Sigma factor

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.

Domain organization, promoter recognition and structural organization of the σ⁷⁰ family. (a) The domain organization of σ factors from Groups 1, 3 and 4 are illustrated above σ⁷⁰ consensus E. coli promoter DNA. (b) Organization of E. coli σ70 in an RNA polymerase transcription initiation complex. (PDB 4YLN).

By sequence similarity, most sigma factors are σ⁷⁰-like (InterPro: IPR000943). 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 (InterPro: IPR000394) type. They are functional sigma factors, but they have significantly different primary amino acid sequences.[8]

Protein domain infoboxes

Sigma70 region 1.1 Identifiers Symbol Sigma70_r1_1 Pfam PF03979 InterPro IPR007127 Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

Sigma70 region 1.2 Crystal structure of Thermus aquaticus RNA polymerase sigma subunit fragment containing regions 1.2 to 3.1 Identifiers Symbol Sigma70_r1_2 Pfam PF00140 InterPro IPR009042 PROSITE PDOC00592 SCOP2 1sig / SCOPe / SUPFAM Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

Sigma70 region 2 Crystal structure of a sigma70 subunit fragment from Escherichia coli RNA polymerase Identifiers Symbol Sigma70_r2 Pfam PF04542 Pfam clan CL0123 InterPro IPR007627 PROSITE PDOC00592 SCOP2 1sig / SCOPe / SUPFAM Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

Sigma70 region 3 Solution structure of sigma70 region 3 from Thermotoga maritima Identifiers Symbol Sigma70_r3 Pfam PF04539 Pfam clan CL0123 InterPro IPR007624 SCOP2 1ku2 / SCOPe / SUPFAM Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

Sigma70 region 4 Solution structure of sigma70 region 4 from Thermotoga maritima Identifiers Symbol Sigma70_r4 Pfam PF04545 Pfam clan CL0123 InterPro IPR007630 SCOP2 1or7 / SCOPe / SUPFAM Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

Sigma70 region 4.2 Crystal structure of Escherichia coli sigma70 region 4 bound to its -35 element DNA Identifiers Symbol Sigma70_r4_2 Pfam PF08281 Pfam clan CL0123 InterPro IPR013249 SCOP2 1or7 / SCOPe / SUPFAM Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

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.

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.[9] 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.

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 [14] for a model and empirical data of this phenomenon).

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.[15] 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.

Left: illustration of genes whose promoters can be recognized by both sigma 70 (green) and sigma 38 (blue). Shown are the RNA polymerases, carrying the two different sigma factors, and either of them can bind to the promoter region (grey rectangle). Right: Model proposed in [15] of these genes. The model consists of a two-step process of gene expression (transcription followed by translation). The rate constant from transcription (k_t) accounts for the possibility of binding by either RNAP (those carrying sigma 70, and those carrying sigma 38). The model also includes translation (rate constant kt), and RNA and protein degradation to “nothing” represented by the “slashed zero glyph”.

• Ekkehard Bautz

• Sigma+Factor at the US National Library of Medicine Medical Subject Headings (MeSH)