Special care to prevent proteolysis during yeast RNA polymerase B purification leads to the appearance of two forms of enzymes, BI and BII, with different molecular weight (465000 and 435000, respectively). The two forms of enzyme can be separated by ion‐exchange chromatography or polyacrylamide gel electrophoresis. Their subunit structures were compared by sodium dodecylsulfate gel electrophoresis, the only observed difference between the two enzymes is in the molecular weight of the heaviest subunit which is 220000 for enzyme BI and 180000 for enzyme BII. Otherwise, the two enzymes have seven common subunits of molecular weights 150000, 45000, 26000, 22500, 14500, 12500 and 9000. Two additional polypeptide chains of 32000 and 16500 Mr are dissociated from the enzyme upon polyacrylamide gel electrophoresis or DEAF Sephadex chromatography.
The largest subunit of enzyme BI (Mr 220000) can be specifically cleaved in vitro by a yeast protease extract, generating a polypeptide chain indistinguishable from the largest subunit of enzyme BII. This proteolytic cleavage of enzyme BI in vitro is inhibited by phenylmethylsulfonyl fluoride and does not significantly change the activity of the enzyme with single‐stranded or double‐stranded DNA as template. The precursor‐product relationship of the different forms of class B RNA polymerises in eukaryotic cells is discussed.