Limited digestion of RNA polymerase from Escherichia coli by trypsin (effect of rifamycin and DNA on the integrity of sigma subunit)

A modified polyacrylamide gel electrophoresis technique is used to separate the polypeptides after digestion of $\text{E. coli}$ RNA polymerase with various concentration of trypsin. The subunits β and β′ and two large breakdown products of molecular weight of 147,000 and 141,000 are distinctly separated. At a very low level of trypsin σ and α are not cleaved while two major breakdown products of molecular weights of 110,000 and 43,000 appear from the larger subunits. At a still higher level of trypsin σ is converted to a polypeptide of molecular weight of 86,000 and other small fragments. DNA protects, to some extent, the σ and this polypeptide and also β and the two large breakdown products from trypsin digestion. It is also observed that rifamycin, an inhibitor of RNA synthesis, enhances the tryptic digestion of σ, only in the absence of MgCl₂.