The sigma70 family of sigma factors

Abstract

Members of the sigma70 family of sigma factors are components of the RNA polymerase holoenzyme that direct bacterial or plastid core RNA polymerase to specific promoter elements that are situated 10 and 35 base-pairs upstream of transcription-initiation points. Members of the sigma70 family also function as contact points for some activator proteins, such as PhoB and lambda(cl), and play a role in the initiation process itself. The primary sigma factor, which is essential for general transcription in exponentially growing cells, is reversibly associated with RNA polymerase and can be replaced by alternative sigma factors that co-ordinately express genes involved in diverse functions, such as stress responses, morphological development and iron uptake. On the basis of gene structure and function, members of the sigma70 family can broadly be divided into four main groups. Sequence alignments of the sigma70 family members reveal that they have four conserved regions, although the highest conservation is found in regions 2 and 4, which are involved in binding to RNA polymerase, recognizing promoters and separating DNA strands (so-called 'DNA melting'). The division of the linear sequence of sigma70 factors into four regions is largely supported by recent structural data indicating that primary sigma factors have three stable domains that incorporate regions 2, 3 and 4. Furthermore, structures of the RNA polymerase holoenzyme have revealed that these domains of sigma70 are spread out across one face of RNA polymerase. These structural data are starting to illuminate the mechanistic role of sigma factors in transcription initiation.

Figure 1

Phylogenetic relationships between members of the σ⁷⁰ family of sigma factors from four diverse bacteria: E. coli (E); Caulobacter cresentus (CC or C); B. subtilis (B); and Mycobacterium tuberculosis (M). For C. cresentus, gene numbers from the annotated genome sequence are given. Note that the primary and related factors comprise groups 1 and 2, the group 3 σ factors are divided into functionally related groups (sporulation, flagellar biosynthesis, general stress and heat shock), and the divergent ECF factors comprise group 4. Particularly striking is the distance between the ECF subfamily and other members of the σ⁷⁰ family, as well as divergence within the ECF subfamily itself. The unrooted tree was constructed using the Phylip programs PROTDIST and NEIGHBOUR from a multiple amino-acid sequence alignment made by the program ClustalW. Only conserved regions 2 and 4 were included in the alignments.

Figure 2

Structural characteristics of E. coli σ⁷⁰. (a) The protein sequence has been divided into four regions on the basis of sequence conservation with other members of the σ⁷⁰ family. Residues in the carboxy-terminal part of region 4 (subregion 4.2) form a helix-turn-helix motif that contacts the -35 element of the promoter. Residues from conserved regions 2 and 3 cooperate to mediate recognition of the -10 region and melting of the DNA. A residue in the amino-terminal part of region 3 (3.0) contacts the conserved TG motif in the extended -10 element of certain promoters that do not require a -35 region. Residues from an α helix in region 2 that corresponds to the conserved subregions 2.3 and 2.4 interact intimately with the -10 element. Subregion 2.3 is thought to interact primarily with single-stranded DNA in the open complex (dashed arrow). The three domains of the σ factor observed by X-ray crystallography (σ₂, σ₃ and σ₄) are indicated underneath the linear structure. Note that the protein domains correspond closely (although not precisely) with the regions assigned by sequence comparisons. (b) A model for the interaction of RNA polymerase holoenzyme (containing, β,β ', two α, and ω one subunit in addition to the σ factor) with promoter DNA. The model is based on crystallographic analyses of σ domains, holoenzyme, and holoenzyme-model DNA complexes [10,14,15,25]. The major functional domains of the σ factor are shown in dark grey. The bold arrow indicates the direction of transcription. Although the template strand in the transcription bubble passes underneath the β unit and the σ₂ domain, the path of the DNA is shown throughout its length. Adapted from [21].