Sigma factors are essential in regulating gene expression in E. coli, allowing regulons (large groups of genes) to be controlled. Sigma factors are small proteins that bind to RNA polymerase, forming a holoenzyme that can then bind to the DNA template. They (sigma factors) can have their concentration in the cell regulated, allowing different regulons to be expressed.
Different sigma factors are able to control different groups of genes – this can increase the survival chances of the organism (in this case E. coli).
There are 7 sigma factors found in E. coli:
1 Sigma-70 is the dominant sigma factor found in E. coli, being found during the log growth phase. This is frequently seen in laboratory growth, where the log phase is dominant due to the high levels of nutrients and optimal temperatures provided. In natural environments, it is more likely there will be stresses on the cell, resulting in other sigma factors being used.
2 Sigma-38 is the general cell stress response sigma factor found in E. coli. This factor is typically more dominant when log-phase growth is not possible, where bacterial densities are reaching the maximum concentration for the environment.
3 Sigma-32 is the heat shock response and cytoplasmic stress sigma factor. This allows the upregulation of chaperone proteins and denatured protein degradation pathways. These proteins allow the maintenance of protein structure at higher temperatures, or degrading denatured proteins before they coagulate in the cytoplasm (which can induce apoptosis / cell death).
4 Sigma-28 controls flagellar and motility genes. The formation of a flagellar apparatus is through a sigma cascade, ensuring proteins are expressed in the correct order to assemble the protein complex correctly. An example is FliA, a protein that activates sigma-28, inducing the expression of the filament after the motor complex.
5 Sigma-54 is involved in the nitrogen starvation response. Proteins encouraging the uptake of extracellular nitrogen are upregulated, (hopefully) increasing the presence of nitrogen within the cell and thus improving the survival chances. There is no known anti-sigma factor for sigma-54.
6 Sigma-19 controls ferric citrate transport, being present when there is low iron.
7 Sigma-24 is involved in the extra-cytoplasmic stress response, and extreme heat shock.