The DNA synthesizing subunit of polymerase-primase from calf thymus

Evolution and degeneration of eukaryotic DNA replication system

Several molecular forms of DNA polymerases have been identified in eukaryotic cells. Although three DNA polymerases alpha, delta, and epsilon, have been well studied and indicated to be involved in nuclear DNA replication process, it remains unclear how this hetero-polymerase system might have arisen. Here I wish to consider its past and future, viewed in the context of molecular evolution. Comparative analysis has revealed some nucleotides and/or amino acids to be conserved in DNA polymerase delta, in polymerase domains III and IV, which have disappeared in DNA polymerase alpha. Furthermore, the codon usage for serine residues in conserved domains of DNA polymerase alpha varies and is not as conservative as for DNA polymerase delta. Recently and in the present study, I have reported that DNA polymerase delta could substitute for the function of DNA polymerase alpha in vitro, and proposed the hypothesis that eukaryotic DNA polymerase alpha arose due to symbiotic contacts. This 'exogenous' polymerase would be expected to be excluded from the eukaryotic DNA replication system, and my analysis in the present study suggests it is about to degenerate.

Single-stranded DNA binding protein from calf thymus. Purification, properties, and stimulation of the homologous DNA-polymerase-alpha-primase complex

A binding protein for single-stranded DNA (ssDNA) was purified from calf thymus to near homogeneity by chromatography on DEAE-cellulose, blue-Sepharose, ssDNA-cellulose and FPLC Mono Q. The most purified fraction consisted of four polypeptides with molecular masses of 70, 55, 30, and 11 kDa. The polypeptide with the molecular mass of 55 kDa is most likely a degraded form of the largest polypeptide. The complex migrated as a whole on both glycerol gradient ultracentrifugation (s = 5.1 S) and gel filtration (Stokes' radius approximately 5.1 nm). Combining these data indicates a native molecular mass of about 110 kDa, which is in accord with a 1:1:1 stoichiometry for the 70 + 55/30/11-kDa complex. The ssDNA binding protein (SSB) covered approximately 20-25 nucleotides on M13mp8 ssDNA, as revealed from both band shift experiments and DNase I digestion studies. The homologous DNA-polymerase-alpha-primase complex was stimulated by the ssDNA binding protein 1.2-fold on poly(dA).(dT)14 and 10-13-fold on singly primed M13mp8 DNA. Stimulation was mainly due to facilitated DNA synthesis through stable secondary structures, as demonstrated by the vanishing of many, but not all, pausing sites. Processivity of polymerase-primase was not affected on poly(dA).(dT)14; with poly(dT).(rA)10 an approximately twofold increase in product lengths was observed when SSB was present. The increase was attributed to a facilitated rebinding of polymerase alpha to an already finished DNA fragment rather than to an enhancement of the intrinsic processivity of the polymerase. Similarly, products 300-600 nucleotides long were formed on singly primed M13 DNA in the presence of SSB, in contrast to 20-120 nucleotides when SSB was absent. DNA-primase-initiated DNA replication on M13 DNA was inhibited by SSB in a concentration-dependent manner. However, with less sites available to begin with RNA priming, more homogeneous products were formed.