InterPro domain: IPR013324

The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme [ 1 ]. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. 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. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [ 2 , 3 ].

The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. All plastid sigma factors belong to the superfamily of sigmaA/sigma70 and have sequences homologous to the conserved regions 1.2, 2, 3, and 4 of bacterial sigma factors [ 4 ].

This entry represents regions 3 and 4 (or sigma3 and sigma4 domains) found in several sigma factors, often in conjunction with the sigma2 domain ( IPR013325 ). Both regions 3 and 4 are present in Sigma70 [ 5 ], Sigma28 (FliA), and SigA [ 6 ], while region4 is also found in SigmaF [ 7 ] and RpoE. Regions 3 and 4 have a nucleotide-binding 3-helical core structure, consisting of a closed or partly open bundle with a right-handed twist. Some other nucleotide-binding proteins are thought to contain domains with a similar topology.

1. Structure and function of bacterial sigma factors. Annu. Rev. Biochem. 57, 839-72
2. Sigma factors from E. coli, B. subtilis, phage SP01, and phage T4 are homologous proteins. Nucleic Acids Res. 14, 6745-63
3. The sigma 70 family: sequence conservation and evolutionary relationships. J. Bacteriol. 174, 3843-9
4. Plastid sigma factors: Their individual functions and regulation in transcription. Biochim. Biophys. Acta 1847, 770-8
5. Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. Cell 87, 127-36
6. Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Mol. Cell 9, 527-39
7. Crystal structure of the Bacillus stearothermophilus anti-sigma factor SpoIIAB with the sporulation sigma factor sigmaF. Cell 108, 795-807