- Protein family review
- Open Access
The σ70family of sigma factors
© BioMed Central Ltd 2003
- Published: 3 January 2003
Members of the σ70 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 σ70 family also function as contact points for some activator proteins, such as PhoB and λcl, and play a role in the initiation process itself. The primary σ factor, which is essential for general transcription in exponentially growing cells, is reversibly associated with RNA polymerase and can be replaced by alternative σ 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 σ70 family can broadly be divided into four main groups. Sequence alignments of the σ70 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 σ70 factors into four regions is largely supported by recent structural data indicating that primary σ 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 σ70 are spread out across one face of RNA polymerase. These structural data are starting to illuminate the mechanistic role of σ factors in transcription initiation.
- Flagellum Biosynthesis
- Specific Promoter Element
- Distinct Intermediate State
- Bacterium Streptomyces Coelicolor
The bacterial core RNA polymerase complex, which consists of five subunits (ββ'α2ω), 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 σ factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme. The vast majority of σ factors belong to the so-called σ70 family, reflecting their relationship to the principal σ factor of Escherichia coli, σ70. a second family of σ factors, the σ54 family, comprises proteins that are functionally similar to, but structurally distinct from, σ70 of E. coli. Here, we limit ourselves to the σ70 family.
Members of the σ70 family direct RNA polymerase to specific promoter elements that are usually 5-6 base-pairs (bp) in length and are centred 10 and 35 bp upstream (positions -10 and -35) of the transcription initiation site. They also function in the melting of promoter DNA and the early stages of elongation of transcripts. The discovery of the σ factor as a dissociable RNA polymerase subunit  heralded the subsequent finding that RNA polymerase recruits alternative σ factors as a means of switching on specific regulons . Multiple members of the σ70 family have since been discovered in most bacteria, with up to 63 encoded by a single genome, in the case of the antibiotic-producing bacterium Streptomyces coelicolor . Furthermore, σ70-related factors have been discovered in higher plants, in which they act together with a bacterial-type RNA polymerase to direct transcription in the plastid .
For historical reasons the nomenclature of the σ superfamily is complex. In E. coli and several other Gram-negative bacteria, σ factor genes are designated rpo (for RNA polymerase subunit), whereas in most Gram-positive bacteria the genes are designated sig. The proteins may be designated σ with a superscript reflecting the molecular weight or gene name, or may have an arbitrary single-letter designation. In the post-genomic era, the situation has naturally become further complicated with the realization that some organisms have more σ factors than there are letters in the alphabet.
The crystal structure of the σ2 domain has been solved for two primary σ factors (σ70 of E. coli and σA of Thermus aquaticus) [10,11], and one ECF σ factor (σR of S. coelicolor) . Discounting a non-conserved region that occurs between subregions 1.2 and 2.4 in some primary σ factors, each σ2 domain is composed of a bundle of three α helices that is virtually identical in all three structures analyzed. The second helix of this bundle is a major point for contact with a coiled-coil domain in the β' 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 (Figure 2b).
The σ3 domain, which is less conserved between members of the σ70 family, and is absent from ECF σ factors, is also a three-helix domain, the first helix of which contains the residues implicated in contacting DNA upstream of extended -10 promoters . The σ4, domain has two pairs of α helices; the carboxy-terminal pair forms a helix-turn-helix motif that contacts the promoter DNA in the region from -30 to -38 [10,14]. The spectacular crystallographic views obtained recently of the σ70 factor in the holoenzyme complex [14,15] revealed that the σ2, σ3 and σ4, domains extend across a wide area of the RNA polymerase, with an interface between the core complex and σ70 of more than 8000 Å2. Also revealed was a gap of approximately 45 Å between the σ3 and σ4 domains, taken up by a 33-residue linker (the 'σ3-σ4 linker') that, strikingly, travels close to the active site of RNA polymerase and through the channel from which the growing transcript exits the RNA polymerase complex before connecting with the σ4 domain.
