Sigma factor explained

A sigma factor (σ factor or specificity factor) is a protein needed for initiation of transcription in bacteria.^{[1] [2]} It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoters. It is homologous to archaeal transcription factor B and to eukaryotic factor TFIIB.^[3] The specific sigma factor used to initiate transcription of a given gene will vary, depending on the gene and on the environmental signals needed to initiate transcription of that gene. Selection of promoters by RNA polymerase is dependent on the sigma factor that associates with it.^[4] They are also found in plant chloroplasts as a part of the bacteria-like plastid-encoded polymerase (PEP).^[5]

The sigma factor, together with RNA polymerase, is known as the RNA polymerase holoenzyme. Every molecule of RNA polymerase holoenzyme contains exactly one sigma factor subunit, which in the model bacterium Escherichia coli is one of those listed below. The number of sigma factors varies between bacterial species.^{[1] [6]} E. coli has seven sigma factors. Sigma factors are distinguished by their characteristic molecular weights. For example, σ⁷⁰ is the sigma factor with a molecular weight of 70 kDa.

The sigma factor in the RNA polymerase holoenzyme complex is required for the initiation of transcription, although once that stage is finished, it is dissociated from the complex and the RNAP continues elongation on its own.

Specialized sigma factors

Different sigma factors are utilized under different environmental conditions. These specialized sigma factors bind the promoters of genes appropriate to the environmental conditions, increasing the transcription of those genes.

Sigma factors in E. coli:

• σ⁷⁰(RpoD) – σ^A – the "housekeeping" sigma factor or also called as primary sigma factor (Group 1), transcribes most genes in growing cells. Every cell has a "housekeeping" sigma factor that keeps essential genes and pathways operating.^[1] In the case of E. coli and other gram-negative rod-shaped bacteria, the "housekeeping" sigma factor is σ⁷⁰.^[1] Genes recognized by σ⁷⁰ all contain similar promoter consensus sequences consisting of two parts.^[1] Relative to the DNA base corresponding to the start of the RNA transcript, the consensus promoter sequences are characteristically centered at 10 and 35 nucleotides before the start of transcription (−10 and −35).
• σ¹⁹ (FecI) – the ferric citrate sigma factor, regulates the fec gene for iron transport and metabolism
• σ²⁴ (RpoE) – extreme heat stress response and the extracellular proteins sigma factor
• σ²⁸ (RpoF/FliA) – the flagellar synthesis and chemotaxis sigma factor
• σ³² (RpoH) – the heat shock sigma factor, it is turned on when the bacteria are exposed to heat. Due to the higher expression, the factor will bind with a high probability to the polymerase-core-enzyme. Doing so, other heatshock proteins are expressed, which enable the cell to survive higher temperatures. Some of the enzymes that are expressed upon activation of σ³² are chaperones, proteases and DNA-repair enzymes.
• σ³⁸ (RpoS) – the starvation/stationary phase sigma factor
• σ⁵⁴ (RpoN) – the nitrogen-limitation sigma factor

There are also anti-sigma factors that inhibit the function of sigma factors and anti-anti-sigma factors that restore sigma factor function.

Structure

By sequence similarity, most sigma factors are σ⁷⁰-like . They have four main regions (domains) that are generally conserved:

N-terminus --------------------- C-terminus 1.1 2 3 4

The regions are further subdivided. For example, region 2 includes 1.2 and 2.1 through 2.4.

Domain 1.1 is found only in "primary sigma factors" (RpoD, RpoS in E.coli; "Group 1"). It is involved in ensuring the sigma factor will only bind the promoter when it is complexed with the RNA polymerase.^[7] Domains 2-4 each interact with specific promoter elements and with RNAP. Region 2.4 recognizes and binds to the promoter −10 element (called the "Pribnow box"). Region 4.2 recognizes and binds to the promoter −35 element.^[7]

Not every sigma factor of the σ⁷⁰ family contains all the domains. Group 2, which includes RpoS, is very similar to Group 1 but lacks domain 1. Group 3 also lacks domain 1, and includes σ²⁸. Group 4, also known as the Extracytoplasmic Function (ECF) group, lack both σ1.1 and σ3. RpoE is a member.^[7]

Other known sigma factors are of the σ⁵⁴/RpoN type. They are functional sigma factors, but they have significantly different primary amino acid sequences.^[8]

