TABLE 1.
DNA fragments used in binding studiesa
| Marbox type | Sequence of one strand of the marbox fragment at the indicated position |
|||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | |
| Consensus | A | Y | N | G | C | A | C | N | N | W | N | N | R | Y | Y | A | A | A | C | N |
| Promoter | ||||||||||||||||||||
| acnA | A | A | C | C | C | A | A | A | T | T | G | A | T | A | A | A | A | G | A | G |
| acrAB | A | T | G | G | C | A | C | G | A | A | A | A | A | C | C | A | A | A | C | A |
| fpr | A | A | G | G | C | T | C | A | A | T | C | G | A | T | C | A | A | A | T | C |
| fumC | A | T | G | G | C | A | C | G | A | A | A | G | A | C | C | A | A | A | C | A |
| inaA | A | C | G | A | C | A | C | G | T | T | T | C | A | T | T | A | A | G | A | T |
| marRAB | A | T | G | C | C | A | C | G | T | T | T | T | G | C | T | A | A | A | T | C |
| mdaB | T | T | T | G | C | A | C | A | T | T | T | T | G | C | T | A | A | T | T | T |
| mdtG | A | G | A | G | C | T | T | T | T | A | T | C | G | C | T | A | A | A | T | C |
| micF | A | C | A | G | C | A | C | T | G | A | A | T | G | T | C | A | A | A | A | C |
| nfsB | A | G | C | G | C | A | T | T | T | T | T | C | T | C | G | C | T | T | A | C |
| pqiA | A | A | A | G | C | A | G | A | A | A | C | T | G | T | A | A | A | A | C | G |
| poxB | G | A | G | G | C | A | C | T | A | A | C | G | G | T | T | A | A | A | T | A |
| sodA | A | C | G | G | C | A | T | T | G | A | T | A | A | T | C | A | T | T | T | T |
| ybjC | A | A | A | G | C | T | A | T | A | A | C | T | G | T | T | A | A | A | C | A |
| yhbW | A | T | A | G | C | T | C | A | C | T | T | T | G | T | T | A | A | C | A | A |
| zwf | A | T | C | G | C | A | C | G | G | G | T | G | G | A | T | A | A | G | C | G |
a
Both strands of the 20-mer marbox from each promoter were synthesized and annealed and used in the binding experiments. Each marbox is shown in the forward orientation (22). Although there is no base preference at position 20, which is why we refer to the marbox as being 19 bp in length, binding in vitro requires a 20-bp fragment (22). At position 12, 6 of the 16 marbox sequences have a T at this position (boldface). At positions 17 and 18, 9 of the 16 marboxes have an A at both positions; underlining shows where there is no A; only the sodA and nfsB marboxes have no A at either position.