PROSITE documentation PDOC00592

Sigma-70 factors family signatures

Sigma factors [1] are bacterial transcription initiation factors that promote the attachment of the core RNA polymerase to specific initiation sites and are then released. They alter the specificity of promoter recognition. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.

With regard to sequence similarity, sigma factors can be grouped into two classes: the sigma-54 and sigma-70 families. The sigma-70 family includes, in addition to the primary sigma factor, a wide variety of sigma factors, some of which are listed below:

• Bacillus sigma factors involved in the control of sporulation-specific genes: sigma-E (sigE or spoIIGB), sigma-F (sigF or spoIIAC), sigma-G (sigG or spoIIIG), sigma-H (sigH or spo0C) and sigma-K (sigK or spoIVCB/spoIIIC).
• Escherichia coli and related bacteria sigma-32 (gene rpoH or htpR) involved in the expression of heat shock genes.
• Escherichia coli and related bacteria sigma-27 (gene fliA) involved in the expression of the flagellin gene.
• Escherichia coli sigma-S (gene rpoS or katF) which seems to be involved in the expression of genes required for protection against external stresses.
• Myxococcus xanthus sigma-B (sigB) which is essential for the late-stage differentiation of that bacteria.

Alignments of the sigma-70 family permit the identification of four regions of high conservation [2,3]. Each of these four regions can in turn be subdivided into a number of sub-regions. We developed signature patterns based on the two best conserved sub-regions. The first pattern corresponds to sub-region 2.2; the exact function of this sub-region is not known although it could be involved in the binding of the sigma factor to the core RNA polymerase. The second pattern corresponds to sub-region 4.2 which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors. The second pattern starts one residue before the N-terminal extremity of the HTH region and ends six residues after its C-terminal extremity.