The DNA Polymerase

DNA polymerases encoded by fungal linear plasmids are of the viral B type, like enzymes from adenoviruses and phages which display a replication mode employing protein primers (Ito and Braithwaite 1991; Kempken et al. 1992; Rohe et al. 1992). As already mentioned, however, linear plasmid encoded DNA polymerases carry the TPs as an N-terminal extension. Though suggested earlier (Oeser and Tudzynski 1989; Chan et al. 1991; Meinhardt and Rohe 1993), this structure was experimentally proven rather late for pGKL2 of Kluyveromyces lactis and later for pMLP1 of Pleurotus ostreatus (Takeda et al. 1996; Kim et al. 2000). Except for a weakly conserved motif (SYKN), there is only, if at all, a hardly detectable similarity among TP regions of distantly related plasmid DNA polymerases and the respective proteins from bacteriophages and adenoviruses, suggesting extended structural diversities. It remains totally obscure at present if, how, and where the TP is split off from the polymerase during replication. For the Neurospora plasmid kalilo, the molecular mass of the TP was determined to be approximately 120 kDa

(Vierula et al. 1990). It was suggested that it actually may represent the full-size TP-DNA polymerase fusion protein (Chan et al. 1991). On the contrary, however, for pMLP1 of Pleurotus ostreatus, as well as another linear plasmid, pMLP2, it was shown that TPs comprise only 70 and 72 kDa, respectively; consistently, DNA polymerase domains were immunologically not detectable, providing evidence for in vivo processing of the protein (Kim et al. 2000). Also, the molecular mass (approx. 36 kDa) of the TP of pGKL2 (Stam et al. 1986; Takeda et al. 1996) rules out a full-size TP-DNA protein. Replication initiation has been studied in detail for phage phi29; it was proven that the initiation complex consisting of TP and DNA polymerase starts DNA synthesis at the ends of the template. Dissociation of the above complex occurs shortly after elongation has begun, i.e., after the synthesis of approximately six nucleotides (Mendez et al. 1997; Kamtekar et al. 2006).

The highly processive phi29 DNA polymerase replicates the entire phage genome unassisted by a helicase or sliding clamp. Such unique features rely on the terminal protein region 2 (TPR2), which is similarly inserted in all DNA polymerases using protein primers. The TPR2 domain forms a doughnutlike structure, which enables high processivity and facilitates separation of template and nontemplate strands before entry into the polymerase active site (Kamtekar et al. 2004; Rodriguez et al. 2005). TPR2-like domains in linear plasmid encoded DNA polymerases (Dufour et al. 2000, 2003; Rodriguez et al. 2005) are assumed to compare functionally to the phi29 enzyme (Jeske et al. 2006a).

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