Whereas the function of the essential group 1 σ70 factors is to direct general transcription, the accessory σ factors of groups 2-4 usually function to turn on specific gene sets in response to an appropriate signal. Their functions can be divided into three very broad categories: stress responses, development and ancillary metabolism. The wide variety of stress responses controlled by members of the σ70 family includes the stationary phase and general stress responses (mediated by, for example, σS in E. coli and σB in Bacillus subtilis), intracellular and extracytoplasmic protein misfolding (regulated in E. coli by σ32 and σE, respectively), oxidative stress (e.g. σR in S. coelicolor), osmotic stress (σM in B. subtilis) and cell-wall stress (controlled by, for example, σE in S. coelicolor and σW in B. subtilis). Developmental programs under the control of σ70 family members include flagella biosynthesis (involving σD in B. subtilis and σF in Salmonella typhimurium), endospore formation (mediated by, for example, σE, σK, σF and σG in B. subtilis), and exospore formation (σWhiG in S. coelicolor). Ancillary metabolic functions that are controlled by σ factors include iron uptake (σFecI in E. coli and σPvds in pseudomonads). There are clearly many more functions to be discovered, especially amongst members of the ECF subfamily; for example, in S. coelicolor the function of only three of its 49 ECF σ factors is understood.
The activity of σ factors, and the consequent activity of the promoters they recognize, can be controlled at many different levels: de novo synthesis (at the transcriptional or translational level), by post-translational processing, by proteolytic degradation, and by post-translational inhibition. Indeed, some σ factors, such as σS factor of E. coli, are regulated at most of these levels . Of widespread importance is post-translational inhibition by so-called anti-σ factors, proteins that reversibly bind to the σ factor thereby preventing its interaction with the core RNA polymerase [17,18]. In these cases, the signal that leads to the activation of the σ factor and the induction of the σ regulon somehow modify the σ-binding activity of the anti-σ factor.
Recent structural studies together with an extensive catalog of biochemical data are starting to shed light on the function of σ70 family members in transcription initiation. Once they become part of the holoenzyme, the promoter-recognition determinants of subregions 2.4 and 4.2 of the σ factor are solvent-exposed and appropriately separated. This conformation allows subregions 2.4 and 4.2 to interact with the -10 and -35 elements, respectively, to form a so-called 'closed' complex in which the promoter DNA remains base-paired. At promoters that lack -35 regions or have -35 elements that deviate significantly from the consensus sequence, the σ4, domain can stimulate formation of the closed complex by contacting activator proteins, such as λcI, which is bound upstream, or PhoB, which is bound downstream of the complex on the DNA .
In the following stage, the DNA in the region from position -11 to +4, which partially overlaps with the -10 element, melts in a process called isomerization, the mechanistic details of which are unresolved but probably include several kinetically distinct intermediate states. Once separated, the two DNA strands take different paths, with the template strand approaching the active site of the RNA polymerase and the non-template strand being held by conserved aromatic residues in region 2.3 of the σ factor that had previously been implicated in DNA melting . The σ factor may also play a role in the next stage, that of de novo RNA synthesis, by donating a disordered loop from the σ3-σ4 linker into the active site of the RNA polymerase; this might perhaps stabilize the initiating nucleotide . Alternatively, the disordered loop may stabilize the open complex by preventing reannealing close to the transcription start site . Finally, after a nascent RNA of 8-10 nucleotides has been synthesized, the σ factor is released or moves out of the way to allow elongation to proceed further and RNA polymerase to escape the promoter. The discovery that the σ3-σ4 linker is located in the RNA exit channel of the RNA polymerase suggests a mechanism of promoter clearance that involves the nascent RNA displacing the linker, in turn weakening the interaction between the core RNA polymerase and the σ4 domain and ultimately the rest of the σ factor [14,15]. Interestingly, σ70 of E. coli can in some instances interact with the exposed non-template strand early in the elongation process, and these interactions can lead to transient pausing of the elongation complex . Furthermore, recent evidence suggests that σ70 may remain associated with the core RNA polymerase complex during the elongation process [23,24].
The recent structural information on primary σ factors has had a major impact on our understanding of the mechanistic role of the σ70 family of σ factors in transcription initiation. Numerous puzzles remain, however. It is not clear how transcription-activator proteins can modulate the complex conformational changes that accompany promoter recognition and melting. The timing and extent of release of the σ factor during the transition to the transcript-elongation phase is a topic of continuing controversy. Finally, the extent to which σ factors might be retained in early, or perhaps later, elongation complexes and might mediate a sequence-responsive pause in transcription is not resolved. Although a reasonably detailed picture of the action of σ70 can now be envisaged, the sequence divergence noted within the σ70 family raises questions about how other family members mediate promoter recognition and melting and how they interact with their regulators. Finally, the many bacterial genome sequencing projects have revealed a huge gap in our understanding of the biological function of the many newly discovered σ factors. Even in some of the best characterized model systems, such as B. subtilis, there is a frustrating lack of knowledge regarding the regulation, roles, and possible redundancies among the various σ factors.
