Translesion Synthesis during

Quach N, Myron GF, Shibata D. In vitro mutation artifacts after formalin fixation and error prone translesion synthesis during PCR. BioMed Central 2004 4 1-11. http //www.biomedcentral.eom/1472-6890/4/l. 

DNA adducts most likely reflects increased DNA repair such as nucleotide excision repair and postreplication repair including translesion synthesis, gap filling, and template switching during replication (27,28). 

Purified yeast Pol is able to perform limited nucleotide insertions opposite several DNA lesions such as TT (6-4) photoproduct, AAF-dG adduct, and (+) or ( )-trans-anti-BPDE-N2-dG adduct. Furthermore, Pol also catalyzes extension synthesis from opposite many types of lesions with varying efficiencies, including an AP site, cis-syn TT dimer, (64) photoproduct, AAF-dG adduct, (+) or (-)-trans-an//-BPDE-/V2-dG adduct, and an acrolein-derived dG adduct. Therefore, it has been proposed that Pol functions both as an insertion polymerase and an extension polymerase. It appears that the extension activity of Pol is versatile. Thus, it is believed that Pol is a major extension polymerase during translesion synthesis in eukaryotes. 

Opposite the 3 T of a TT dimer, Pol is unable to insert a nucleotide in vitro, although it is active for translesion synthesis opposite the 5 T of the dimer. Thus, other translesion polymerases are required to bypass the 3 T of the TT dimer and other lesions for which Pol is inactive. During translesion synthesis, the active site... 

Although the molecular defect of XPV is very different from that of the other XP patients (XPA, XPB, XPC, XPD, XPE, XPF, and XPG), who are deficient in nucleotide excision repair, the clinical manifestations of the diseases are quite similar. This is not surprising because the defect in either Polq or nucleotide excision repair results in a common problem genomic overload of TT dimers and perhaps other CPDs for error-prone translesion synthesis by other bypass polymerases during replication. The result is predictable elevated cytotoxicity and mutagenesis induced by the UV component of the sunlight, which constitute the cellular bases of XP diseases. 

It appears that multiple mechanisms exist for translesion synthesis, due to the involvement of multiple bypass polymerases. In the simplest case, one polymerase inserts a nucleotide opposite the lesion, and then the same polymerase extends the synthesis from opposite the lesion. This constitutes the one-polymerase two-step mechanism (Figure 22.23). Examples of this mode of translesion synthesis include the bypass of a TT dimer by Polr and the bypass of a (-)-trans-anU-bcn/o a ]pyrene-A 2-dG by PoIk. In a more complex scheme, following nucleotide insertion opposite the lesion by one polymerase, subsequent extension synthesis is catalyzed by another polymerase. This constitutes the two-polymerase two-step mechanism (Figure 22.23). PolC is believed to be the major extension polymerase during translesion synthesis by the two-polymerase two-step mechanism. Additionally, PoIk and Polr may also catalyze extension synthesis during the bypass of some selected lesions. 

Pol V is upregulated from <15 to 200 copies per cell approximately 45 minutes after SOS induction. Pol V is a heterotrimer with a subunit composition of UmuD 2C (see Fig. 6a). UmuC contains the catalytic domain of Pol V. UmuD is the product of RecA-mediated proteolytic cleavage of UmuD. Importantly, Pol V function requires RecA, and the mechanism by which RecA stimulates Pol V activity has been under investigation for several years (57). Recent data indicate that RecA nucleoprotein filaments act in trans to stimulate Pol V (see Fig. 6a) (57, 58). Interestingly, RecA hlaments in cis (immediately 5 to Pol V on the DNA template) do not stimulate Pol V (59). Pol V and SSB may cooperate to displace RecA from DNA (57, 60). Alternatively, recent data indicate that RecA may be removed by UvrD helicase, as UvrD is also induced during the SOS response, but whether UvrD plays a direct role in translesion synthesis is currently an open question (61, 62). 

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.

Fischhaber, P.L., Gerlach, V.L., Feaver, W.J., Hatahet, Z., Wallace, S.S., and Friedberg, E.C. (2002) Human DNA polymerase K bypasses and extends beyond thymine glycols during translesion synthesis in vitro, preferentially incorporating correct nucleotides. J. Biol. Chem., 277, 37604-37611. 

The translesion synthesis DNA polymerases also confer selective advantage on E. coli during long periods in stationary phase-the growth advantage in stationary phase (GASP) phenotype [97]. Finally, Pol IV is particularly elevated in stationary phase (around 7500/cell) and is implicated in adaptive mutagenesis [98]. 

Iwai, S and Sale, J.E. (2008) REV1 restrains DNA polymerase C, to ensure frame fidelity during translesion synthesis of UV photoproducts in vivo. Nucleic Acids Res., 36, 6767-6780. 

DNA-dependent DNA polymerases are responsible for directing the synthesis of new DNA from deoxyribo-nucleotide triphosphates (dNTPs) opposite an existing DNA template, which contains the genetic information critical to an organism s survival. To properly preserve this information, during each round of catalysis, a polymerase must accurately select and catalyze the insertion of a complementary nucleotide (dNTP) substrate, from a pool of four structurally similar molecules, into a nascent DNA strand. Present across all three domains of life, including Archaea, Bacteria, and Eukaryota, polymerases are necessarily and diversely utilized during DNA replication, recombination, repair, and translesion synthesis (TLS). 

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.)...

Baynton, K., Bresson-Roy, A., and Fuchs, R. P. P. (1999). Distinct roles for Revlp and Rev7p during translesion synthesis in Saccharomyces cerevisiae. Mol. Micro. 34, 124-133. 

Fig. 10. Switches between replicative and specialized DNA polymerases during translesion synthesis, (a) Pol III holoenzyme is able to elongate a primer in the vicinity of a lesion provided its 3 -extremity is located four or more nucleoddes dovmstream from the lesion site. If the primer is shorter, the proofreading exonuclease that is associated with Pol III degrades the primer (Fuji and Fuchs, 2004). (b) Minimal conditions for robust Pol V-mediated TLS. Two cofactors are essential for efficient Pol V-mediated lesion bypass (i) a DNA substrate onto which the / clamp is stably loaded,...

Lenne-Samuel, N., Wagner, J., Etienne, H., and Fuchs, R. P. (2002). The processivity factor /3 controls DNA polymerase IV traffic during spontaneous mutagenesis and translesion synthesis in vivo. EMBO Rep. 3, 45-49. 

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

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