Dimer bypass

Figure 1. Schematic presentation of (A) DNA repair mechanisms 1. Photoreactivation also known as photoenzymatic repair, and 2. Nucleotide excision repair where the lesion damaged by exposure to UV-B is reversed (photoreactivation) or expelled (nucleotide excision repair) (B) DNA damage tolerance mechanisms 1. Dimer bypass and 2. Recombinational repair where replication proceeds around the lesion and the gap is filled in by adenine (dimer bypass) or a homologous sequence is inserted (recombinational repair).

Washington, M.T., Johnson, R.E., Prakash, S., and Prakash, L. (2000) Accuracy of thymine-thymine dimer bypass by Saccharomyces cerevisiae DNA polymerase q. Proc. Natl. Acad. Sci. 

Nelson, J.R., Lawrence, C.W., and Hinkle, D.C. (1996) Thymine-thymine dimer bypass by yeast DNA polymerase... 

McCulloch, S. D., Kokoska, R. J., Masutani, C., Iwai, S., Hanaoka, F., and Kunkel, T. A. (2004). Preferential cis-syn thymine dimer bypass by DNA polymerase h occurs with biased fidelity. Nature 427, 97-100. 

There are multiple systems for naming organolithium compounds. In one, CeHsLi is named phenyl lithium and w-C4H9Li is w-butyl lithium. In another, these species are named Uthiobenzene and 1-lithiobutane, respectively, when the lithium atom is regarded as a substituent on the hydrocarbon parent. A third nomenclature approach assumes these species are ionic salts, e.g. the above two compounds are called lithium phenylide and lithium butylide. We will bypass any questions of aggregation by referring to these compounds by their monomeric names (e.g. phenyl lithium and not dimeric phenyl lithium, phenyl lithium dimer nor diphenyl dilithium), and where monomeric species are actually meant, we will make this explicit. 

In mammalian cells, at least eight DNA polymerases are present. DNA polymerase a is involved in the initiation of DNA synthesis at DNA replication origins and lagging strand synthesis (Wang, 1991). DNA polymerase 7is a mitochondrial DNA polymerase (Wang, 1991). Recently, bypass polymerases, such as DNA polymerase V, t. and Chave also been identified (Lindahl and Wood, 1999). These DNA polymerases are capable of continuing DNA synthesis even through bulky DNA lesions—such as UV-induced pyrimidine-dimers in the template strand (Lindahl and Wood, 1999). 

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. 

In contrast to TT dimers, TT (6-4) photoproducts cannot be bypassed by Polq alone in vitro. Instead, Polq is able to insert a G opposite the 3 T of the TT (6-4) photoproduct before aborting DNA synthesis. The resulting intermediate of translesion synthesis is a substrate for extension synthesis by Pol . Coordination between these two polymerases could therefore achieve bypass of TT (6-4) photoproducts by the two-polymerase two-step mechanism of translesion synthesis. This indeed occurs in yeast cells and is the major mechanism of G mis-insertion opposite the 3 ... 

In some cases, the damaged portion of DNA is bypassed during the replication phase but otherwise replication continues. The recombinational or post replication pathway then inserts a homologous complementary DNA strand into the site opposite of the dimer damage (Figure 1). The dimer damage is left unrepaired and replication continued such that the complementary strand is error-free. This type of repair is known to occur in bacteria. 

Pol32 in the bypass and mutation induction of an abasic site, T-T (6-4) photoadduct and T-T cis-syn cyclobutane dimer. Genetics, 169, 575-582. 

Although Pol V replicates undamaged templates with relatively low fidelity (10 3 to 10-4) [76], one striking quality is Pol V s ability to accurately bypass UV photoproducts (e.g., inserting dATP opposite thymine-thymine (TT) cyclobutane pyrimidine dimers (CPDs) [76]). Analysis of insertion tendencies opposite a variety of adducts/lesions led to the observation that Pol V seems to have two insertion modes (i) correct dNTP insertion and (ii) default dATP insertion [37]. UV light is a frequently encountered form of DNA damage for which a translesion synthesis DNA polymerase might be important and since TT CPDs are the major UV lesion... 

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