Sigma is a specificity factor. It directs RNA polymerase to the promoter and ensures that transcription is initiated only where it is supposed to be initiated.
The very fact that RNA polymerase depends upon a specificity factor to direct the RNA polymerase to the correct promoter immediately offers a mechanism for controlling transcription. Different sigma factors direct the RNA polymerase to different promoters, and their regulate the expression of different genes (Table 4.2).
The E. coli sigma factor is σ70—so called because the protein is 70 kD in size, which is sometimes abbreviated as Eσ70, referring to the corresponding holoenzyme containing this sigma factor.
E. coli also has six alternative sigma factors that are used in special circumstances:
Table 4.2 σ factors and their function
| Sigma factor | Gene | Function |
|---|---|---|
| σ70 | rpoD | Principal sigma factor. |
| σ54 | rpoN (ntrA, glnF) | Nitrogen-regulated gene transcription. |
| σ32 | rpoH | Heat-shock gene transcription. |
| σS | rpoS | Gene expression in stationary phase cells. |
| σF | rpoF | Expression of flagellar operons. |
| σE | rpoE | Involved in heat-shock and oxidative stress responses; regulates the expression of extracytoplasmic proteins. |
| σFecl | fecl | Regulates the fec genes for iron dicitrate transport. |
σ32 is required for the expression of heat-shock genes, i.e., the genes that are only expressed when the cell is exposed to a high temperature and it must make special proteins in order to survive. Some parts of the sequence of theσ32 can be recognized in other bacterial sigma factors.
σ54 is present all the time and it is required for the expression of many genes that are involved for the nitrogen metabolism. The σ54 has a very different sequence and structure than the other sigma factors in E. coli and most bacteria; thus, there are at least two different families of sigma factor proteins in bacteria.