Table 1.
Effector predictions in 15 GENSOR units with no reported effector in RegulonDB, and a connectivity value of 1.
| GENSOR unit | Ligand binding domain | Predicted effectors | Prediction status | Evidence | Reference |
|---|---|---|---|---|---|
| FabR | Fatty acids attached to acyl-ACP | Validated | Gel mobility shift assay | Zhu et al., 2009 | |
| UlaR | DeoR C terminal sensor domain (Pfam:PF00455) | Ascorbate-6P | Validated | Gel mobility shift assay | Garces et al., 2008 |
| Dan | Bacterial regulatory helix-turn-helix protein, lysR family (Pfam:PF00126) | Tartrate | Supporting evidence | Change in gene expression due to addition of the compound (β-galactosidase assay) | Kim et al., 2009 |
| FeaR | AraC-binding-like domain (Pfam:PF14525) | Hyacinthin (phenyl acetaldehyde) | Supporting evidence | Inference from operon dynamics | Zeng and Spiro, 2013 |
| HcaR | LysR substrate binding domain (Pfam:PF03466) | 3-(5,6-Dihydroxycyclohexa-1,3-dien-1-yl)propanoate | Supporting evidence | Inference from operon dynamics | Turlin et al., 2001 |
| MtlR | Mannitol-1P | Supporting evidence | Inference from operon dynamics | Figge et al., 1994 | |
| KdgR | Bacterial transcriptional regulator (Pfam:PF01614) | 2-Keto-3-deoxygluconate-6-P | Supporting evidence | 2-Keto-3-deoxyguconate has been reported as effector of KdgR ortholog in Erwinia chrysanthemi | Nasser et al., 1992 |
| MngR | UTRA domain (Pfam:PF07702) | 2 (Alpha-D-mannosyl-6-phosphate)-D-glycerate | Supporting evidence | Change in gene expression due to addition of the external form of the compound (microarray). Mutation of downstream enzymes did not affect induction. | Sampaio et al., 2004 |
| AscG | Periplasmic binding protein-like domain (Pfam:PF13377) | Arbutin-6P, beta-D-cellibiose-6P | New | ||
| CaiF | Gamma-butyrobetaine, crotonobetainyl-CoA, carnityl-CoA, gamma-butyrobetaine-CoA | New. Supported by dynamics of the GENSOR unit (see text). Evidence against other predictions. | Mobility shift assay reflected no binding of L-carnitine or crotonobetaine | Buchet et al., 1999 | |
| YiaJ | Bacterial transcriptional regulator (Pfam:PF01614) | Xylulose-5P, 2-3,dioxo-L-gulonate, 3-keto-L-gulonate, 3-keto-L-gulonate 6-P | New. Evidence against other predictions (see text). | 80 candidate effectors did not show changes in target gene expression | Ibañez et al., 2000 |
| CsiR | FCD domain (Pfam:PF07729) | L-Glutamate, ketoglutarate, succinate semialdehyde | New | ||
| GatR | DeoR C terminal sensor domain (Pfam:PF00455) | Galactitol 1-phosphate, keto-L-tagatose 6-phosphate, tagatofuranose 1,6-diphosphate | New | ||
| RtcR | RNA terminal-2′,3′-cyclic-phosphate | New | |||
| CadC | Cadaverine, lysine | Evidence against mode of action | Anchored to the membrane; works as a one-component system. Responds to PH stress. | Buchner et al., 2015 | |
Ligand-binding domains identified in TF sequences are shown alongside their Pfam identifiers. Predicted effectors were inferred from the GENSOR unit topology; the prediction status indicates whether the prediction has been validated in the literature, evidence exists that supports or contradicts the hypotheses, or that predictions are new. ‘Evidence’ column indicates the relevant experiments that have been reported in the literature.