Table 2. All genes investigated in this study categorized according to their regulatory architecture, given as (number of activators, number of repressors).
The regulatory architectures as listed reflect only the binding sites that would be able to be recovered within our 160 bp constructs, but include both newly discovered and previously known binding sites. In those cases where binding sites that appear in RegulonDB or Ecocyc are omitted from this tally, the Section 'Explanation of included binding sites' in Appendix 4 has the reasoning, for each relevant gene, why the binding sites are not shown. The table also lists the number of newly discovered binding sites, previously known binding sites, and number of identified transcription factors. The evidence used for the transcription factor identification is given in the final column. 'Bioinformatic' evidence implies that discovered position weight matrices were compared to known transcription factor position weight matrices. The literature sites column contains only those sites that are both expected to be and are, in actuality, observed in the Reg-Seq data.
| Architecture | Promoter | Newly discovered binding sites | Literature binding sites | Identified binding sites | Evidence |
|---|---|---|---|---|---|
| (0, 0) | acuI | 0 | 0 | 0 | |
| aegA | 0 | 0 | 0 | ||
| arcB | 0 | 0 | 0 | ||
| cra | 0 | 0 | 0 | ||
| dnaE | 0 | 0 | 0 | ||
| ecnB | 0 | 0 | 0 | ||
| fdoH | 0 | 0 | 0 | ||
| holC | 0 | 0 | 0 | ||
| hslU | 0 | 0 | 0 | ||
| htrB | 0 | 0 | 0 | ||
| minC | 0 | 0 | 0 | ||
| modE | 0 | 0 | 0 | ||
| ycgB | 0 | 0 | 0 | ||
| mscL | 0 | 0 | 0 | ||
| pitA | 0 | 0 | 0 | ||
| poxB | 0 | 0 | 0 | ||
| rlmA | 0 | 0 | 0 | ||
| rumB | 0 | 0 | 0 | ||
| sbcB | 0 | 0 | 0 | ||
| sdaB | 0 | 0 | 0 | ||
| tar | 0 | 0 | 0 | ||
| ybdG | 0 | 0 | 0 | ||
| ybiP | 0 | 0 | 0 | ||
| ybjT | 0 | 0 | 0 | ||
| yehT | 0 | 0 | 0 | ||
| yfhG | 0 | 0 | 0 | ||
| ygdH | 0 | 0 | 0 | ||
| ygeR | 0 | 0 | 0 | ||
| yggW | 0 | 0 | 0 | ||
| ynaI | 0 | 0 | 0 | ||
| yqhC | 0 | 0 | 0 | ||
| zapB | 0 | 0 | 0 | ||
| zupT | 0 | 0 | 0 | ||
| amiC | 0 | 0 | 0 | ||
| (0, 1) | araC | 0 | 1 | 0 | |
| bdcR | 1 | 0 | 1 | Known binding location (NsrR) (Partridge et al., 2009) | |
| coaA | 1 | 0 | 0 | ||
| dicC | 0 | 1 | 0 | ||
| dinJ | 1 | 0 | 0 | ||
| ybeZ | 1 | 0 | 0 | ||
| idnK | 1 | 0 | 1 | Mass- Spectrometry (YgbI) | |
| leuABCD | 1 | 0 | 1 | Mass- Spectrometry (YgbI) | |
| mscM | 1 | 0 | 0 | ||
| yedK | 1 | 0 | 1 | Mass- Spectrometry (TreR) | |