Work on σ factors in the laboratory of JDH is supported by the National Institutes of Health and by the BBSRC and the Wellcome Trust in the laboratory of MSBP.
- Burgess RR, Travers AA, Dunn JJ, Bautz EK: Factor stimulating transcription by RNA polymerase. Nature. 1969, 221: 43-46. A seminal paper describing the discovery of the σ subunit of RNA polymerase.View ArticleGoogle Scholar
- Losick R, Pero J: Cascades of sigma factors. Cell. 1981, 25: 582-584. A classical minireview summarizing early studies on the role of σ factor cascades in the development of phage SPO1 and endospore formation in B. subtilis.View ArticleGoogle Scholar
- Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, et al: Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature. 2002, 417: 141-147. 10.1038/417141a. Complete sequence of the S. coelicolor genome, a genome that encodes 63 σ factors.View ArticleGoogle Scholar
- Isono K, Shimizu M, Yoshimoto K, Niwa Y, Satoh K, Yokota A, Kobayashi H: Leaf-specifically expressed genes for polypeptides destined for chloroplasts with domains of σ70 factors of bacterial RNA polymerases in Arabidopsis thaliana. Proc Natl Acad Sci USA. 1997, 94: 14948-14953. 10.1073/pnas.94.26.14948. The first description of genes that encode σ70-like sigma factors in multicellular eukaryotes.View ArticleGoogle Scholar
- Lonetto M, Gribskov M, Gross CA: The σ70 family: sequence conservation and evolutionary relationships. J Bacteriol. 1992, 174: 3843-3849. A classical review of the structure, function and evolutionary relationships between bacterial σ factors.Google Scholar
- Helmann JD: The extracytoplasmic function (ECF) sigma factors. Adv Microb Physiol. 2002, 46: 47-110. A comprehensive review of the ECF subfamily of σ factors.View ArticleGoogle Scholar
- Lonetto MA, Brown KL, Rudd KE, Buttner MJ: Analysis of the Streptomyces coelicolor sigE gene reveals the existence of a subfamily of eubacterial RNA polymerase sigma factors involved in the regulation of extracytoplasmic functions. Proc Natl Acad Sci USA. 1994, 91: 7573-7577. The discovery of the ECF subfamily of σ factors.View ArticleGoogle Scholar
- Wösten MM: Eubacterial sigma-factors. FEMS Microbiol Rev. 1998, 22: 127-150. 10.1016/S0168-6445(98)00011-4. A comprehensive review of bacterial factors.View ArticleGoogle Scholar
- Barne KA, Bown JA, Busby SJ, Minchin SD: Region 2.5 of the Escherichia coli RNA polymerase σ70 subunit is responsible for the recognition of the 'extended-10' motif at promoters. EMBO J. 1997, 16: 4034-4040. 10.1093/emboj/16.13.4034. The isolation of a new rpoD mutant defines a region of σ70involved in contacting promoters with 'extended-10' elementsView ArticleGoogle Scholar
- Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O, Trester-Zedlitz ML, Darst SA: Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Mol Cell. 2002, 9: 527-539. Crystal structures of the stable σ2, σ3 and σ4 domains of Thermus aquaticus and of the σ4 domain complexed with promoter DNA.View ArticleGoogle Scholar
- Malhotra A, Severinova E, Darst SA: Crystal structure of a σ70 subunit fragment from E. coli RNA polymerase. Cell. 1996, 87: 127-136. Crystal structure of conserved subregions 1.2-2.4 of E. coli σ70.View ArticleGoogle Scholar
- Wei L, Stevenson CEM, Burton N, Jakimowicz P, Paget MSB, Buttner MJ, Lawson DM, Kleanthous C: Identification and structure of the anti-sigma factor-binding domain of the disulphide-stress regulated sigma factor factor σR from Streptomyces coelicolor. J Mol Biol. 2002, 323: 225-236. 10.1016/S0022-2836(02)00948-8. Crystal structure of conserved region 2 of an ECF σ factor.View ArticleGoogle Scholar
