Table 3.

Differentially expressed genes that are related to catabolic activity in E. coli O157:H7 curli variants

Function group and gene name	ID	Product	COGa	Fold upregulation in RM6607Rb
Fatty acid uptake or metabolism
fadE	Z0278	Putative acyl-CoA dehydrogenase	COG1960I	5.7
hdhA	Z2624	NAD-dependent 7-α-hydroxysteroid dehydrogenase	COG1028IQR	2.0
fadD	Z2848	Acyl-CoA synthetase, long-chain fatty acid–CoA ligase	COG0318IQ	5.4
fadJ	Z3604	Multifunctional fatty acid oxidation complex subunit α	COG1250I	3.6
fadI	Z3605	3-Ketoacyl–CoA thiolase	COG0183I	3.1
fadL	Z3608	Long-chain fatty acid outer membrane transporter	COG2067I	4.4
ucpA	Z3691	Short-chain dehydrogenase	COG1028IQR	4.3
fadA	Z5366	3-Ketoacyl–CoA thiolase	COG0183I	4.2
fadB	Z5367	Multifunctional fatty acid oxidation complex subunit α	COG1250I	5.9
acs	Z5668	Acetyl-CoA synthetase	COG0365I	5.0
phoH	Z1522	PhoB dependent, putative ATPase, involved in lipid metabolism and RNA modification	COG1702T	3.7
Amino acid uptake or metabolism
gltL	Z0802	ATP-binding protein of glutamate/aspartate transport system	COG1126E	2.4
gltK	Z0803	Glutamate/aspartate transport system permease	COG0765E	3.0
gltJ	Z0804	Glutamate/aspartate transport system permease	COG0765E	2.5
glnH	Z1033	Glutamine ABC transporter periplasmic protein	COG0834ET	2.3
Z2223	Z2223	Hemin-binding lipoprotein	COG0747E	3.8
Z2224	Z2224	Transport system permease protein	COG0601EP	2.4
Z2276	Z2276	Transport system permease protein	COG1177E	6.7
Z2277	Z2277	Transport system permease protein	COG1176E	3.8
Z2278	Z2278	ATP-binding component of a transport system	COG3842E	5.5
Z2279	Z2279	Transport protein	COG0687E	5.7
fliY	Z3010	Cystine transporter subunit	COG0834ET	6.4
hisP	Z3568	Histidine/lysine/arginine/ornithine transporter subunit	COG4598E	4.2
hisM	Z3569	Histidine transport, membrane protein M	COG4160E	2.1
hisQ	Z3570	Histidine transport system permease protein	COG4215E	2.7
hisJ	Z3571	Histidine-binding periplasmic protein of high-affinity histidine transport system	COG0834ET	2.8
argT	Z3572	Lysine-, arginine-, and ornithine-binding periplasmic protein	COG0834ET	3.9
oppD	Z2022	Oligopeptide ABC transporter ATP-binding protein	COG0444EP	2.2
dppA	Z4961	Dipeptide transport protein	COG0747E	2.4
ylbB	Z0671	Putative hydantoin utilization protein	COG0624E	2.9
cstA	Z0740	Carbon starvation protein, cAMP-CRP dependent, involved in peptide utilization.	COG1966T	3.0
cstC	Z2780	Acetylornithine δ-aminotransferase, participates in catabolism of amino acids	COG4992E	4.9
dadA	Z1952	d-Amino acid dehydrogenase subunit, catalyzes oxidative deamination of d-amino acids	COG0665E	2.1
ydjS	Z2776	Succinylglutamate desuccinylase, hydrolyzes N-succinyl-l-glutamate to succinate and l-glutamate, participates in arginine and proline metabolism	COG2988E	4.5
Z2777	Z2777	Succinylarginine dihydrolase, catalyzes hydrolysis of 2-N-succinylarginine into 2-N-succinylornithine, ammonia, and carbon dioxide in arginine degradation	COG3724E	6.0
Z2779	Z2779	Arginine succinyltransferase, participates in arginine and proline metabolism	COG3138E	5.8
Z3717	Z3717	Putative ethanolamine utilization protein EutP	COG4917E	2.6
gcvH	Z4241	Glycine cleavage system protein H	COG0509E	2.2
gcvT	Z4242	Glycine cleavage system aminomethyltransferase T	COG0404E	2.2
aspA	Z5744	Aspartate ammonia lyase, participates in alanine and aspartate metabolism and nitrogen metabolism	COG1027E	5.3
Carbohydrate uptake or metabolism
nagE	Z0826	Phosphotransferase system N-acetylglucosamine-specific transporter subunit IIABC	COG1263G	2.5
Z2192	Z2192	ABC transporter ATP-binding protein	COG1129G	2.5
ycjV	Z2463	ABC transporter ATP-binding protein	COG3839G	2.1
ugpE	Z4819	Glycerol-3-phosphate transporter membrane protein, related to uptake of glycerol-3-phosphate	COG0395G	2.4
ugpA	Z4820	Glycerol-3-phosphate transporter permease	COG1175G	3.1
ugpB	Z4822	Glycerol-3-phosphate transporter periplasmic binding protein	COG1653G	3.2
xylF	Z4991	d-Xylose transporter subunit XylF	COG4213G	2.0
rbsB	Z5252	d-Ribose transporter subunit RbsB	COG1879G	2.3
Z5691	Z5691	Ribose ABC transporter ATP-binding protein	COG1129G	2.1
Z5839	Z5839	ABC transporter ATP-binding protein	COG1129G	2.2
Z2189	Z2189	Autoinducer-2 ABC transporter, periplasmic autoinducer-2-binding protein LsrB, sugar ABC transporter	COG1879G	2.7
ytfQ	Z5838	Periplasmic binding domain of ABC-type YtfQ-like transport systems	COG1879G	2.7
mgsA	Z1314	Methylglyoxal synthase, participates in pyruvate metabolism	COG1803G	2.4
yneB	Z2188	Aldolase, catalyzes a reversible aldol reaction	COG1830G	2.6
manB	Z3194	Phosphomannomutase, participate in fructose and mannose metabolism	COG1109G	2.0
yeiQ	Z3431	Putative oxidoreductase, may be related to metabolic pathways	COG0246G	3.5
yihM	Z5409	Hypothetical protein contains conserved domain pfam01261 (AP_endonuc_2) and COG1082 [IolE], may be related to carbohydrate transport and metabolism	COG1082G	2.6

^aThe COG category was assigned based on the annotation for E. coli O157:H7 strain EDL933.

^bThe ratio of normalized hybridization intensities of the gene in RM6607R to that in RM6607W. All genes listed passed the significance test as detailed in Materials and Methods.