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Table 5 Genes compared to LB either with highest logFC or RPKM values on radish sprouts and in spinach medium or genes known from an association to plants 1

From: Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces

Gene tag

Product

LB

LB-pH9

LB-pH4

LB-15°C

LB-nitrite

LB-antibiotics

LB-solid

minimal medium

spinach juice

radish sprouts

feces

Z0070

L-arabinose isomerase

1 (4)

−0.5 (2)

1.2 (2)

−1.3 (1)

1.7 (13)

0.0 (1)

−5.6 (0)

−1.1 (1)

0.1 (3)

3.1 (23)

−5.6 (0)

Z1106

HCP oxidoreductase, NADH-dependent

1 (3)

−1.1 (1)

−4.8 (0)

−4.8 (0)

0.3 (4)

−4.8 (0)

0.4 (2)

0.7 (4)

7.7 (443)

2.1 (9)

1.1 (1)

Z1107

hydroxylamine reductase

1 (2)

0.2 (1)

−4.7 (0)

2.1 (7)

0.2 (2)

−4.7 (0)

1.5 (2)

−1.1 (1)

8.3 (356)

2.3 (5)

−4.7 (0)

Z1109

aquaporin Z

1 (9)

3.0 (41)

1.3 (4)

4.1 (130)

3.4 (88)

−5.6 (0)

−1.4 (1)

1.1 (12)

0.2 (6)

3.8 (70)

−5.6 (0)

Z1390

hydrogenase 1 large subunit

1 (2)

0.2 (1)

−5.0 (0)

−1.1 (1)

1.0 (4)

−5.0 (0)

−5.0 (0)

1.3 (4)

7.6 (255)

0.5 (2)

−5.0 (0)

Z1670

curli production assembly/transport component, 2nd curli operon

1 (24)

1.6 (43)

1.0 (8)

2.1 (88)

1.2 (54)

−7.3 (0)

−3.1 (1)

0.3 (18)

−0.9 (7)

1.2 (32)

0.5 (6)

Z1671

curli assembly protein CsgF

1 (7)

2.3 (21)

−4.6 (0)

2.0 (26)

−0.4 (5)

−4.6 (0)

−4.6 (0)

0.9 (9)

−4.6 (0)

2.4 (24)

−4.6 (0)

Z1672

curli assembly protein CsgE

1 (12)

2.2 (35)

2.3 (11)

1.5 (30)

0.9 (23)

−5.3 (0)

−0.1 (4)

1.2 (19)

−2.0 (2)

2.2 (34)

−5.3 (0)

Z1673

DNA-binding transcriptional regulator CsgD

1 (39)

1.9 (83)

1.6 (19)

0.0 (33)

0.4 (50)

−7.6 (0)

−3.4 (1)

0.6 (37)

−3.4 (2)

1.3 (56)

−1.8 (2)

Z1675

curlin minor subunit

1 (20)

3.1 (114)

−6.3 (0)

2.9 (138)

2.9 (156)

0.4 (7)

−1.1 (3)

2.5 (75)

1.2 (28)

6.0 (803)

−0.4 (3)

Z1676

cryptic curlin major subunit

1 (46)

5.3 (1143)

0.6 (13)

2.0 (168)

3.3 (472)

0.5 (18)

−0.5 (11)

3.8 (440)

−0.3 (23)

5.6 (1336)

−7.5 (0)

Z1697

biofilm formation regulatory protein BssS

1 (113)

2.4 (386)

2.5 (116)

6.7 (10874)

4.4 (2326)

1.5 (89)

3.7 (512)

1.5 (219)

3.0 (556)

6.1 (4555)

4.7 (530)

Z2243

nitrite extrusion protein 2

1 (0)

2.5 (1)

3.2 (1)

5.8 (19)

4.4 (8)

−2.1 (0)

−2.1 (0)

2.4 (1)

2.1 (1)

7.0 (30)

3.7 (1)

Z2315

azoreductase

1 (21)

−1.1 (6)

−0.4 (3)

0.5 (25)

−0.8 (11)

1.8 (19)

0.8 (12)

1.5 (39)

1.1 (25)

4.1 (213)

2.9 (26)

Z2479

DNA-binding transcriptional activator PspC

1 (17)

1.5 (31)

−0.4 (2)

1.9 (57)

1.4 (46)

−0.1 (5)

−5.7 (0)

0.8 (20)

−0.9 (6)

4.1 (182)

7.2 (470)

Z2480

phage shock protein B

1 (25)

1.4 (39)

−0.2 (4)

1.9 (80)

1.2 (55)

−5.5 (0)

−0.3 (7)

−0.9 (8)

0.0 (15)

3.9 (228)

6.8 (482)

Z2482

phage shock protein PspA

1 (64)

0.8 (63)

0.8 (18)

2.0 (206)

0.5 (81)

−0.4 (12)

0.6 (31)

0.6 (59)

0.6 (56)

4.8 (1077)

6.5 (970)

Z2591

acid shock protein precursor

1 (37)

−0.9 (13)

5.3 (261)

−6.6 (0)

−0.9 (20)

−6.6 (0)

−6.6 (0)

−1.5 (9)

1.8 (80)

7.5 (4178)

−6.6 (0)