- Young BA, Anthony LC, Gruber TM, Arthur TM, Heyduk E, Lu CZ, Sharp MM, Heyduk T, Burgess RR, Gross CA: A coiled-coil from the RNA polymerase β' subunit allosterically induces selective nontemplate strand binding by σ70. Cell. 2001, 105: 935-944. 10.1016/S0092-8674(01)00398-1. A 48-residue coiled-coil domain from the β' subunit of RNA polymerase is sufficient to stimulate recognition of the -10 region non-template strand by σ70.View ArticleGoogle Scholar
- Vassylyev DG, Sekine S, Laptenko O, Lee J, Vassylyeva MN, Borukhov S, Yokoyama S: Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature. 2002, 417: 712-719. 10.1038/nature752. Crystal structure of the RNA polymerase holoenzyme of Thermus thermophilus.View ArticleGoogle Scholar
- Murakami KS, Masuda S, Darst SA: Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution. Science. 2002, 296: 1280-1284. 10.1126/science.1069594. Crystal structure of the RNA polymerase holoenzyme of Thermus aquaticus.View ArticleGoogle Scholar
- Hengge-Aronis R: Signal transduction and regulatory mechanisms involved in control of the σS (RpoS) subunit of RNA polymerase. Microbiol Mol Biol Rev. 2002, 66: 373-395. 10.1128/MMBR.66.3.373-395.2002. A review of the E. coli stationary phase sigma factor σS.View ArticleGoogle Scholar
- Hughes KT, Mathee K: The anti-sigma factors. Annu Rev Microbiol. 1998, 52: 231-286. 10.1146/annurev.micro.52.1.231. This article and  are comprehensive reviews of anti-σ factors.View ArticleGoogle Scholar
- Helmann JD: Anti-sigma factors. Curr Opin Microbiol. 1999, 2: 135-141. 10.1016/S1369-5274(99)80024-1. See .View ArticleGoogle Scholar
- Gross CA, Chan C, Dombroski A, Gruber T, Sharp M, Tupy J, Young B: The functional and regulatory roles of sigma factors in transcription. Cold Spring Harb Symp Quant Biol. 1998, 63: 141-155. A detailed review of the role of the σ factor in transcription initiation.View ArticleGoogle Scholar
- Juang YL, Helmann JD: A promoter melting region in the primary sigma factor of Bacillus subtilis. Identification of functionally important aromatic amino acids. J Mol Biol. 1994, 235: 1470-1488. 10.1006/jmbi.1994.1102. The characterization of mutants in subregion 2.3 of Bacillus subtilis σA that are specifically impaired in open-complex formation.View ArticleGoogle Scholar
- Young BA, Gruber TM, Gross CA: Views of transcription initiation. Cell. 2002, 109: 417-420. A review that places the recent RNA polymerase structural studies into the wider context.View ArticleGoogle Scholar
- Ring BZ, Yarnell WS, Roberts JW: Function of E. coli RNA polymerase sigma factor σ70 in promoter-proximal pausing. Cell. 1996, 86: 485-493. This article provides evidence that σ70 remains bound to core RNA polymerase when contacts between the σ factor and the -10 promoter element are broken, and then moves to a pause-inducing sequence further downstream.View ArticleGoogle Scholar
- Bar-Nahum G, Nudler E: Isolation and characterization of σ70 retaining transcription elongation complexes from Escherichia coli. Cell. 2001, 106: 443-451. Identification of σ70-retaining elongation complexes, which are especially prevalent during stationary phase and have a higher ability to support multiple rounds of initiation compared to elongation complexes lacking σ70.View ArticleGoogle Scholar
- Mukhopadhyay J, Kapanidis AN, Mekler V, Kortkhonjia E, Ebright YW, Ebright RH: Translocation of σ70 with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA. Cell. 2001, 106: 453-463. In the majority of transcription complexes, σ70 is not released from RNA polymerase upon transition from initiation to elongation.View ArticleGoogle Scholar
- Murakami KS, Masuda S, Campbell EA, Muzzin O, Darst SA: Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science. 2002, 296: 1285-1290. 10.1126/science.1069595. The first structural study of RNA polymerase holoenzyme complexed with promoter DNA.View ArticleGoogle Scholar