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. 2014 May 9;15:353. doi: 10.1186/1471-2164-15-353

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

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)

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.