TABLE 2.
Genes regulated by iron, with or without Fur
| ORFa | Gene | Functionb | fur/WTc | Low iron/high irond |
|---|---|---|---|---|
| Negatively regulated by Fur and iron | ||||
| Vibriobactin biosynthesis | ||||
| VC0774 | vibA (79) | 8.5 | 9.7 | |
| VC0771 | vibB (79) | 11.7 | 10.1 | |
| VC0773 | vibC (79) | 11.0 | 14.7 | |
| VC0780 | vibD (81) | 2.7 | NDe | |
| VC0772 | vibE (79) | 8.7 | 11.0 | |
| VC2209 | vibF (8) | 7.7 | 10.6 | |
| VC0775 | vibH (81) | 3.0 | 5.6 | |
| Siderophore transport | ||||
| VC2211 | viuA | OMTf vibriobactin (9, 66) | 5.4 | 15.4 |
| VC0475 | irgA | OMT enterobactin (23, 25, 49) | 32.5 | 18.8 |
| VCA0232 | vctA | OMT enterobactin (49) | 11.3 | 14.3 |
| VC0200 | fhuA | OMT ferrichrome (63) | 5.4 | 10.2 |
| VC2210 | viuB | Iron removal from catechol siderophores (7) | 7.9 | 15.0 |
| VC0776 | viuP | PBPg catechols (82) | 4.5 | 6.1 |
| VC0777 | viuD | IMTh catechols (82) | 4.2 | 5.5 |
| VC0778 | viuG | IMT catechols (82) | 4.2 | 15.6 |
| VC0779 | viuC | IMT catechols (82) | 3.2 | 3.5 |
| VCA0227 | vctP | PBPg catechols (49) | 4.8 | 8.9 |
| VCA0228 | vctD | IMT catechols (49) | 2.3 | 4.6 |
| VCA0229 | vctG | IMT catechols (49) | 2.3 | 4.1 |
| VCA0230 | vctC | IMT catechols (49) | 3.7 | 7.9 |
| VC0201 | fhuC | IMT ferrichrome (63) | 3.4 | 5.8 |
| Heme transport | ||||
| VCA0576 | hutA | OMT (34, 35, 48) | 20.4 | 37.3 |
| VCA0914 | hutB | IMT (53) | 10.4 | ND |
| VCA0915 | hutC | IMT (53) | 2.7 | 5.8 |
| VCA0916 | hutD | IMT (53) | 3.3 | 8.4 |
| VCA0907 | hutZ | Heme binding (80) | 8.2 | ND |
| Miscellaneous transporters | ||||
| VC0284 | OMT ligand unknowni | 3.6 | 5.3 | |
| VC2078 | feoA | Ferrous ironj | 3.8 | 4.1 |
| VC2077 | feoB | Ferrous ironj | 3.6 | 5.2 |
| VC0608 | fbpA | Inorganic ironj | 2.7 | ND |
| TonB systems | ||||
| VCA0910 | tonB1 (53) | 17.1 | 50.0 | |
| VCA0911 | exbB1 (53) | 18.7 | 32.1 | |
| VCA0912 | exbD1 (53) | 13.0 | 23.9 | |
| VC1544 | tonB2 (53) | 7.1 | 6.2 | |
| VC1546 | exbB2 (53) | 6.5 | 11.8 | |
| VC1545 | exbD2 (53) | 6.0 | 7.6 | |
| Enzymes | ||||
| VC1542 | ligA-2 | Ligase (linked to tonB2 operon) | 2.2 | 2.4 |
| VC1573 | fumC | Fumarate dehydratase | 9.1 | 13.8 |
| VC2694 | sodA | Superoxide dismutase | 7.5 | 23.8 |
| VCA0063 | ptrB | Protease II (48) | 4.9 | 7.3 |
| Regulatory proteins | ||||
| VC0474 | irgB | Regulator of irgA (24) | 1.7 | 2.3 |
| VCA0231 | vctR | Linked to vctA, function unknown (49) | 8.7 | 10.5 |
| Iron storage | ||||
| VC0364 | bfd | 3.7 | 3.2 | |
| VC0365 | bfr | 3.7 | 3.2 | |
| Unknown function | ||||
| VC0091 | Putative O-methyl transferase for polyketide biosynthesis, COG3315 | 4.8 | 4.4 | |
| VC1264 | irpA | Function unknown, COG3487 | 5.4 | 10.0 |
| VC1265 | Putative thioloxidoreductase, linked to irpA, COG3488 | 3.1 | 3.0 | |
| VC1266 | Hypothetical periplasmic lipoprotein, linked to irpA, COG3489 | 2.7 | 3.9 | |
| VC1267 | Hypothetical, linked to irpA, COG3490 | 2.9 | 4.2 | |
