Table 4.
An Example of the TU's Used to Infer the Behavior of Multiple Regulated Systems
| Protein function | Coregulated group | Regulated promoter(s) | Evidence | Reference | Hypothesis |
|---|---|---|---|---|---|
| Activators | CRP-MalT | malk, malE | CRP triggers MalT repositioning to an appropriate activating position | (Richet et al. 1991) | Both activators are required |
| CRP-FNR | ansB | Both proteins make independent contacts with RNApol-activating transcription | (Busby and Ebright 1997) | Both activators are required | |
| CRP-MelR | melAB | MelR and CRP bind cooperatively at the promoter forming a complex that activates transcription in a codependent manner | (Wade et al. 2001) | Both activators are required | |
| IHF-NR(l), IHF-Xy1R, IHF-NarL | sigma54 promoters and narG | The first protein bends DNA in such a way that the second protein can interact directly with RNApol. Both are required for maximal activation. The presence of IHF alone (bending protein) does not activate transcription | (Goosen and van de Putte 1995) | One specific activator is sufficient | |
| FNR-NarL | napF | Both are required for maximal activation. NarL (proximal site) can activate transcription a few folds compared with the control, but FNR is unable to do it. | (Darwin et al. 1998) | One specific activator is sufficient | |
| DnaA-FIS | nrd | Both are required for maximal activation. DnaA causes more activation than FIS. | (Jacobson and Fuchs 1998) | One specific activator is sufficient | |
| Dual | CRP-CytR | deo | CytR functions as CRP corepressor, causing CRP to repressed transcription | (Rasmussen et al. 1996) | One repressor is sufficient |
| CRP-Lacl | lacZYA | When Lacl is bound, CRP is unable to reach its regulatory site | (Lewis et al. 1996; Matthews, 1996) | One repressor is sufficient | |
| CRP-AraC | araBAD | When AraC is bound, CRP is unable to activate transcription. | (Lee et al. 1981, 1992) | One repressor is sufficient | |
| FNR-FIS-HNS | nirB | FNR anaerobic activation is repressed by the presence of FIS and HNS. | (Wu et al. 1998; Browning et al. 2000) | One repressor is sufficient | |
| NarL-NarP, -IHF | nirB | NarL-NarP complex displaces IHF repression, permitting RNApol to initiate transcription. | (Wu et al. 1998; Browning et al. 2000) | The activator displaces the repressor activity | |
| Repressor | CRP-GalR | gal | The GalR repressor could bind alone to its operators' sites, generating repression. When the repressor HU binds, the repression of gal promoter increases. The proteins repress independently, but maximal repression is reached when both are present | (Aki and Adhya 1997) | One repressor is sufficient |
| FNR-ArcA(over two different promoters) | cyoAB, sdh | The proteins show independent repression, but maximal repression is reached when both are present. | (Cotter and Gunsalus 1992) | One specific repressor is sufficient | |
| ArcA-Betl | betT | The proteins repress independently, but maximal repression is reached when both are present | (Lamark et al. 1996) | One specific repressor is sufficient | |
| TyrR-TrpR | aroLM | TyrR represses in absence of TrpR, but TrpR is unable to repress alone | (Lawley and Pittard 1994) | One specific repressor is sufficient |