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 2 List of differentially expressed genes showing altered metabolic profile of 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
Transport
phoE	Z0302	Outer membrane phosphoporin protein	−1.89	0.027
ybaL	Z0597	Cation:proton antiport protein	−1.48	0.004
ybbA	Z0648	ABC transporter ATP-binding protein	−1.59	5.4E-04
ybbP	Z0649	Oxidoreductase	−1.7	0.02
nagE	Z0826	N-acetylglucosamine PTS permease	−2.30	0.022
glnQ	Z1031	Glutamine ABC transporter ATP-binding	−3.09	0.006
glnH	Z1033	Glutamine ABC transporter periplasmic protein	−3.66	0.004
potF	Z1081	Putrescine ABC transporter periplasmic-binding protein	−4.42	4.0E-04
potG	Z1082	Putrescine ABC transporter ATP-binding protein	−4.00	9.0E-04
potH	Z1083	Putrescine ABC transporter membrane protein	−2.98	1.5E-02
potI	Z1084	Putrescine ABC transporter membrane	−2.92	9.0E-03
lolA	Z1237	Periplasmic chaperone for translocation of lipoproteins to outer membrane	−1.48	0.037
ompA	Z1307	Outer membrane porin A	−2.50	8.6E-06
ybaL	Z1672	Cation:proton antiporter	−1.48	0.004
VybbA	Z1673	ATP-binding protein of ABC transporter	−1.59	5.0E-04
ybbP	Z1677	Membrane component of ABC transporter protein	−1.59	5.0E-04
yceL (mdtH)	Z1702	Multidrug efflux transporter	+1.40	0.024
narK	Z2000	Nitrite/nitrate antiporter	+2.79	0.059
gabP	Z3961	Gamma-aminobutyrate transporter	−5.33	1.0E-03
yhaO	Z4463	Permease for D-serine transport	+2.76	0.01
livF	Z4824	Leucine/isoleucine/valine transporter ATP-binding subunit	−2.06	0.04
nirC	Z4728	Transport of nitrite	+3.95	0.03
dppF	Z4957	Dipeptide transporter ABC-binding unit	−2.61	0.03
dppD	Z4958	Dipeptide transporter ABC-binding unit	−2.40	0.04
dppA	Z4961	Dipeptide transporter protein	−2.52	0.03
yigM	Z5348	Biotin transporter	+1.36	0.03
Amino acid biosynthesis
thrB	Z0003	Homoserine kinase	−2.18	0.01
thrC	Z0004	Threonine synthase	−2.17	0.03
leuD	Z0080	Isopropylmalate isomerase small subunit	−2.66	0.01
leuC	Z0081	Isopropylmalate isomerase large subunt	−2.34	0.04
asnB	Z0821	Asparagine synthetase B	−3.07	0.049
asnB	Z2491	Glutamine synthetase	−2.93	0.02
hisC	Z3183	Histidinol-phosphate aminotransferase	−1.79	0.03
hisH	Z3185	Imidazolr glycerol phosphate synthase	−1.78	0.03
hisA	Z3186	Imidazole-4-carboxamide isomerase	−1.84	0.02
hisF	Z3187	Imidazole glycerol phosphate synthase	−1.86	0.01
hisI	Z3188	Bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase	−1.82	0.02
lysA	Z4156	Diaminopimelate decarboxylase	+2.39	0.03
ilvN	Z5164	Acetolactate synthase I regulatory subunit	−2.08	0.02
ilvB	Z5165	Isoleucine/valine biosynthesis	−2.02	0.01
asnA	Z5245	Asparagine synthetase	−3.47	0.04
aspA	Z5744	Aspartate ammonia-lyase	+2.04	0.04
Amino acid degradation
goaG	Z2486	4-aminobutyrate transferase	−6.75	2.5E-04
ordL	Z2487	γ-glutamylputrescine oxidase	−6.79	0.01
aldH	Z2488	γ-glutamyl-γ-aminobutyraldehyde	−5.52	1.1E-03
gabD	Z3959	Succinate-semialdehyde dehydrogenase I	−4.12	5.0E-03
gabT	Z3960	4-aminobutyrate aminotransferase	−5.66	5.0E-03
Carbohydrate/Energy metabolism
aceF	Z0125	Dihydrolipoamide acetyltransferase	−2.00	0.02
yaeM	Z0184	1-deoxy-D-xylulose 5-phosphate reductoisomerase	−1.33	0.03
malZ	Z0501	Maltodextrin glucosidase	−2.13	0.041
ybdR	Z0752	Zn-dependent oxidoreductase	−2.70	3.0E-04
sdhA	Z0877	Succinate dehydrogenase flavoprotein subunit	−3.11	0.044
sucA	Z0880	2-oxoglutarate dehydrogenase E1	−2.73	0.047
sucB	Z0881	Dihydrolipoamide succinyltransferase	−2.62	0.039
sucC	Z0882	Succinyl-CoA synthetase subunit beta	−2.64	0.029
sucD	Z0883	Succinyl-CoA synthetase subunit alpha	−2.37	0.054