| VC1543 | Hypothetical, linked to tonB2 (53) | 3.9 | 4.1 | |
| VC1547 | exbB related, linked to tonB2 (53) | 4.6 | 9.2 | |
| VC1548 | Hypothetical, linked to tonB2 (53) | 7.9 | 13.3 | |
| VC1572 | Hypothetical, linked to fumC | 9.4 | 8.9 | |
| VC1688 | Hypothetical | 2.6 | 2.9 | |
| VC2076 | Hypothetical, linked to feoAB | 2.4 | 2.7 | |
| VC2695 | rRNA methylase, linked to sodA, COG0219 | 2.7 | 5.0 | |
| VCA0043 | Putative acyl transferase, COG2388 | 4.3 | 3.8 | |
| VCA0216 | Hypothetical membrane, linked to VCA0215 and VCAφ217 | 3.7 | 7.2 | |
| VCA0233 | Hypothetical, linked to vctA, COG3553 (49) | 6.0 | 5.7 | |
| VCA0234 | Hypothetical, linked to vctA (49) | 4.8 | 8.9 | |
| VCA0909 | hutW | Unknown, linked to hutZ (80) | 20.0 | 52.1 |
| VCA0908 | hutX | Unknown, linked to hutZ (80) | ND | 51.3 |
| VCA0976 | Hypothetical | 19.6 | 53.4 | |
| VCA0977 | ABC transporter, linked to VCA0776, COG4172 | 12.7 | 20.5 | |
| VCA1041 | Putative phosphomannomutase, COG1109 | 2.8 | 2.5 | |
| Positively regulated by Fur and by iron | ||||
| VCA0678 | napA | Periplasmic nitrate reductase | 0.44 | 0.18 |
| VCA0679 | napB | Periplasmic nitrate reductase | 0.43 | 0.16 |
| VCA0680 | napC | Periplasmic nitrate reductase | 0.58 | 0.30 |
| VCA0677 | napD | Maturation of nitrate reductase | 0.43 | 0.16 |
| VCA0676 | napF | Periplasmic nitrate reductase | 0.41 | 0.24 |
| VC1973 | menB | Menaquinone biosynthesis | ND | 0.41 |
| Negatively regulated by iron, independently of Fur | ||||
| VC1112 | bioB | Biotin biosynthesis | 0.86 | 3.6 |
| VC2227 | purN | Purine biosynthesis | 1.0 | 2.8 |
| VC2415 | pdhR | Pyruvate dehydrogenase repressor | 0.93 | 3.4 |
| VCA0215 | Hypothetical, linked to VCA0216 | 1.1 | 3.2 | |
| VCA0217 | GGDEF motif protein, linked to VCA0216, COG2199 | 1.2 | 3.2 | |
| VCA0262 | Hypothetical | 0.95 | 3.2 | |
| Positively regulated by iron, independently of Fur | ||||
| VC1216 | Hypothetical, GGDEF motif protein, COG2199 | 0.97 | 0.34 | |
| VC1343 | Peptidase M20, COG2195 | 0.89 | 0.43 | |
| VC1371 | Hypothetical | 0.97 | 0.49 | |
| VC1514 | Hypothetical | 1.2 | 0.23 | |
| VC1515 | Putative formate dehydrogenase-specific chaperone, COG3381 | 1.0 | 0.33 | |
| VC1516 | Iron-sulfur cluster binding protein, COG1145 | 0.95 | 0.37 | |
| VCA0784 | Putative reductase, COG3007 | 0.95 | 0.50 |
a
ORF designation from TIGR database (33).
b
The reference(s) for previously identified genes is indicated. For genes of unknown function, the cluster of orthologous groups (COG) (70) number is included if available.
c
Mean expression ratio of fur mutant relative to wild-type parental strain O395.
d
Mean expression ratio of wild-type strain O395 grown in the absence relative to the presence of iron supplementation.
e
ND, not determined. Data for this gene did not pass the quality filters.
f
OMT, outer membrane transporter.
g
PBP, periplasmic binding protein.
h
IMT, inner membrane transporter.
i
A. R. Mey, unpublished data.
j
E. E. Wyckoff, unpublished data.