Part of the cell · Essential ion and nutrient transport
Pulling nutrients in from outside
On the cell picture: Transport systems
The medium is rich in phosphate, nitrogen, sulfur and metals, but none of it crosses the membrane by itself. Each element has one dedicated doorway.
Proteins in the model: 98
Part of the model's 1051 proteins. Each group below is a book group, counted in the working count after the repeats and non-first-cell groups were removed. The proteins are not yet matched gene by gene.
| Group | Proteins |
|---|---|
| Ion Channels and Transporters | 12 |
| P-Type ATPase | 7 |
| Metal ion transporters | 5 |
| Aquaporins | 1 |
| Symporter and antiporter | 6 |
| ABC transporters | 3 |
| Nutrient uptake | 2 |
| Sugar transporters | 5 |
| Carbon source transporters | 3 |
| Amino acid transporters | 5 |
| Co-factor transporters | 3 |
| Folate transporters | 3 |
| Phosphate transport | 5 |
| Magnesium transport | 4 |
| Additional amino acid transport | 3 |
| SAM transporters | 4 |
| Third amino acid transport | 3 |
| Fatty Acid transport | 2 |
| Additional phosphate transport | 2 |
| Nucleotide/serine/ethanolamine | 3 |
| Additional ABC transport | 2 |
| TrkA family potassium uptake | 3 |
| Drug efflux pumps | 5 |
| Sodium/proton pumps | 5 |
| Specialized transporters | 2 |
Its pathways
- ATP-coupled transportatlas pathway14
- Ion exchangeatlas pathway9
- Potassium balanceatlas pathway3
- Channels and ion uptakeatlas pathway2
- Substrate recognitionatlas pathway1
- Not yet placed in a pathwayto sort33
If it fails
An element sitting in abundance outside can no longer get in. The cell starves in the middle of plenty, with its biosynthetic pathways fully intact.
Cannot take the nutrient in · 1–2 generations
What it depends on
- Building and maintaining the membraneA membrane provides the physical environment in which transport channels and carriers operate.Book pp. 500–503
- Turning hydrogen into usable energyATP or ion gradients drive active transport, depending on transporter type.Book pp. 499, 502–503
- Reading genes into RNA, Building proteins and folding themTranslation supplies channels, pumps, and other transport proteins.Book pp. 501–503
What it supplies
- Mineral ions (not a separate group in the tree)Transporters bring required ions into the cell and export excess ions.Book pp. 499, 502–503
- Making the twenty amino acidsUptake supplies nitrogen, sulfur, or other environmental substrates needed by the selected biosynthetic routes.Book pp. 500, 502–503
- Switching genes on and offUptake and transport determine intracellular nutrient and ion availability, providing inputs to selected regulatory responses.Book pp. 502–503
- Holding the internal balanceIon transport and solute exchange maintain intracellular pH, osmolarity, and nutrient balance.Book pp. 502–504
Dependencies are curated from the book at the level of the map’s systems and are not measured protein contacts. See all systems together.
How it is built and controlled
Counts from UniProt annotations of this group’s proteins.
Its place in the control layer
None of this group’s proteins appear in the information, signaling, regulation, machine-signal or assembly lists.
From the control-layer pages. Which genes a regulator controls is mostly inferred from related bacteria, because Aquifex has no genetic system for testing it directly.
Origins
What needs to be explained
How did selective permeability and active transport develop while maintaining a useful compartment?
What needs explaining. Explain selective membrane passage, energy coupling and regulation under the resources available to the proposed early system.
