DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli

Madelung, Michelle; Kronborg, Tina; Doktor, Thomas Koed; Struve, Carsten; Krogfelt, Karen Angeliki; Møller-Jensen, Jakob

doi:10.1186/s12866-017-1008-4

BMC Microbiology

Table 2 Sequenced inserts, gene name and protein product. UTI89 genome coordinates of identified inserts, and position relative to proximal genes. Colony identifiers are ordered in accordance to sequence start and end sites. Colonies marked in bold were used for GFP expression analysis. Differential fluorescence is reported as GFP fluorescence fold change of select UTI89/pMWLib clones grown in human urine versus LB

From: DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli

Gene	Protein	Gene start	Insert sequence start	Insert sequence end	Colony ID	Fold change in mean GFP signal
argA	N-acetylglutamate synthase	3139678	3139160	3139678	8, 57	13.5
argA	N-acetylglutamate synthase	3139678	3139113	3139736	45	13.5
argC	N-acetyl-gamma-glutamyl-phosphate reductase	4439034	4438574	4439108	60	8.2
argC	N-acetyl-gamma-glutamyl-phosphate reductase	4439034	4438733	4439183	84
argE	Acetylornithine deacetylase	4438919	4439100	4438541	4, 93	14.1
argE	Acetylornithine deacetylase	4438919	4439305	4438787	42	14.1
argG	Argininosuccinate synthase	3538472	3538296	3538904	51	4.3
argG	Argininosuccinate synthase	3538472	3538143	3538627	82	4.3
artJ	Arginine-binding periplasmic protein 2	861650	862067	861578	16	7.9
asnA	asparagine synthetase A	4188023	4187539	4188150	1, 24, 38, 46, 49, 86	1.4
asnB	asparagine synthetase B	674199	674321	673791	30	Lower in urine
			674541	673908	35
			674162	673571	72
manZ	PTS system mannose-specific transporter subunit IID	1930575	1930463	1930677	35	Lower in urine
ecnA	entericidin A	4648116	4647814	4648373	17	2.1
ecnB	entericidin B	4648352	4647814	4648373	17	2.1
ilvC	Ketol-acid reductoisomerase	4218632	4218651	4219116	20	4.5
ilvC	Ketol-acid reductoisomerase	4218632	4218333	4218799	83	4.5
ilvG	Acetolacetate synthase 2 catalytic subunit	4211428	4210930	4211421	7, 10	13.8
metA	Homoserine O-succinyltransferase	4462506	4462367	4462876	2	2.4
			4462142	4462760	9, 11
			4462396	4462910	34, 52, 53, 66, 73, 79, 90
			4462388	4463001	81
metC	Cystathionine beta-lyase	3362694	3362313	3362827	76	2.7
metE	5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase	4277928	4277452	4277904	6, 26, 67	25.4
			4277357	4277878	13, 44, 58, 87
			4277611	4278191	74
metF	5,10-methylenetetrahydrofolate reductase	4416931	4416691	4417181	18, 23, 31	42.5
potF	putrescine ABC transporter substrate-binding protein	854834	854439	855001	5	2.4
potF	putrescine ABC transporter substrate-binding protein	854834	854460	855009	43	2.4
serA	D-3-phosphoglycerate dehydrogenase	3236056	3236446	3236125	41	3.9
yaiM	hypothetical protein	395196	395661	395108	41	3.9
UTI89_C1129	outer membrane heme/hemoglobin receptor	1122532	1122106	1122627	91	Lower in urine
UTI89_C4885	hypothetical protein	4787503	4787381	4787460	91	Lower in urine
yajB	ACP phosphodieterase	439176	439346	438767	25	Lower in urine
ybdH	hypothetical protein	617328	617543	617035	3, 15, 36, 54, 69, 85, 88, 92	9.5
			617447	617035	89
			617636	617023	21, 50, 56, 77
			617691	617083	28, 78
			617543	617107	61
ybdL	aminotransferase	617488	617206	617798	33, 37, 47	5.0
ybdL	aminotransferase	617488	617323	617815	62	5.0
yeaR	Hypothetical protein	1912199	1912872	1912250	65	6.6
yibI	Hypothetical protein	4027446	4027775	4027295	19, 70, 75	5.6
yibI	Hypothetical protein	4027446	4027590	4027356	68	5.6
Unannotated gene			48649	49106	12, 14, 22, 27, 32, 39, 40, 48, 55, 59, 64, 71, 80, 94, 95	Non-fluorescent
Unannotated gene			48681	49177	63	Non-fluorescent
Opposite strand of yagV			315403	315898	29	Could not be cultivated in urine

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ISSN: 1471-2180

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