Control layer
Gene regulatory network
Which genes are switched on, when, and by what.
The switches that are kept
The kept set keeps one general sigma factor and a few regulators. The atlas groups the PII and Fur proteins as “Switching genes on and off”.
| Aquifex protein | Evidence (UniProt) | Home pathway |
|---|---|---|
| RNA polymerase sigma factor SigA | Inferred from related proteins | Transcription |
| 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 |
| RNA polymerase-binding transcription factor DksA | Inferred from related proteins | Not yet placed in a pathway |
| Transcription termination/antitermination protein NusG | Seen as a protein | Transcription |
| Transcription termination/antitermination protein NusA | Inferred from related proteins | Transcription |
Sigma factors
The Aquifex genome encodes 6 sigma factors and related proteins, including RpoN and FliA, which in other bacteria switch on nitrogen and flagellar genes. Only RpoD, the housekeeping sigma factor, is among the kept proteins.
RNA switches
Many bacteria also regulate genes with riboswitches: stretches of messenger RNA that bind a small molecule and change shape. These are RNA, not protein, and the atlas does not yet map them for Aquifex.
Source: Winkler, Nahvi & Breaker, Nature 419:952–956 (2002)
How sure the links are
No Aquifex gene has been knocked out, so which genes each regulator controls is inferred from related bacteria, not shown in Aquifex itself.
The origins question
How did genes come to be switched on only when they are needed?
Regulators often appear to have developed from enzymes or binding domains that already recognised a molecule. RNA switches that bind metabolites suggest that regulation could have begun in RNA.
The scenario keeps one general sigma factor out of six in the genome, plus PII and Fur regulators. A constant setting needs little regulation. The design analysis asks where regulation is essential at all, and whether those essential links show demand-responsive production that has to be in place from the start.
Hallmarks that apply.
Sources
- Jacob & Monod, Journal of Molecular Biology 3:318–356 (1961)
- Burgess et al., Nature 221:43–46 (1969)
- Protein lists and evidence levels: UniProt proteome UP000000798