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.