| rapA | 1 | 0 | 1 | Growth condition Knockout (GlpR), Bioinformatic (GlpR) | |
| sdiA | 1 | 0 | 0 | ||
| tff-rpsB-tsf | 1 | 0 | 1 | Growth condition Knockout (GlpR), Bioinformatic (GlpR), Knockout (GlpR) | |
| thiM | 1 | 0 | 0 | ||
| tig | 1 | 0 | 1 | Growth condition Knockout (GlpR), Bioinformatic (GlpR), Knockout (GlpR) | |
| ybiO | 1 | 0 | 0 | ||
| ydjA | 1 | 0 | 0 | ||
| yedJ | 1 | 0 | 0 | ||
| phnA | 1 | 0 | 1 | Mass- Spectrometry (YciT) | |
| mutM | 1 | 0 | 0 | ||
| rhlE | 1 | 0 | 1 | Growth condition Knockout (GlpR), Bioinformatic (GlpR), Mass- Spectrometry (GlpR) | |
| uvrD | 1 | 0 | 1 | Bioinformatic (LexA) | |
| dusC | 1 | 0 | 0 | ||
| ftsK | 0 | 1 | 0 | ||
| znuA | 0 | 1 | 0 | ||
| znuCB | 0 | 1 | 0 | ||
| (1, 0) | waaA-coaD | 1 | 0 | 0 | |
| rcsF | 1 | 0 | 0 | ||
| groSL | 1 | 0 | 0 | ||
| mscS | 1 | 0 | 0 | ||
| thrLABC | 1 | 0 | 0 | ||
| yeiQ | 1 | 0 | 1 | Growth condition Knockout (FNR), Bioinformatic (FNR) | |
| ycbZ | 1 | 0 | 0 | ||
| ygjP | 1 | 0 | 0 | ||
| lac | 0 | 1 | 0 | Bioinformatic (CRP) | |
| yehS | 1 | 0 | 0 | ||
| yehU | 1 | 0 | 1 | Growth condition Knockout (FNR), Bioinformatic (FNR) | |
| (0, 2) | pcm | 2 | 0 | 0 | |
| yecE | 2 | 0 | 1 | Mass- Spectrometry (HU) | |
| yjjJ | 2 | 0 | 1 | Growth condition Knockout (MarA), Bioinformatic (MarA) | |
| dcm | 2 | 0 | 1 | Mass- Spectrometry (HNS) | |
| (1, 1) | arcA | 2 | 0 | 2 | Growth condition Knockout (FNR), Bioinformatic (FNR), Mass- Spectrometry (FNR, CpxR) |
| dgoR | 0 | 2 | 0 | Bioinformatic (CRP) Bioinformatic (DgoR) | |
| ykgE | 2 | 0 | 2 | Growth condition Knockout (FNR), Bioinformatic (FNR), Mass- Spectrometry(YieP) Knockout (YieP) | |
| ymgG | 2 | 0 | 0 | ||
| (2, 0) | asnA | 2 | 0 | 0 | |
| fdhE | 2 | 0 | 2 | Growth condition Knockout (FNR, ArcA), Bioinformatic (FNR, ArcA), Knockout (ArcA) | |
| xylF | 0 | 2 | 0 | ||
| (1, 2) | marR | 0 | 3 | 0 | Mass- Spectrometry (MarR) |
| aphA | 3 | 0 | 2 | Growth condition Knockout (FNR), Bioinformatic (FNR), Mass- Spectrometry (DeoR) | |
| iap | 3 | 0 | 0 | ||
| ilvC | 3 | 0 | 1 | Mass- Spectrometry (IlvY) (Rhee et al., 1998) | |
| (2, 1) | maoP | 3 | 0 | 3 | Growth condition Knockout (GlpR), Bioinformatic (GlpR), Knockout (PhoP, HdfR, GlpR) |
| rspA | 1 | 2 | 1 | Mass- Spectrometry (DeoR) | |
| (2, 2) | ybjX | 4 | 0 | 4 | Bioinformatic (2 PhoP sites), Mass- Spectrometry (HNS, StpA) |
| (3, 0) | araAB | 0 | 3 | 0 | |
| xylA | 0 | 3 | 0 | ||
| yicI | 3 | 0 | 0 | ||
| (0, 3) | ompR | 0 | 3 | 0 | |
| ybjL | 3 | 0 | 0 | ||
| (0, 4) | relBE | 0 | 4 | 0 | Mass- Spectrometry (RelBE) |