Z2949

trehalose-6-phosphate synthase

1 (20)

2.0 (49)

0.3 (4)

0.9 (32)

3.0 (151)

−2.2 (1)

0.1 (7)

1.0 (26)

2.3 (57)

2.6 (74)

1.3 (9)

Z2950

trehalose-6-phosphate phosphatase

1 (16)

2.7 (66)

0.6 (4)

1.5 (41)

3.2 (141)

−1.1 (2)

−0.2 (5)

1.0 (20)

2.2 (45)

3.7 (133)

1.4 (8)

Z2951

partial high-affinity L-arabinose transport system; membrane protein, fragment 2

1 (4)

0.0 (3)

−4.6 (0)

−0.6 (2)

0.6 (6)

−4.6 (0)

−4.6 (0)

−4.6 (0)

−4.6 (0)

2.3 (12)

−4.6 (0)

Z2953

L-arabinose transporter ATP-binding protein

1 (8)

1.4 (13)

0.7 (2)

0.4 (9)

1.7 (27)

−6.6 (0)

−0.5 (2)

−1.1 (2)

−0.4 (4)

1.5 (14)

−6.6 (0)

Z2954

L-arabinose-binding periplasmic protein

1 (43)

1.4 (70)

−2.1 (2)

−0.3 (29)

1.2 (95)

−8.4 (0)

−2.6 (2)

−4.8 (1)

−3.2 (3)

1.3 (60)

−8.4 (0)

Z3425

PTS system fructose-specific transporter subunits IIBC

1 (3)

1.8 (7)

1.5 (1)

1.5 (8)

1.3 (7)

−5.4 (0)

−0.2 (1)

0.4 (3)

5.9 (112)

3.2 (17)

−5.4 (0)

Z3426

1-phosphofructokinase

1 (4)

0.0 (2)

−4.9 (0)

2.1 (15)

1.2 (9)

−4.9 (0)

0.3 (2)

1.6 (8)

5.9 (139)

2.7 (16)

−4.9 (0)

Z3427

bifunctional PTS system fructose-specific transporter subunit IIA/HPr protein

1 (2)

0.9 (2)

−4.3 (0)

1.2 (4)

−0.6 (1)

−4.3 (0)

2.7 (5)

1.3 (3)

7.3 (192)

4.0 (21)

−4.3 (0)

Z3511

UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase

1 (122)

−1.9 (19)

−2.2 (4)

−0.4 (76)

−1.0 (58)

−0.8 (17)

−2.9 (5)

−4.0 (5)

−4.8 (2)

0.3 (87)

−4.2 (1)

Z3512

undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase

1 (75)

−2.5 (7)

−0.5 (9)

−1.8 (18)

−2.2 (15)

−1.5 (7)

−3.9 (2)

−5.5 (1)

−3.6 (3)

−0.7 (27)

−3.2 (1)

Z3513

bifunctional UDP-glucuronic acid decarboxylase/UDP-4-amino-4-deoxy-L-arabinose formyltransferase

1 (88)

−3.3 (5)

−1.7 (4)

−1.3 (29)

−2.2 (17)

−2.4 (4)

−3.2 (3)

−2.8 (7)

−4.3 (2)

−0.4 (39)

−4.5 (1)

Z3515

4-amino-4-deoxy-L-arabinose transferase

1 (64)

−1.8 (11)

−1.6 (3)

0.7 (91)

−0.7 (39)

−1.8 (5)

−1.8 (6)

−2.4 (8)

−3.0 (5)

−0.4 (28)

−9.7 (0)

Z5648

phage shock protein G

1 (2)

3.1 (11)

6.4 (31)

4.0 (29)

2.8 (14)

4.5 (13)

2.1 (3)

3.0 (11)

2.2 (6)

7.7 (257)

8.5 (140)

Z5717

arginine:agmatin antiporter

1 (5)

0.2 (3)

−5.7 (0)

−3.2 (0)

1.3 (11)

−5.7 (0)

−0.5 (1)

3.9 (46)

7.5 (528)

1.8 (9)

−5.7 (0)

Z5719

biodegradative arginine decarboxylase

1 (3)

−0.1 (2)

0.3 (1)

−1.7 (1)

−1.4 (1)

−6.0 (0)

−6.0 (0)

0.3 (3)

8.3 (647)

1.2 (4)

−6.0 (0)

Z5734

lysine decarboxylase 1

1 (1)

1.6 (2)

−4.0 (0)

−0.1 (1)

0.6 (1)

−4.0 (0)

−4.0 (0)

−4.0 (0)

7.6 (107)

0.5 (1)

−4.0 (0)

Z5735

lysine/cadaverine antiporter

1 (0)

0.6 (0)

3.2 (1)

−2.1 (0)

0.6 (1)

−2.1 (0)

2.1 (1)

−2.1 (0)

5.3 (10)

−2.1 (0)

−2.1 (0)

  1. 1For each gene, the first number indicates the logFC of a certain condition compared to LB; RPKM values are shown in parentheses. Significantly differentially expressed genes are in bold (i.e., p values ≤ 0.05 in edgeR). Note that Z3511-Z3515 are not only active on sprouts, but also in LB medium. For a graphic version, indicating the magnitude of the absolute value of logFC in shades of grey, see Additional file 4.
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