Bacterial σ factors are essential components of the RNA polymerase and determine the promoter specificity (Helmann and Chamberlin, 1988a). All bacteria possess one primary (or housekeeping) σ factor that is responsible for the basal expression level of most genes. Most bacterial genomes also encode alternative σ factors, which can redirect RNA polymerases to initiate transcription from alternative promoters after substituting the primary σ factor (Helmann and Chamberlin, 1988a).

Extracytoplasmic function (ECF) σ factors constitute the largest and most diverse subfamily of alternative σ factors (Butcher et al., 2008; Helmann, 2002). These small proteins contain only two domains, named regions σ2 and σ4, which are required for both RNA polymerase interaction and recognition of the bipartite sequence motif that forms an alternative promoter.

Major features of ECF signal transduction:

1. ECF σ factors facilitate a cytoplasmic transcriptional response to environmental signals.
2. ECF σ factors usually autoregulate their own expression.
3. ECF genes are usually co-expressed with gene(s) that encode cognate anti-σ factor(s).
4. In the absence of a stimulus, the anti-σ factor tightly binds the σ factor, thereby keeping it inactive.
5. Upon receiving a proper signal, the anti-σ factor is inactivated (either by degradation through a cascade of regulated proteolytic steps, or confromational changes). Both mechanisms result in the release and consequent activation of the ECF σ factor, which can then redirect gene expression to its target promoters after recruitment by the RNA polymerase core enzyme.

Review and classification of ECF σ factors

• The third pillar of bacterial signal transduction: phylogenomic classification of the extracytoplasmic function (ECF) σ factor protein family.
  Staroń, A., Sofia, H.J., Dietrich, S., Ulrich, L.E., Liesegang, H., Mascher, T.
  Mol. Microbiol., 2009 (epub).

Related ECF literature

• The role of anti-sigma factors in gene regulation.
  Brown, K.L. and Hughes, K.T.
  Mol Microbiol., 1995, 16:397-404.
• Environmental sensing and the role of extracytoplasmic function (ECF) sigma factors
  Butcher, B.G., Mascher, T., and Helmann, J.D.
  Bacterial Physiology - a Molecular Approach El-Sharoud, W.M. (ed). 2008; Berlin, Heidelberg: Springer-Verlag GmbH, 233-261.
• The functional and regulatory roles of sigma factors in transcription.
  Gross, C.A., Chan, C., Dombroski, A., Gruber, T., Sharp, M., Tupy, J., and Young, B.
  Cold Spring Harb. Symp. Quant. Biol., 1998, 63:141-155.
• Multiple sigma subunits and the partitioning of bacterial transcription space.
  Gruber, T.M., and Gross, C.A.
  Annu. Rev. Microbiol., 2003, 57:441-466.
• Structure and function of bacterial sigma factors.
  Helmann, J.D., and Chamberlin, M.J.
  Annu. Rev. Biochem., 1988a, 57:839-872.
• Anti-sigma factors.
  Helmann, J.D.
  Curr. Opin. Microbiol., 1999, 2:135-141.
• The extracytoplasmic function (ECF) sigma factors.
  Helmann, J.D.
  Adv. Microb. Physiol., 2002, 46:47-110.