TABLE 1.
PdhR-bound DNA fragmentsa
| Group and no. of clones | Upstream gene | SELEX fragment | Downstream gene |
|---|---|---|---|
| A (SELEX fragments within spacer regions) | |||
| 48 | aroP← | (0122011) S (0122303) | →pdhR |
| 14 | cyoA← | (0450896) S (0451132) | ←ampG |
| 3 | yfiD← | (2714930) S (2715311) | →ung |
| 2 | ycfD→ | (1167498) S (1167753) | →ndh |
| B (SELEX fragments on open reading frames) | |||
| 2 | wcaA← | (2135986) S (wzc) (2136196) | ←wzb |
| 1 | ygeD← | (2974235) S (aas) (2974451) | →galR |
| 1 | degP→ | (0182534) S (cdaR) (0182770) | ←yaeH |
| 1 | ybiS← | (0857353) S (ybiT) (0857554) | ←ybiU |
| 1 | yhiD→ | (3964400) S (yhjE) (3964580) | ←yhjG |
a
Using the genomic SELEX method, a total of 73 DNA fragments have been isolated as complexes with the purified PdhR protein, which were all cloned into the sequencing vector. Group A clones contained the sequences from spacer regions between the indicated neighboring genes, while group B clones carried the sequences within the indicated coding frames. The numbers on both sides of each SELEX (S) fragment indicate the boundaries in the E. coli genome map (27). The arrows indicate the direction of transcription of the neighboring genes. The genes shown in boldface type indicate the PdhR regulation targets.