Control layer
Signaling pathways
How the cell senses a change and turns it into a response.
What the minimal cell keeps
The kept set keeps very little dedicated signaling. These proteins sense starvation, nitrogen and iron.
| Aquifex protein | Evidence (UniProt) | Home pathway |
|---|---|---|
| Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase | Inferred from related proteins | Nutrient and metabolic state |
| RNA polymerase-binding transcription factor DksA | Inferred from related proteins | Not yet placed in a pathway |
| Nitrogen regulatory protein P-II | Seen as a protein | Not yet placed in a pathway |
| Transcriptional regulator (FurR family) | Inferred from related proteins | Transcription control |
| Ferric uptake regulation protein | Inferred from related proteins | Transcription control |
What the minimal cell leaves out
Most bacteria use two-component systems: a sensor kinase that detects a change and passes a phosphate to a response regulator. The Aquifex genome encodes 5 sensor kinases and 1 response regulator. None of them is among the kept proteins. Its 32 flagellar proteins are also left out, and it has no chemotaxis proteins.
Why so little
The scenario fixes a constant environment: hydrogen, oxygen, CO₂ and minerals at 95 °C. A cell that never has to switch between food sources or swim towards them needs few sensors. In a changing environment the list would be longer.
The origins question
How could sensing a change become linked to a useful response?
In a stable setting little sensing is needed, and simple feedback, such as a product slowing its own formation, can come from binding alone.
Even the minimal set links a measured state, such as starvation or iron level, to a matched change in gene activity. The design analysis asks whether such matched links can be built one step at a time, with a benefit at each step.
Hallmarks that apply.
Sources
- Cashel & Gallant, Nature 221:838–841 (1969)
- Nixon, Ronson & Ausubel, PNAS 83:7850–7854 (1986)
- Protein lists and evidence levels: UniProt proteome UP000000798