Multiple Sigma Subunits

Multiple Sigma Subunits

In vitro transcription experiments with the E. coli RNA polymerase haveshown that the σ subunit is required for initiation at promoters, but that σ is not required for elongation activity. In fact, the σ subunit comes offthe polymerase when the transcript is between 2 and 10 nucleotides long. Polymerase lacking the σ subunit, core polymerase, binds ran-domly to DNA and initiates nonspecifically or from nicks, but it rarely initiates from promoters. These results raise an interesting question: If the σ subunit is required for promoter recognition, then could different σ subunits be used to specify transcription from different classes ofgenes? The answer is yes.

Although many years of searching were required, sigma subunits specific for more than five different specific classes of genes have been found in E. coli. Most transcription is initiated by the σ⁷⁰ subunit. Not only in E. coli, but in all types of cells, heat shock induces the synthesis of about 40 proteins that aid in surviving the stressful conditions. One of the proteins induced in E. coli by heat shock is a σ factor that recognizes promoters located in front of other heat shock responsive genes. Other σ factors are used for transcription of nitrogen regulated genes, the flagellar and chemotaxis genes, and genes induced under oxidative stress.

Developmentally regulated genes are another area in which the specificity provided by σ factors proves useful. Bacillus subtilis forms spores under some conditions. Synthesizing a spore requires conversion of one cell into two drastically different cells. One ultimately becomes the spore, and the other completely surrounds the maturing spore and synthesizes the protective cell wall of the spore. Cascades of different sigma factors turn on the appropriate genes in these two cell-types.

Eukaryotic polymerases appear to contain an analog of the σ subunit. This protein is required for correct initiation, reduces nonspecific initiation, and competes for binding to the polymerase with the bacterial σ subunit.