Pathway · 2 proteins
Nutrient and metabolic state
Regulatory and signaling proteins provide candidate state-dependent controls.
How it works
- The annotations include PII-like signaling proteins, a PII uridylyltransferase family, RelA/SpoT-related proteins and cyclic-nucleotide signaling enzymes. These represent different candidate ways to connect metabolic state to regulation.
- Diguanylate cyclase and phosphodiesterase activities can respectively make and break down cyclic di-GMP; CdaA-family enzymes make cyclic di-AMP. PII modification and stringent-response chemistry are separate signaling routes.
- The balance of synthesis, degradation and receptor interactions determines the response. Putative or bifunctional annotations do not establish which activity operates in a particular VF5 growth condition.
Grouped by the atlas’s curated pathway map. The table order is not a proven reaction order.
Its proteins
| Protein | EC | Reaction (UniProt) | Metal or cluster | Amino acids | Certainty |
|---|---|---|---|---|---|
| Diadenylate cyclase | 2.7.7.85 | 2 ATP = 3',3'-c-di-AMP + 2 diphosphate | — | 256 | Unspecified |
| Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase | 3.1.7.2 | guanosine 3',5'-bis(diphosphate) + H2O = GDP + diphosphate + H(+) | Mn(2+) | 696 | Unspecified |
Also part of this pathway
These proteins are described under another pathway, but also take part here.
| Protein | EC | Reaction (UniProt) | Metal or cluster | Amino acids | Certainty |
|---|---|---|---|---|---|
| UPF0166 protein aq_450Home: Not yet placed in a pathway | — | — | — | 105 | Step named |
Origins
How could a cell sense its own state and respond before signal molecules existed?
How it was discovered
- 1950sEarl Sutherland finds that many hormones act by producing cyclic AMP inside the cell, the first known second messenger (Nobel Prize 1971).Brooker, Biology, p. 194
None of the books searched discusses the origin of signalling molecules.
Second messengers amplify a signal and spread it fast. The two proteins in this pathway make and remove the alarm signals cyclic di-AMP and ppGpp, which slow growth when nutrients run short. A signal is useful only if something reads it and acts on it.
From the books: Brooker, Biology, p. 194.
The wider question for this part of the cell: origins for conserved, but we cannot say what they do.
Sources
- Atlas pathway grouping from the VF5 reference-genome system map (Deckert et al. 1998; Braakman & Smith 2014)
Other pathways in this group: tRNA charging · Biosynthesis of various nucleotide sugars · Purine metabolism · Bacterial secretion system · Glyoxylate and dicarboxylate metabolism · Starch and sucrose metabolism · Homologous recombination · Fructose and mannose metabolism · Streptomycin biosynthesis · Other carbon fixation pathways · Nicotinate and nicotinamide metabolism · Not yet placed in a pathway