DNA polymerase switching

Figure 6 Mechanisms of translesion synthesis, (a) Activation mechanism of Pol V during translesion synthesis. Pol V is a heterotrimer composed of subunits UmuC, D 2 UmuC is the catalytic domain, and UmuD is the product of RecA mediated proteolysis. Translesion synthesis by Pol V is activated by the presence of a RecA filament in trans. (b) Model of DNA polymerase switching during translesion synthesis. Pol III and Pol IV each bind to a p protomer at a conserved hydrophobic protein binding pocket (QL[S/D]LF). 1. Pol III is arrested at the site of DNA damage, whereas Pol IV is held in an inactive state away from the DNA. 2. Pol IV gains hold of the primer terminus from Pol III at the stall site Pol III is now held away from the DNA. 3. Pol IV extends the DNA past the lesion. 4. Pol III regains hold of the primer terminus from Pol IV.

Friedberg EC, Lehmann AR, Fuchs RP. Trading places how do DNA polymerases switch during translesion DNA synthesis Mol. Cell 2005 18 499-505. 

Fig. 5. Models for DNA polymerase switching during translesion synthesis. (A) Model for lesion bypass by a single TLS polymerase. (B) Model for lesion bypass by two TLS polymerases, wherein the first polymerase inserts a nucleotide opposite the damaged site and the second extends the aberrant primer terminus. (See Color Insert.)...

With the discovery of DNA polymerases specialized in TLS, it became clear that lesion bypass and mutagenesis would entail several DNA polymerase switches, with the replicative DNA polymerase being transiently replaced in the vicinity of the lesion by one (or several) specialized polymerases before resuming high-fidelity replication. This new paradigpi for the mechanism of TLS and mutagenesis was dubbed the DNA polymerase switch model (Gordonnier and Fuchs, 1999). 

Zhang Z, Zhang S, Lin SH, Wangb X, Wu L, Lee EY, Lee MY. Strucmre of monoubiquitinated PCNA implications for DNA polymerase switching and Okazaki fragment maturation. Cell Cycle. 2012 11 2128-36. 

To summarize, terminase inhibitors point the way toward a switch in strategy for developing HCMV inhibitors, with the aim of achieving a quality different from that of established DNA polymerase inhibitors. Intervention with viral DNA maturation arrests the replicative cycle at the DNA cleavage and packaging step, leading to an accumulation of empty procapsids and unprocessed concatemeric DNA. 

Fig. 2. Strategies for uniform labeling of double-stranded DNA. (A) Nick translauon involves the 5 - 3 exonuclease and DNA polymerase functions of E. coli DNA polymerase 1 in the translocation of a single-strand break in a DNA strand. Trcuislocation of the breakpoint occurs in the 5 - 3 direction as a result of concomitant nucleotide hydrolysis and polymerization. (B) Template switching involves the extension of a DNA chain at a single-strand break, in a reaction where DNA is duplicated, rather than replaced as in nick treuislation.

Figure 3 Kinetic steps during DNA synthesis favor incorporation of correct dNTPs. Most often the DNA polymerase selects the correct dNTP that forms a correct Watson-Crick base pair with the template strand (pathway 1, left). The chemistry of correct dNTP incorporation is rapid, and it allows the polymerase to proceed rapidly to incorporate subsequent dNTPs. The chemistry of incorporating an incorrect dNTP is slow (pathway 2, right), and subsequent elongation of the mispaired 3 terminus is also slow. These two kinetic barriers provide time for the primed template to switch into the proofreading 3 -5 exonuclease active site, where removal of the mispaired 3 terminus is rapid. The excised and fully base paired primed site then switches back to the DNA polymerase active site (dashed arrow).

Yuzhakov A, Kelman Z, O Donnell M. Trading places on DNA-a three-point switch underlies primer handoff from primase to the replicative DNA polymerase. Cell 1999 96 153-163. 

Juarez R, Ruiz JF, Nick McElhinny SA, Ramsden D, Blanco L. A specific loop in human DNA polymerase mu allows switching between creative and DNA-instructed synthesis. Nucleic Acids Res. 2006 34 4572-4582. 

Tujo distinct polymerases are needed to copy a eukaryotic replicon. An initiator polymerase called polymerase a begins replication but is soon replaced by a more processive enzyme. This process is called polymerase switching because one polymerase has replaced another. This second enzyme, called DNA polymerase 5, is the principal replicative polymerase in eukaryotes (Table 28.2). 

Translesion synthesis Y-family polymerases and the polymerase switch. DNA Repair, 6, 891-899. 

Members of the newly discovered low-fidelity Y Family are exonuclease deficient, possess TLS abilities, and include eukaryotic Pol r/, Pol t, Pol k, and REVl, and Sulfolobus solfataricus DNA polymerase IV (Dpo4). Pol rj, Pol L, and Pol k have all been shown to interact with the deoxycytidyltransferase, REVl, which may act as a scaffold during polymerase switching, the process by which the aforementioned TLS polymerases are coordinated in their projected participation in either DSB repair (Pol r/), BER (Pol t), NER (Pol k), and SHM (Pol rj and Pol i) (reviewed in Rattray and Strathern, Prakash Lehmann etal Lehmann, Kannouche and... 

Komissarova, N., and Kashlev, M. (1997a). RNA polymerase switches between inactivated and activated states by translocating back and forth along the DNA and the RNA./. Biol. Chem. 272, 15329-15338. 

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