<p>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 [<cite idref="PUB00000061"/>]. 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.</p> <p> 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 [<cite idref="PUB00004340"/>, <cite idref="PUB00002181"/>]. </p><p> Each sigma2 domain is composed of a bundle of three alpha-helices that is virtually identical in all structures analyzed to date [<cite idref="PUB00010647"/>]. The second helix of this bundle is a major point for contact with a coiled-coil domain in the beta' subunit of the core RNA polymerase complex. The third helix of the bundle includes conserved residues along one face that are involved in DNA melting and in recognition of the -10 promoter element. The sigma3 domain, which is less conserved between members of the sigma70 family is also a three-helix domain, the first helix of which contains the residues implicated in contacting DNA upstream of extended -10 promoters. The sigma4, domain has two pairs of alpha helices; the carboxy-terminal pair forms a helix-turn-helix motif that contacts the promoter DNA in the region from -30 to -38.</p>