Purification and characterization of DNA polymerase III from Bacillus subtilis

DNA polymerase III from Bacillus subtilis has been purified about 4,500-fold. Disc gel electrophoresis of the purified fraction reveals a single major protein band which co-migrates with the polymerase activity. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the polymerase yields a single, 166,000 dalton band. The hydrodynamic properties of the enzyme are ionic strength-dependent. The average values from determinations in high and low salt are 7.6 S for the sedimentation coefficient and 52 A for the Stokes radius. These two parameters indicate a molecular weight for the native enzyme of 160,000. Therefore, the enzyme appears to contain a single, long, polypeptide chain. The enzyme has no endonuclease activity but does have single strand specific exonuclease activity. Hydrolysis is initiated exclusively from the 3' terminus yielding 5' mononucleotides, and a dinucleotide is the limit of digestion. The exonuclease activity has an ionic strength dependence of pH optimum similar to that of the polymerase but appears to be more fastidious in its divalent metal requirement. The mode of attack by the enzyme is strictly distributive. The activity of the exonuclease decreases markedly with increasing substrate size. Two opposing mechanisms account quantitatively for this effect--intrinsic competitive inhibition by interior substrate nucleotides and increasing accessibility of the substrate terminus to the enzyme with increasing chain length. The polymerase synthesizes DNA in the 5' leads to 3' direction and the apparent Km for each of the deoxyribonucleoside triphosphates is about 1 muM. The polymerase replicates RNA-primed, phiX174 DNA in the presence of Escherichia coli elongation Factors I and II. In contrast to polymerase III, B. subtilis DNA polymerase II has no detectable nuclease activity.