ALTERNATIVE σ FACTORS
They direct RNAP to initiate transcription at specific
promoters to allow differential expression of a particular
subset of genes.
First described for Bacillus subtilis & phages SP01/SP82
Now ten different families.
And a common feature in all bacteria
e.g. – E. coli – 7 factors
The specificity of RNAP for promoter sequences can be
modified by different σ factors. Some are absolutely
specific for their own promoter sequences. Others have
promoter specificities that overlap with other sigma
Need to know some sigma factors. Sigma 70 most
Phage have different sigma factors for different life stages.
Sigma 70 recognizes early genes. Makes sigma factors
for middle/late genes.
Sigma S is similar to sigma 70 and used for stationary
Don’t know many sigma factors.
Sigma factors have evolutionary tree that is devided into
1. How many sigma factors can bacteria have?
2. What does it depend on? The different conditions that
the bacteria can live under. Presence of a certain
substrate. Stresses. Changes in life cycle.
3. What does it help with?
M. genitalium: smallest genome. One sigma factor.
S. coelicolor: soil bacteria with large genome. Over 60
This gives flexibility in promoter use. And depends upon
Types of σ Regulation
1. Concentration A. Synthesis
B. Protein stability
2. Activity modulated by modification
A. Cleavage of protein sequence
B. Interaction with inhibitors (anti sigma factors)
σS – Stationary Phase
When cells stop growing exponentially, many genes no
longer needed. Instead, slow growth stationary phase
genes are turned on. 3
Many of these genes are transcribed by σS
Encoded by rpoS. Sometimes called sigma 38.
Not the only stationary phase–specific alternative σ factor,
but the major one.
Given that exponential bacterial growth is not normal… (in
real conditions). Perhaps high levels of sigma S is normal
Also expressed under cell stress
At exponential growth: Sigma S = 0/cell. Sigma 70 =
At stationary phase: Sigma 70 = 300/cell
σS shares many promoter specificities with σ70. Some
promoters are recognized by both σ factors. Unusual
since most alternative sigma factors are specific for a
class of genes. Sigma S controls many genes.
Regulation of σS (rpoS) mainly occurs at level of
transcription, but also at post-translational stages and
protein stability 4
σH (σ32) and σE (σ24)
When E. coli growth temperatures reach > 40 C, new
genes are expressed. Heat shock resonse. Or
This involves the expression of approx. 20 new proteins.
Heat Shock (HS) is a universal phenomenon since
organisms from bacteria to mammals do it, and express
many of the same proteins.
HS genes encode
Proteases and a family of proteins called chaperones
which refold thermally denatured proteins.
σH recognizes a completely new promoter sequence, so
all HS genes require σH and core RNAP.
These genes are expressed at a basal level at normal
temperatures so low levels of sigma 32 (sigma H) are
σH gene is recognized by σ70 at 40 C. Levels of σH
increase 20 fold during HS. T 1/2= 1 min therefore this is a
fast response both increasing and decreasing. Short half
life means quick disappearance when stimulus is not
This is mostly due to an increase in translational
efficiency; the mRNA is easier to translate at higher temps
(less folding energy to get sigma H secondary structure).
Sigma H half life also increases at higher temperatures.
When temperatures rise to 50 C, HS is more extreme, and
continuous synthesis of HS proteins is required.
Rarely found at normal temperatures, σH & σE become
abundant above 40 C.
σE does not recognize σH or σ70 promoters (these genes
are for thermotolerance). But instead indir