Protein domain infoboxes

Symbol: Sigma70_r1_1 Sigma70 region 1.1 Pfam: PF03979 Interpro: IPR007127

Symbol: Sigma70_r1_2 Sigma70 region 1.2 Pfam: PF00140 Interpro: IPR009042 Prosite: PDOC00592 Scop: 1sig

Symbol: Sigma70_r2 Sigma70 region 2 Pfam: PF04542 Pfam Clan: CL0123 Interpro: IPR007627 Prosite: PDOC00592 Scop: 1sig

Symbol: Sigma70_r3 Sigma70 region 3 Pfam: PF04539 Pfam Clan: CL0123 Interpro: IPR007624 Scop: 1ku2

Symbol: Sigma70_r4 Sigma70 region 4 Pfam: PF04545 Pfam Clan: CL0123 Interpro: IPR007630 Scop: 1or7

Symbol: Sigma70_r4_2 Sigma70 region 4.2 Pfam: PF08281 Pfam Clan: CL0123 Interpro: IPR013249 Scop: 1or7

Retention during transcription elongation

The core RNA polymerase (consisting of 2 alpha (α), 1 beta (β), 1 beta-prime (β'), and 1 omega (ω) subunits) binds a sigma factor to form a complex called the RNA polymerase holoenzyme. It was previously believed that the RNA polymerase holoenzyme initiates transcription, while the core RNA polymerase alone synthesizes RNA. Thus, the accepted view was that sigma factor must dissociate upon transition from transcription initiation to transcription elongation (this transition is called "promoter escape"). This view was based on analysis of purified complexes of RNA polymerase stalled at initiation and at elongation. Finally, structural models of RNA polymerase complexes predicted that, as the growing RNA product becomes longer than ~15 nucleotides, sigma must be "pushed out" of the holoenzyme, since there is a steric clash between RNA and a sigma domain. However, σ⁷⁰ can remain attached in complex with the core RNA polymerase in early elongation^[9] and sometimes throughout elongation.^[10] Indeed, the phenomenon of promoter-proximal pausing indicates that sigma plays roles during early elongation. All studies are consistent with the assumption that promoter escape reduces the lifetime of the sigma-core interaction from very long at initiation (too long to be measured in a typical biochemical experiment) to a shorter, measurable lifetime upon transition to elongation.

Sigma cycle

It had long been thought that the sigma factor obligatorily leaves the core enzyme once it has initiated transcription, allowing it to link to another core enzyme and initiate transcription at another site. Thus, the sigma factor would cycle from one core to another.However, fluorescence resonance energy transfer was used to show that the sigma factor does not obligatorily leave the core. Instead, it changes its binding with the core during initiation and elongation. Therefore, the sigma factor cycles between a strongly bound state during initiation and a weakly bound state during elongation.

Sigma factor competition

The number of RNAPs in bacterial cells (e.g., E. coli) have been shown to be smaller than the number of sigma factors. Consequently, if a certain sigma factor is overexpressed, not only will increase the expression levels of genes whose promoters have preference for that sigma factor, but it will also reduce the probability that genes with promoters with preference for other sigma factors.^{[11] [12] [13] [14]}

Meanwhile, transcription initiation has two major rate limiting steps: the closed and the open complex formation. However, only the dynamics of the first step depends on the concentration of sigma factors. Interestingly, the fastest is the closed complex formation relative to the open complex formation, the less responsive is a promoter to changes in sigma factors’ concentration (see for a model and empirical data of this phenomenon).

Genes with dual sigma factor preference

While most genes of E. coli can be recognized by an RNAP with one and only one type of sigma factor (e.g. sigma 70), a few genes (~ 5%) have what is called a “dual sigma factor preference”,^[15] that is, they can respond to two different sigma factors, as reported in RegulonDB.^[16] The most common ones are those promoters that can respond to both sigma 70 and to sigma 38 (iIlustrated in the figure) . Studies of the dynamics of these genes showed that when the cells enter stationary growth they are almost as induced as those genes that have preference for σ38 alone. This induction level was shown to be predictable from their promoter sequence. A model of their dynamics is shown in the figure. In the future, these promoters may become useful tools in synthetic genetic constructs in E. coli.