Hurdles
- H-TR-1Getting nutrients inThe problem. A cell's membrane blocks ions, sugars, amino acids and nucleotides, so each nutrient needs a transporter.Why it is hard. Tight membranes are needed to hold gradients and keep contents, yet they stop nutrients; leaky membranes let nutrients in but lose contents.Molecular machinesStage 2: One step shown on its ownShown: Fatty-acid vesicles let some nucleotides in while keeping larger molecules inside.In the books: 152 open problems on transport systems ↗
- H-TR-2SelectivityThe problem. Transporters must tell apart very similar molecules and ions; the potassium channel lets K⁺ through about a thousand times more readily than Na⁺, although Na⁺ is smaller.Why it is hard. That discrimination depends on precise atomic positions inside the protein (Doyle et al. 1998).Molecular machinesStage 0: Not yet addressed by experimentShown: not yet addressed by experiment.In the books: 152 open problems on transport systems ↗
- H-TR-3Powered uptakeThe problem. Importing nutrients against their concentration needs energy: ATP-driven pumps of several subunits, or coupling to an ion gradient.Why it is hard. The pump and the energy supply must work together; transport also consumes part of the energy the cell produces.Molecular machinesStage 0: Not yet addressed by experimentShown: not yet addressed by experiment.In the books: 152 open problems on transport systems ↗
- H-TR-4Insertion and orientationThe problem. Transport proteins must be threaded into the membrane the right way round, by the Sec translocon and YidC.Why it is hard. The insertion machines are themselves membrane proteins that needed inserting.Molecular machinesStage 0: Not yet addressed by experimentShown: not yet addressed by experiment.In the books: 152 open problems on transport systems ↗
- H-TR-5System balanceThe problem. Influx, efflux and internal use must be balanced for every substance.Why it is hard. Imbalance leads to swelling, shrinking, or build-up of toxic levels; balance needs many transporters working together.The integrated cellStage 0: Not yet addressed by experimentShown: not yet addressed by experiment.In the books: 152 open problems on transport systems ↗
Scope. A transporter demonstrated in one organism is an example of a mechanism. Its inclusion in this catalogue does not make that exact protein universal or indispensable in every environment.
Experimental progress. A structure of the BtuCD–F vitamin B12 transporter bound to an ATP analogue reveals a nucleotide-associated state of an ABC uptake system.
What would strengthen a natural account. Steps shown to work together under plausible early-Earth conditions, without a chemist choosing the reagents, purifying the products or changing conditions between steps, would strengthen a natural account of origins in proportion to what they explain. Loss of a claimed dependency or discovery of functional alternatives would weaken the corresponding design argument. Gaps in the record do not supply a numerical likelihood for either explanation.
Observations. Binding sites and channels select transported molecules or ions. ATP or an ion gradient can power transport, depending on the transporter.
Hallmarks that apply.
- H27 Material selection: Binding sites and channels select transported molecules or ions.
- H21 Energy currency: ATP or an ion gradient can power transport, depending on the transporter.
- H36 Homeostatic regulation: Membrane exchange connects nutrient supply to internal balance.
The author’s conclusion. The coordinated features give the author a positive reason to consider design within the wider cellular architecture. For this local system alone, they do not establish that design is uniquely the best historical explanation. The conservative inference is that the system contributes to a cumulative design case, with its weight conditional on the comparative evidence and on how much plausible natural pathways explain.
From the book article Transport Systems, with its scientific references.
How it was discovered
- 1956Monod’s group shows that bacteria use a specific protein, a “permease”, to take up lactose.Rickenberg et al., Annales de l’Institut Pasteur 91:829–857 (1956)
- 1957Jens Skou discovers the sodium–potassium pump, the first known ion-pumping enzyme (Nobel Prize 1997).Skou, Biochimica et Biophysica Acta 23:394–401 (1957)
- 1986Higgins and colleagues recognise a large family of ATP-driven transporters, now called ABC transporters.Higgins et al., Nature 323:448–450 (1986)
- 1998The structure of the bacterial potassium channel KcsA shows how it lets potassium through but not sodium (Nobel Prize 2003).Doyle et al., Science 280:69–77 (1998)
- 2002The first structure of a complete ABC transporter, the vitamin B12 importer BtuCD, is solved.Locher, Lee & Rees, Science 296:1091–1098 (2002)
- 2003The structure of lactose permease shows how a sugar is carried in together with a proton.Abramson et al., Science 301:610–615 (2003)
Each hurdle above is sorted by kind and by how far experiments have got (see “How hurdles are sorted” at the top).
All parts of the cell side by side: origins hub. The book articles:
- Transport Systems: system page · full description · origins