzyme B	128	Sigma70, RpoD17, Irp, Fnr, NagC
mhpR	127	TC	DNA-binding transcriptional activator	284	Sigma70, RpoD17, ArgR, ArcA
mnmC	69	AT	5-Methylaminomethyl-2-thiouridine biosynthesis bifunctional protein	182	Sigma70
motA	9	GC	Flagellar motor stator protein 98	98	FliA, MotAB, CheAW, CpxR
msyB	120	TT	Acidic protein	308	Sigma70, SoxS
mukF	20	GG	Chromosome partition protein	123	Sigma70, RpoD17, Irp, RpoH2, Fnr, NagC
narG	159	TG	Nitrate reductase subunit alpha	154	Sigma70, ArgR
narI	10	GC	Respiratory nitrate reductase subunit gamma 195	195	Sigma70, Crp
nikC	45	AA	Nickel ABC transporter permease subunit	164	Sigma70, RpoD16
nrdD	175	TA	Anaerobic ribonucleoside-triphosphate reductase	350	Sigma70
nuoE	158	TG	NADH-quinone oxidoreductase subunit NuoE	222	Sigma70, Crp
pntA	8, 50	GA	Si-specific NAD(P) transhydrogenase	415	Sigma70
rase	56	AC	4-Hydroxybenzoate octaprenyltransfe	178	Sigma, PurR
rayT	88	CA	REP-associated tyrosine transposase	248	Sigma70
rep	139	TC	ATP-dependent DNA helicase Rep	185	Sigma70
rpoS	156	TG	RNA polymerase sigma factor	315	Sigma70, Crp
rppH	169	TA	RNA pyrophosphohydrolase	396	Sigma70, NarP
rrl	61	AG	23S ribosomal RNA	153	Crp, RpoD15
sanA	67	AT	Outer membrane permeability protein	193	Sigma 70
sdr	149	TG	Short-chain dehydrogenase	99	Sigma70
secA	167	TA	Preprotein translocase subunit SecA	161	Sigma70, RpoD17, Ihf
sgr	132	TC	Helix-turn-helix domain-containing protein	199	Sigma70, ArgR2
speF	90	CA	Ornithine decarboxylase SpeF	128	Sigma70
spy	105	CT	ATP-independent periplasmic protein-refolding chaperone	233	Ihf, Fis, lrp,
tesB	173	TA	Acyl-CoA thioesterase II	133	Sigma70, RpoD16
thiP	99	CT	Thiamine/thiamine pyrophosphate ABC transporter permease	210	Sigma70, OmpR
tolC	115	TT	Outer membrane channel protein	128	ArgR
trpS/pgp	123	TT	Tryptophan–tRNA ligase Phosphoglycolate phosphatase	115	Sigma70
tyrR	134	TC	Transcriptional regulator	147	RpoD19, RpoD17, Crp, OmpR, MetR
ucpA	100	CT	SDR family oxidoreductase	133	Sigma70, Fnr
ugdH	121	TT	UDP-glucose 6-dehydrogenase	294	Sigma70, FlhCD, RpoH2, RpoD17, Fnr, lrp
uhpC	16	GG	MFS transporter family glucose-6-phosphate receptor	174	Sigma70, ArgR
wbbI	5, 29	GA	Beta-1,6-galactofuranosyltransferase	200	Sigma70
wcaL	129	TC	Colanic acid biosynthesis glycosyltransferase	290	Sigma70
weel	24, 75	GT	Beta-1,6-galactofuranosyltransferase	217	Sigma70, RpoD17, RpoD16,RpoD17,RpoD17
wzc	109	CT	Tyrosine-protein kinase	179	Sigma70
ybaT	89	CA	Amino acid permease	171	ArgR2, Ihf, ArcA
ybjX	49	AC	DUF535 domain-containing protein YbjX	145	Sigma70
ycbV	148	TG	Putative fimbrial-like adhesin protein	110	Sigma70, Crp, RpoD15, PhoB, RpoD17, lrp
ychE	131	TC	NAAT family transporter	258	Sigma70, RpoD16, lrp, SoxS, TyrR, GlpR, RpoD18
ydhW	23, 25, 40	GT	Oxidoreductase	183	Sigma70
ydiV	52	AC	EAL domain-containing protein bacteria	241	Sigma70, Crp
yeaW	101	CT	Carnitine monooxygenase subunit	179	Sigma 70
yedE/fdhT	48	AC	Selenium metabolism membrane protein	110	Sigma70
yeeJ	119	TT	Inverse autotransporter adhesin	182	Sigma70
yeiH	135	TC	YeiH family putative sulfate export transporter	114	Sigma70, OxyR, arcA, Fnr, RpoD18, TyrR, Fnr, DeoR, Ihf, ArgR2
yfeX	54	AC	Porphyrinogen peroxidase	167	Sigma70
yhdP	46	AA	AsmA2 domain-containing protein	200	Sigma70
yidR	125	TC	DUF3748 domain-containing galacturonate catabolism protein	174	Sigma70
yihG	151	TG	Putative acyltransferase	186	Sigma70
yneE	98	CG	Bestrophin family inner membrane protein	120	Sigma70
ypfG	64	AG	DUF1176 domain-containing protein	328	Sigma70, RpoH3
	26	GT	Hypothetical protein	211	Sigma 70, ArgR2, Crp
	152	TG	Non-coding, Pseudo genes	186	Sigma70, Fis, Fnr, LexA
	161	TG	Unknown	626	Sigma70

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