See also

• Ekkehard Bautz

Notes and References

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2. Kang JG, Hahn MY, Ishihama A, Roe JH . Identification of sigma factors for growth phase-related promoter selectivity of RNA polymerases from Streptomyces coelicolor A3(2) . Nucleic Acids Research . 25 . 13 . 2566–73 . July 1997 . 9185565 . 146787 . 10.1093/nar/25.13.2566 .
3. Burton SP, Burton ZF . The σ enigma: bacterial σ factors, archaeal TFB and eukaryotic TFIIB are homologs . Transcription . 5 . 4 . e967599 . 6 November 2014 . 25483602 . 4581349 . 10.4161/21541264.2014.967599 .
4. Ho TD, Ellermeier CD . Extra cytoplasmic function σ factor activation . Current Opinion in Microbiology . 15 . 2 . 182–8 . April 2012 . 22381678 . 3320685 . 10.1016/j.mib.2012.01.001 .
5. Schweer J, Türkeri H, Kolpack A, Link G . Role and regulation of plastid sigma factors and their functional interactors during chloroplast transcription - recent lessons from Arabidopsis thaliana . European Journal of Cell Biology . 89 . 12 . 940–6 . December 2010 . 20701995 . 10.1016/j.ejcb.2010.06.016 .
6. Sharma UK, Chatterji D . Transcriptional switching in Escherichia coli during stress and starvation by modulation of sigma activity . FEMS Microbiology Reviews . 34 . 5 . 646–57 . September 2010 . 20491934 . 10.1111/j.1574-6976.2010.00223.x . free .
7. Paget MS . Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution . Biomolecules . 5 . 3 . 1245–65 . June 2015 . 26131973 . 4598750 . 10.3390/biom5031245 . free .
8. Merrick MJ . In a class of its own--the RNA polymerase sigma factor sigma 54 (sigma N) . Molecular Microbiology . 10 . 5 . 903–9 . December 1993 . 7934866 . 10.1111/j.1365-2958.1993.tb00961.x . 84789281 .
9. Kapanidis AN, Margeat E, Laurence TA, Doose S, Ho SO, Mukhopadhyay J, Kortkhonjia E, Mekler V, Ebright RH, Weiss S . Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis . Molecular Cell . 20 . 3 . 347–56 . November 2005 . 16285917 . 10.1016/j.molcel.2005.10.012 . free .
10. Harden TT, Wells CD, Friedman LJ, Landick R, Hochschild A, Kondev J, Gelles J . Bacterial RNA polymerase can retain σ70 throughout transcription . Proc Natl Acad Sci U S A . 113 . 3 . 602–7 . January 2016 . 26733675 . 4725480 . 10.1073/pnas.1513899113 . 2016PNAS..113..602H . free .
11. Jishage . M . Ishihama . A . December 1995 . Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of sigma 70 and sigma 38 . Journal of Bacteriology . en . 177 . 23 . 6832–6835 . 10.1128/jb.177.23.6832-6835.1995 . 0021-9193 . 177550 . 7592475.
12. Jishage . M . Iwata . A . Ueda . S . Ishihama . A . September 1996 . Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of four species of sigma subunit under various growth conditions . Journal of Bacteriology . en . 178 . 18 . 5447–5451 . 10.1128/jb.178.18.5447-5451.1996 . 0021-9193 . 178365 . 8808934.
13. Grigorova . Irina L. . Phleger . Naum J. . Mutalik . Vivek K. . Gross . Carol A. . 2006-04-04 . Insights into transcriptional regulation and σ competition from an equilibrium model of RNA polymerase binding to DNA . Proceedings of the National Academy of Sciences . en . 103 . 14 . 5332–5337 . 10.1073/pnas.0600828103 . 16567622 . 1459355 . 2006PNAS..103.5332G . 0027-8424. free .
14. Kandavalli . Vinodh K. . Tran . Huy . Ribeiro . Andre S. . October 2016 . Effects of σ factor competition are promoter initiation kinetics dependent . Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms . en . 1859 . 10 . 1281–1288 . 10.1016/j.bbagrm.2016.07.011. 27452766 .
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16. Santos-Zavaleta . Alberto . Salgado . Heladia . Gama-Castro . Socorro . Sánchez-Pérez . Mishael . Gómez-Romero . Laura . Ledezma-Tejeida . Daniela . García-Sotelo . Jair Santiago . Alquicira-Hernández . Kevin . Muñiz-Rascado . Luis José . Peña-Loredo . Pablo . Ishida-Gutiérrez . Cecilia . 2019-01-08 . RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12 . Nucleic Acids Research . en . 47 . D1 . D212–D220 . 10.1093/nar/gky1077 . 0305-1048 . 6324031 . 30395280.