Sigma factor in gene expression

A sigma factor is a protein required for the initiation of transcription in bacteria. It is a bacterial

transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoters.
It is similar to archaeal transcription factor B and transcription factor TFIIB present in eukaryotes. 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. They are also found in
plant chloroplasts as a part of the bacteria-like plastid-encoded polymerase (PEP).

Every molecule of RNA polymerase holoenzyme contains exactly one sigma factor subunit. The
number of sigma factors vary between species. E. coli has seven sigma factors and are distinguished by
their molecular weights. These are:

 σ70(RpoD) – σA –the "housekeeping" sigma factor or also called as primary sigma factor.

It is responsible for transcription of most genes in growing cells. Every cell has this sigma
factor and keeps essential genes and pathways operating. In the case of E. coli and other
gram-negative rod-shaped bacteria, the "housekeeping" sigma factor is σ70. Genes
recognized by σ70 all contain similar promoter consensus sequences consisting of two
parts. 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) – necessary for exocytoplasmic 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. Hence expressing other heat shock proteins which enable the cell
to survive at higher temperatures.
 σ38 (RpoS) – the starvation/stationary phase and stress sigma factor
 σ54 (RpoN) – recognizes genes for nitrogen metabolism
 σ70 represents sigma factor with a molecular weight of 70 kDa.

Experiment

 Sigma factor-sigma E (sigma 24) has been known for maintaining the induction of the
heat shock response of Escherichia coli at high temperatures. The gene encoding for
sigma E was found in this experiment using a genetic screen designed to isolate trans‐
acting mutations that abolish expression from either htrA or rpoHP3, two promoters
recognized uniquely by sigma E‐containing RNA polymerase. Such a screen was
attained by transducing strains carrying a single copy of either phtrA‐lacZ or rpoHP3‐
lacZ fusions with mutagenized bacteriophage P1 lysates and screening for Lac‐ mutant
colonies at 22 degrees C. Lac‐ mutants were subsequently tested for inability to grow at
43 degrees C. Only those Lac‐ Ts‐ mutants that were unable to accumulate heat shock
proteins at 50 degrees C were retained for further characterization. In a complementary
approach, those genes which when cloned on a multicopy plasmid led to higher
constitutive expression of the sigma E regulon were characterized and mapped. Both
approaches identified the same gene, rpoE, mapping at 55.5 min on the E.coli genetic
map and encoding a polypeptide of 191 amino acid residues. The wild‐type and a
mutant rpoE gene products were over‐expressed and purified. It was found that the
purified wild‐type sigma E protein, when used in in vitro run‐off transcription assays in
combination with core RNA polymerase, was able to direct transcription from the htrA
and rpoHP3 promoters, but not from known sigma 70‐dependent promoters. In vivo and
in vitro analyses of rpoE transcriptional regulation showed that the rpoE gene is
transcribed from two major promoters, one of which is positively regulated by sigma E
itself.