Transcriptional regulation by alternative sigma (σ) factors

▶Sigma factors: The α β β’ ω core enzyme of RNA polymerase is unable to start transcription at promoter sites. In order to specifically recognize the consensus –35 and –10 elements of general promoters, it requires the σ factor subunit. This subunit is only required for transcription initiation, being released from the core enzyme after initiation and before RNA elongation takes place.

Thus, σ factors appear to be bifunctional proteins that simultaneously can bind to core RNA polymerase and recognize specific promoter sequences in DNA.

Many bacteria, including E. coli, produce a set of σ factors that recognize different sets of promoters. Transcription initiation from single promoters or small groups of promoters is regulated commonly by single transcriptional repressors (such as the lac repressor) or transcriptional activators (such as the cAMP receptor protein, CRP). However, some environmental conditions require a massive change in the overall pattern of gene expression in the cell. Under such circumstances, bacteria may use a different set of σ factors to direct RNA polymerase binding to different promoter sequences. This process allows thediversion of the cell’s basic transcription machinery to the specific transcription of different classes of genes.

▶Promoter recognition: The binding of an alternative σ factor to RNA polymerase can confer a new promoter specificity on the enzyme responsible for the general RNA synthesis of the cell. Comparisons of promoters activated by polymerase complexed to specific σ factors show that each σ factor recognizes a different combination of sequences centered approximately around the –35 and –10 sites. It seems likely that σ factors themselves contact both of these regions, with the –10 region being most important. The σ70 subunit is the most common σ factor in E. coli which is responsible for recognition of general promoters which have consensus –35 and –10 elements.

▶Heat shock: The response to heat shock is one example in E. coli where gene expression is altered significantly by the use of different σ factors. When E. coli is subjected to an increase in temperature, the synthesis of a set of around 17 proteins, called heat-shock proteins, is induced. If E. coli is transferred from 37 to 42°C, this burst of heat-shock protein synthesis is transient. However if the increase in temperature is more extreme, such as to 50°C, where growth of E. coli is not possible, then the heat-shock proteins are the only proteins synthesized. Thepromoters for E. coli heat-shock protein-encoding genes are recognized by a unique form of RNA polymerase holoenzyme containing a variant σ factor, σ32, which is encoded by the rpoH gene. σ32 is a minor protein which is much lessabundant than σ70. Holoenzyme containing σ32 acts exclusively on promoters of heat-shock genes and does not recognize the general consensus promoters of most of the other genes . Heat-shock promoters accordingly have different sequences to other general promoters which bind to σ70.

5 7▶Sporulation in Bacillus subtilis: Vegetatively growing B. subtilis cells form bacterial spores in response to a sub-optimal environment. The formation of a spore (or sporulation) requires drastic changes in gene expression, including the cessation of the synthesis of almost all of the proteins required for vegetative existence as well as the production of proteins which are necessary for the resumption of protein synthesis when the spore germinates under more optimal conditions.

The process of spore formation involves the asymmetrical division of the bacterial cell into two compartments, the forespore, which forms the spore, and the mother cell, which is eventually discarded. This system is considered one of the most fundamental examples of cell differentiation. The RNA polymerase in B. subtilis is functionally identical to that in E. coli. The vegetatively growing B.subtilis contains a diverse set of σ factors. Sporulation is regulated by a further set of σ factors in addition to those of the vegetative cell. Different σ factors are specifically active before cell partition occurs, in the forespore and in the mother cell. Cross-regulation of this compartmentalization permits the forespore and mother cell to tightly co-ordinate the differentiation process.

▶Bacteriophage σ factors:  Some bacteriophages provide new σ subunits to endow the host RNA polymerase with a different promoter specificity and hence to selectively express their own phage genes (e.g. phage T4 in E. coli and SPO1 in B. subtilis). This strategy is an effective alternative to the need for the phage to encode its own complete polymerase (e.g. bacteriophage T7). The B. subtilis bacteriophage SPO1 expresses a ‘cascade’ of σ factors in sequence to allow its own genes to be transcribed at specific stages during virus infection. Initially, early genes are expressed by the normal bacterial holoenzyme. Among these early genes is the gene encoding σ28, which then displaces the bacterial σ factor from the RNA polymerase. The σ28-containing holoenzyme is then responsible for expression of the middle genes. The phage middle genes include genes 33 and 34 which specificy a further σ factor that is responsible for the specific transcription of late genes. In this way, the bacteriophage uses the host’s RNA polymerase machinery and expresses its genes in a defined sequential order.


Key Notes

  • Sigma factors: The sigma (σ) factor is responsible for recognition of consensus promoter sequences and is only required for transcription initiation. Many bacteria produce alternative sets of σ factors.


  • Promoter recognition: In coli, σ70 is responsible for recognition of the –10 and –35 consensus sequences. Differing consensus sequences are found in sets of genes which are regulated by the use of alternative σ factors.


  • Heat shock: Around 17 proteins are specifically expressed in coli when the temperature is increased above 37°C. These proteins are expressed through transcription by RNA polymerase using an alternative sigma factor σ32. σ32 has its own specific promoter consensus sequences.


  • Sporulation in Bacillus subtilis: Under nonoptimal environmental conditions, subtilis cells form spores through a basic cell differentiation process involving cell partitioning into mother cell and forespore. This process is closely regulated by a set of σ factors which are required to regulate each step in this process.


  • Bacteriophage σ factors: Many bacteriophages synthesize their own σ factors in order to ‘take over’ the host cell’s own transcription machinery by substituting the normal cellular σ factor and altering the promoter specificity of the RNA polymerase. subtilis SPO1 phage expresses a cascade of σ factors which allow a defined sequence of expression of early, middle and late phage genes.