Pathway · 2 proteins
Transcription control
Sigma factors and DNA-binding regulators affect gene expression.
How it works
- Sigma-factor annotations identify components that help RNA polymerase recognize classes of promoters. The module also includes several DNA-binding regulator families and sigma-54-associated regulators.
- Changes in regulator binding or sigma-factor usage can alter transcription initiation. Sigma-54-dependent activation and regulation by factors such as DksA use different mechanisms; the module does not imply that all these factors assemble together.
- The output is a change in which transcripts are produced and at what rate. Specific targets, binding sites and activating conditions cannot be assigned from family annotations alone.
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 |
|---|---|---|---|---|---|
| Transcriptional regulator (FurR family) | — | — | Zn(2+) | 144 | Unspecified |
| Ferric uptake regulation protein | — | — | Fe cation, Zn(2+), Mn(2+) | 152 | 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 |
|---|---|---|---|---|---|
| RNA polymerase sigma factor SigAHome: Transcription | — | — | — | 575 | Step named |
Origins
How could genes be switched on and off before regulator proteins existed?
Lehninger suggests that riboswitch aptamers may derive from RNAs that once bound cofactors needed for metabolism in an RNA world.
A regulator must sense a condition and act on the right genes. The two regulators in this pathway are iron-sensing Fur proteins, which bind DNA only when iron is plentiful and switch off uptake genes. Sensor, switch and target have to match.
From the books: Nelson & Cox, Lehninger Principles of Biochemistry, p. 1134.
The wider question for this part of the cell: origins for switching genes on and off.
Sources
- Atlas pathway grouping from the VF5 reference-genome system map (Deckert et al. 1998; Braakman & Smith 2014)
Other pathways in this group: Not yet placed in a pathway