Table 3. Observed native architectures and predictions of where in parameter space their observation is expected.
| Organism | Phosphorelay | Ratios of abundance (order of magnitude) | Estimated proteins per cell h | Predicted operational regions |
|---|---|---|---|---|
| Escherichia coli | TorS:TorR (M3) | 1:1:1:10 | 100:1000 | k1, k2>10−1s−1a |
| EvgS:EvgA (M3) | 1:1:1:100 | 100:10000 | k1, k2>10−1s−1a | |
| BarA:UvrY (M3) | 1:1:1:10 | 1000:10000 | k1, k2>10−1s−1a | |
| ArcB:ArcA (M3) | 1:1:1:10 | 10000:1000000 | k1, k2>10−1s−1a | |
| RcsC:RcsD:RcsB (M2) | 1:1:1:100 | 1000:1000:100000 | k1>10−1s−1b | |
| Shigella flexneri | BarA:UvrY (M3) | 1:1:1:1 | 1000:1000 | M1 or M2′ |
| ArcB:ArcA (M3) | 1:1:1:10 | 10000: 100000 | k1>10−1s−1c | |
| Shewanella oneidensis | ||||
| SO0859:SO0860 (M3) | 1:1:1:1 | 100000:100000 | k1>10−1s−1d | |
| Desulfovibrio vulgaris | DVU_3062:DVU_3061 (M3) | 1:1:1:1 | 100000:100000 | k1>10−1s−1d |
| Saccharomyces cerevisiae | Sln1:Ypd1:Ssk1 (M2) | 1:1:1:1 | 1000:1000:1000 | e |
| Sln1:Ypd1:Skn7 (M2) | 1:1:1:1 | 1000:1000:1000 | e | |
| Schizosaccharomyces pombe | Mak1:Mpr1:Mcs4 (M2) | 1:1:1:10 | 1000:1000:10000 | f |
| Mak2:Mpr1:Mcs4 (M2) | 1:1:1:10 | 1000:1000:10000 | f | |
| Mak3:Mpr1:Mcs4 (M2) | 1:1:1:10 | 1000:1000:10000 | f | |
| Bacillus subtilis | KinA:Spo0F:Spo0B:Spo0A (M1) | 1:100:1:100 | 12:4200:110:1700 | k1, k2<10−1s−1.g |
| KinB:Spo0F:Spo0B:Spo0A (M1) | 1:100:1:100 | 93:4200:110:1700 | k1, k2<10−1s−1.g | |
| KinC:Spo0F:Spo0B:Spo0A (M1) | 1:100:1:100 | 82:4200:110:1700 | k1, k2<10−1s−1.g |
Notes.
As compared to architectures M1, M2, M2′. M4 does not allow for the observed abundance ratio between signal transduction domains.
As compared to M1, the only other architecture that allows for the observed ratio between abundances of signal transduction domains. Regulation by the environment expected at the SK phosphorylation step.
As compared to architectures M1, M2, M2′. M4 does not allow for the observed abundance ratio between signal transduction domains. Regulation by the environment expected at the SK phosphorylation step.
As compared to architectures M1, M2, M2′ and M4. Regulation by the environment expected at the SK phosphorylation step.
See analysis of the system as a Sln1-Ypd1-Skn7-Ssk1 PR in the main text.
Outside the range of protein abundances tested in this work. Nevertheless, comparing the trends of similar abundance ratios for one order of magnitude less suggests that M2 would be the preferred architecture if we pool the abundances of Mac1, Mac2 and Mac 3 proteins together.
Comparison between architectures M1 and M2′, which are the only ones that allow for this ratio of abundance between domains. Consistent with experimental determinations of the rate constants (supplementary materials).
These numbers are calculated by multiplying cell volume (µm3), average number of proteins in cells per µm3, and the protein abundance in parts per million: CellVolume × 6.23 × 108 × Proteinabundances × 10−6.