Part of the cell · Other / function not assignable
Conserved, but we cannot say what they do
Not labelled on the cell picture.
These proteins are kept because closely related organisms, including ones that have thrown away everything they could, still keep them. Their function is not known.
Proteins in the model: 0
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 |
|---|---|
| No book group is assigned to this section in the working count. | |
Its pathways
- tRNA chargingatlas pathway3
- Nutrient and metabolic stateatlas pathway2
- Biosynthesis of various nucleotide sugarsKEGG map7
- Purine metabolismKEGG map6
- Bacterial secretion systemKEGG map5
- Glyoxylate and dicarboxylate metabolismKEGG map4
- Starch and sucrose metabolismKEGG map3
- Homologous recombinationKEGG map3
- Fructose and mannose metabolismKEGG map2
- Streptomycin biosynthesisKEGG map2
- Other carbon fixation pathwaysKEGG map2
- Nicotinate and nicotinamide metabolismKEGG map2
- Not yet placed in a pathwayto sort68
If it fails
Their removal is predicted to be fatal, but we cannot say which step breaks. These are the honest weak points of the model.
Predicted fatal, mechanism unknown · cannot be stated
What it depends on
None listed in the curated set.
What it supplies
None listed in the curated set.
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
Signaling pathways
- What the minimal cell keeps:
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 can the origin of a protein be assessed when its role in the cell is not yet known?
What needs explaining. Account for 109 proteins that related organisms keep, including bacteria that have discarded every gene they could, but whose role in the Aquifex scenario cannot yet be named. 35 have no characterised activity at all. Others have a known chemical activity (38 carry an enzyme number) but no known place in a required system.
Hurdles
- H-UNK-1Function firstThe problem. Many proteins kept by every free-living relative have no known function.Why it is hard. The origin of a role cannot be assessed until the role is known.The integrated cellStage 0: Not yet addressed by experimentShown: not yet addressed by experiment.In the atlas: 207 proteins of the 1,051 whose function is not known ↗
- H-UNK-2Real requirementThe problem. It must be shown which of them are truly needed.Why it is hard. Being kept by related organisms suggests a protein is needed, but does not prove it; no knockout data exist for these organisms.The integrated cellStage 0: Not yet addressed by experimentShown: not yet addressed by experiment.In the atlas: 207 proteins of the 1,051 whose function is not known ↗
- H-UNK-3Place in the cellThe problem. Each protein must be assigned to a pathway or system, with the partners it works with.Why it is hard. Without that, the dependency map of the cell is incomplete.The integrated cellStage 0: Not yet addressed by experimentShown: not yet addressed by experiment.In the atlas: 207 proteins of the 1,051 whose function is not known ↗
- H-UNK-4Hidden dependenciesThe problem. Unknown roles may hide further dependencies between systems.Why it is hard. Each new dependency adds to what must be present together in the first cell.The integrated cellStage 0: Not yet addressed by experimentShown: not yet addressed by experiment.In the atlas: 207 proteins of the 1,051 whose function is not known ↗
- H-UNK-5Protein familyThe problem. Each protein should be placed in a protein family, to see whether related proteins have known functions.Why it is hard. Many have no recognisable relatives outside closely related organisms, so their function cannot be inferred from family.Information and controlStage 0: Not yet addressed by experimentShown: not yet addressed by experiment.In the atlas: 207 proteins of the 1,051 whose function is not known ↗
Many conserved proteins of unknown function turn out, once studied, to belong to known protein families or to do housekeeping work such as modifying tRNAs or repairing damaged metabolites.
A naturalistic account treats them like any other protein: as members of families with a shared history, whose roles can be found by experiment and whose origins can then be assessed in the same way as the rest of the cell.
Until their roles are known, the atlas makes no claim about their origin either way.
The design analysis does not use these proteins as evidence. A hallmark can only be assessed once a protein's function, its partners and the effect of losing it are known, which is the test attached to each hallmark.
What they do show is that the inventory of what a free-living cell needs is larger than what can currently be explained in detail. Even the laboratory minimal cell JCVI-syn3.0 kept 149 genes of unknown function.
Each role discovered here will either add a coordinated function to the cumulative case or remove a claimed requirement. Both outcomes are informative.
How it was discovered
- 1998The complete genome of Aquifex aeolicus is published, including many predicted proteins with no known function.Deckert et al., Nature 392:353–358 (1998)
- 2004Galperin and Koonin argue that conserved proteins of unknown function should be priority targets for experiments.Galperin & Koonin, Nucleic Acids Research 32:5452–5463 (2004)
- 2016The synthetic minimal cell JCVI-syn3.0 keeps 473 genes, of which 149 have no known biological function.Hutchison et al., Science 351:aad6253 (2016)
All parts of the cell side by side: origins hub. The book articles:
- No book article maps to this group.