Table 2.
RcdA target list (SELEX-chip)
| Function | Left | S | Right | Function | ||
|---|---|---|---|---|---|---|
| Hydroxymethyltransferase | panB | < | yadC | < | yadK | |
| tfaX | > | > | appY | Transcription factor | ||
| Lipoate synthase | lipA | < | ybeF | < | ybeF | |
| Transporter | ybjJ | < | > | rcdA | Transcription factor | |
| Outer membrane protein A | ompA | < | sulA | > | sxy | CRP-dependent promoters |
| Biofilm adhesin PGA export | pgaA | < | ycdT | < | insE4 | |
| Transcription factor | csgD | < | > | csgB | Curlin nucleator protein | |
| pinE | > | > | mcrA | 5-Met-C restriction nuclease B | ||
| Antirepressor for YcgE | ycgF | < | > | ycgZ | Connector for RcsB regulation | |
| Conserved protein | ydeI | < | > | ydeJ | Conserved protein | |
| ynfM | > | > | asr | Acid shock periplasm prot | ||
| ydhS | > | ydhT | < | ydhU | ||
| insH6 | < | > | yoeA | Hemin or colicin receptor | ||
| Fimbrial-like adhesin protein | yehA | < | yehB | < | yehC | |
| micF | > | > | rcsD | RcsBC TCS intermediate prot | ||
| pbl | > | ygeK | < | ygeL | ||
| 5S rRNA of rrnD operon | rrfD | < | rrlD | < | alaU | |
| yibG | > | > | yibV | Hypothetical protein | ||
| gltU | > | rrlC | > | rrfC | 5S rRNA of rrnC operon | |
| N-AceNA OM channel protein | nanC | < | > | fimB | On/off regulator of fimA |
Genomic SELEX screening of RcdA-binding sequences was performed under the standard conditions (for details see text). RcdA-bound DNA fragments were subjected to SELEX-chip analysis. The pattern of positions of RcdA-bound DNA fragments are shown in Figure 2. The peak positions of SELEX fragments are shown in “S” column. In some cases, RcdA-binding sites were identified on open reading frames on the indicated genes. The genes located on “Left” and “Right” sides are indicated. The direction of transcription is shown by arrows.