Table 2.
The classification of 10 representative candidate TFs and proposed functions in E. coli K-12 MG1655
| Gene# (b-number) | Classification of candidate TFs (# of TFBSs) | Family Type | Binding sites associated with metabolic pathway | Proposed regulatory roles | Results |
|---|---|---|---|---|---|
| yidZ (b3711) | Type I (118) | LysR | Widespread, intragenic binding | Target genes have diverse functions | Figure 3 |
| yfeC (b2398) | Type II (50) | N/A* | chaAB, panD, grxC, pqqL, hybE, lpp, rpmH, rpmB | yfeC mutant was reported to increase eDNA release (40) | Figure 4 |
| yciT (b1284) | Type II (49) | DeoR | ybiO, ybiV, ybiY | A regulator involved in osmolarity | Figure 5 |
| ydhB# (b1659) | Type II (29) | LysR | ydhB, ydhC | A regulator involved in purine metabolism | Supplementary Figure S6 |
| ybcM (b0546) | Type II (12) | AraC | ybcL, ucpA | A regulator related to stress response | Figure 6 |
| yneJ# (b1526) | Type II (8) | LysR | sad, yneJ | A regulator involved in glutamate metabolism | Supplementary Figure S7 (54) |
| yjhI# (b4299) | Type II (5) | IclR | yjhG, yjhH, yjhI | A regulator related to the energy conversion between pyruvate and glycolaldehyde | Supplementary Figure S8 |
| yfiE# (b2577) | Type II (4) | LysR | yfiE, eamB | A regulator related to the control of a cysteine and O-acetylserine exporter | Supplementary Figure S9 |
| ygbI (b2735) | Type III (1) | DeoR | ygbJ, ygbK | A regulator involved in tartrate metabolism | Figure 7 |
| ynfL# (b1595) | Type III (1) | LysR | ynfL, ynfM | A regulator involved in the control of arabinose efflux transporter | Supplementary Figure S10 |
*N/A indicates no prediction due to the lack of structural information.
Genes# were analyzed and presented in the supplementary material.