nadA	Z0919	Quinolate synthetase	−1.82	0.002
galM	Z0926	Galactose-1-epimerase	−1.33	0.047
galE	Z0929	UDP-galactose-4-epimerase	−1.46	0.019
ybjW	Z1107	Hydroxylamine reductase	+1.98	9/0E-03
galU	Z2012	UTP-glucose-1-phosphate uridylyltransferase	−2.11	0.006
adhE	Z2016	Aldehyde-alcohol dehydrogenase	+2.29	0.01
manX	Z2860	PTS system mannose-specific transporter unit AB	+1.47	0.035
manY	Z2861	PTS enzyme IIC, mannose-specific	+1.55	0.007
manZ	Z2862	PTS system mannose-specific transporter subunit IID	+1.50	0.02
yghA	Z4356	Oxidoreductase	−2.72	0.01
ugpB	Z4822	Glycerol-3-phosphate transporter periplasmic-binding protein	−2.74	0.01
uhpT	Z5156	Sugar phosphate antiporter	+3.22	6.9E-05
mdoB	Z5959	Phosphoglycerol transferase I	−3.00	3.0E-04
Fatty acid and lipid metabolism
pgsA	Z3000	Phosphatidylglycerophosphate synthetase	+1.47	0.01
plsC	Z4372	1-acyl-sn-glycerol-3-phosphate	+1.30	2.3E-03
yrbB	Z4554	Phospholipid ABC transporter	−1.87	2.0E-03
yrbC	Z4555	Phospholipid ABC transporter	−1.97	3.0E-04
Phosphate metabolism
phoU	Z5215	Transcriptional regulator	−2.09	4.0E-03
pstB	Z5216	Phosphate transporter ATP-binding protein	−2.02	0.02
pstA	Z5217	Phosphate transport permease subunit PstA	−2.70	2.0E-03
pstC	Z5218	Phosphate transport permease subunit PstC	−2.52	3.0E-04
pstS	Z5219	Phosphate ABC transporter substrate-binding protein	−5.84	1.4E-07
Sulfur metabolism
cysZ	Z3679	Sulfate transport protein	−1.47	0.03
cysA	Z3687	Sulfate/thiosulfate transporter	+1.50	0.02
cysW	Z3688	Sulfate/thiosulfate permease	+2.16	3.4E-03
cysN	Z4059	Sulfate adenylyltransferase subunit 1	+1.65	0.03
cysJ	Z4074	Sulfite reductase subunit alpha	+2.12	1.2E-03
Protein metabolism
yaeJ	Z0203	Peptidyl-tRNA hydrolase domain-containing protein	−1.36	0.03
rpmE	Z5484	50S ribosomal protein L31	−2.20	0.019
pepA	Z5872	Leucyl aminopeptidase	−1.58	0.02
DNA/RNA metabolism
hisT	Z3580	tRNA pseudouridine synthase A	−1.51	0.02
deoD	Z5986	Purine nucleoside phosphorylase	−1.37	0.04
mazG	Z4096	Nucleoside triphosphate pyrophospho-hydrolase	+1.49	0.02
Cell wall/cell division/cell cycle
murD	Z0098	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase	−1.58	0.02
uppP	Z4410	Undecaprenyl pyrophosphate phosphatase	−1.72	0.01
Cofactors, vitamins, protheticgroups
yaeM	Z0184	1-deoxy-D-xylulose 5-phosphate	−1.33	0.04
nadA	Z0919	Quinolinate synthetase reductoisomerase	−1.82	0.002
btuR	Z2540	Cobinamide adenosyltransferase	−1.31	0.04
nadB	Z3856	L-aspartate oxidase	−1.63	4.0E-03
ggt	Z4813	Gamma-glutamyltranspeptidase	−1.76	2.0E-03
Transcriptional regulation
ykgK	Z0361	LuxR-type transcriptional regulator	−2.49	0.049
marA	Z2170	DNA-binding transcriptional activator MarA	−1.52	0.039
marR	Z2172	MarR family transcriptional repressor	−1.56	0.053
yhgG	Z4765	Transcriptional regulator	+2.12	0.04
Signal transduction
phoB	Z0497	Response regulator belonging to PhoB/PhoR two-component system	−1.53	0.031
phoR	Z0498	Signal sensor component of PhoB/PhoR two-component system	−1.47	0.036
narL	Z1996	Nitrate/citrate response regulator	−1.48	0.064
narK	Z2000	Nitrite/nitrate antiporter	+2.79	0.059
Virulence
cutF (nlpE)	Z0204	Lipoprotein involved with copper homeostasis and adhesion	−1.63	0.004
ykfE	Z0277	C-lysozyme inhibitor	−7.09	5.6E-06
nleB	Z4328	Type III effector	+1.72	0.04
nleE	Z4329	Type III effector	+1.86	0.02
efa-1`	Z4332	Cytotoxin	+1.84	0.01
efa-1`	Z4333	Cytotoxin	+1.93	0.03

^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

Back to article page

ISSN: 1471-2180

Contact us

General enquiries: journalsubmissions@springernature.com

BMC Microbiology

Contact us