Disruption of rcsB by a duplicated sequence in a curli-producing Escherichia coli O157:H7 results in differential gene expression in relation to biofilm formation, stress responses and metabolism

Sharma, V. K.; Bayles, D. O.; Alt, D. P.; Looft, T.; Brunelle, B. W.; Stasko, J. A.

doi:10.1186/s12866-017-0966-x

Table 3 List of differentially expressed genes related to bacteriophages, mobile elements and hypothetical functions in E. coli O157:H7 Congo red-positive isolate

From: Disruption of rcsB by a duplicated sequence in a curli-producing Escherichia coli O157:H7 results in differential gene expression in relation to biofilm formation, stress responses and metabolism

Gene group/gene^a	Gene ID^b	Known or predicted function^b	Fold change	P value
Bacteriophage related
	Z0309	Putative cI repressor protein for prophage CP-933H	+1.43	0.03
	Z1460	Hypothetical protein encoded by bacteriophage Bp-933 W	−4.12	0.01
	Z1922	Hypothetical protein encoded by bacteriophage CP-933X	−2.23	−0.03
	Z1923	Hypothetical protein encoded by bacteriophage CP-933X	−2.38	−0.04
intO	Z2036	Integrase for bacteriophage CP-933O	−1.26	0.01
coxT	Z2970	Regulator for prophage CP-933 T	+4.42	0.04
	Z2971	Phage CP-933 T encoded hypothetical protein	+3.48	0.03
	Z2972	Phage CP-933 T encoded hypothetical protein	+3.70	0.01
	Z2973	Phage CP-933 T encoded hypothetical protein	+4.10	0.01
	Z2974	Phage CP-933 T encoded hypothetical protein	+2.83	0.04
	Z3305	Bacteriophage CP-933 V encoded protein	−1.62	0.01
	Z4330	Transposase	+1.94	0.03
Hypothetical
	Z0005	Unknown	−7.49	4.7E-08
yagU	Z0353	Putative acid resistance	2.29	0.004
yagY	Z0359	Predicted pilus chaperone (cryptic)	−2.13	0.04
yagZ	Z0360	Predicted pilus major subunit	−2.83	0.001
yaiY	Z0475	Predicted inner membrane protein	−33.49	1.6E-12
yaiE	Z0487	Unknown	−1.49	0.01
yajI	Z0513	Unknown	−3.71	1.3E-06
ybcI	Z0682	Predicted inner membrane protein	−2.48	0.004
ybcI	Z0879	Unknown	−2.95	0.04
ybjO	Z1085	Predicted inner membrane protein	−2.35	4.3E-04
ybjX	Z1112	Unknown	−1.51	0.01
ymcD	Z1404	Unknown	+1.48	3.7E-03
ymcD	Z1528	Unknown	+2.11	0.03
yceI	Z1692	Unknown	−2.24	5.0E-03
yceB	Z1700	Unknown	−1.89	5.0E-04
ycfJ	Z1749	Unknown	−24.98	1.5E-14
ycfJ	Z2283	Unknown	−4.39	3.0#-06
ydeH	Z2292	Unknown	+2.69	2.0E-04
ydeF	Z2308	Unknown	+2.83	2.7E-06
ydeF	Z2421	Unknown	+1.79	0.03
yoaG	Z2838	Unknown	+2.54	0.02
	Z2839	Unknown	+2.36	0.04
	Z2893	Unknown	−1.61	0.01
rcnB	Z3275	Putative nickel/cobalt efflux protein	−1.61	0.02
ypeC	Z3656	Unknown	−23.74	1.9E-17
ypfG	Z3722	Unknown	−4.58	9.0E-09
	Z3965	Unknown	−2.33	1.5E-03
	Z4126	Unknown	−4.31	3.0E-04
	Z4151	Unknown	−3.84	7.4E-07
	Z4267	Unknown	+5.52	2.3E-03
	Z4268	Unknown	+4.92	4.3E-06
yggG	Z4280	Unknown	−1.71	0.02
yggG	Z4318	Unknown	+1.30	0.04
ygjT	Z4441	Unknown	−2.25	5.0E-03
yhaM	Z4462	Unknown	+2.34	0.03
yiaB	Z4988	Unknown	−4.71	5.0E-03
yiiF	Z5432	Unknown	+1.52	0.04
yjcO	Z5677	Unknown	+1.28	0.04
yjcO	Z5694	Unknown	−12.64	6.7E-09
yjdA	Z5711	Putative DNA replication function	+2.23	6.4E-06
yjcJ	Z5712	Unknown	+2.79	9.4E-05
yjfN	Z5795	Unknown	−2.58	8.0E-04

^aGene group/gene designations were selected from RAST Server [44]
^bGene ID and known or predicted functions are based on the annotated sequence of E. coli O157:H7 EDL 933 [92]. Symbols + and – represent upregulated and downregulated gene expression, respectively

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