Sigma factor

[1][2] It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoters.

Selection of promoters by RNA polymerase is dependent on the sigma factor that associates with it.

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.

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.

They are functional sigma factors, but they have significantly different primary amino acid sequences.

[8] 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.

This view was based on analysis of purified complexes of RNA polymerase stalled at initiation and at 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.

However, fluorescence resonance energy transfer was used to show that the sigma factor does not obligatorily leave the core.

[11][12][13][14] Meanwhile, transcription initiation has two major rate limiting steps: the closed and the open complex formation.

Domain organization, promoter recognition and structural organization of the σ 70 family. ( a ) The domain organization of σ factors from Groups 1, 3 and 4 are illustrated above σ 70 consensus E. coli promoter DNA. ( b ) Organization of E. coli σ70 in an RNA polymerase transcription initiation complex. (PDB 4YLN).
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”.