trans-Lesion Synthesis Past Bulky Benzo[a]pyrene Diol Epoxide N2-dG and N6-dA Lesions Catalyzed by DNA Bypass Polymerases

Rechkoblit, Olga; Zhang, Yanbin; Guo, Dongyu; Wang, Zhigang; Amin, Shantu; Krzeminsky, Jacek; Louneva, Natalia; Geacintov, Nicholas E.

doi:10.1074/jbc.m201167200

Cited by 186 publications

(193 citation statements)

References 66 publications

Supporting

Mentioning

181

Contrasting

Order By: Relevance

“…Y-family DNA polymerases are involved in the mutagenic bypass of BP adducts (1,3,(13)(14)(15). There are multiple Y-family DNA polymerases in cells.…”

Section: Biochemistrymentioning

confidence: 99%

A structural gap in Dpo4 supports mutagenic bypass of a major benzo[ a ]pyrene dG adduct in DNA through template misalignment

Bauer

Xing²,

Yagi³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

139

View full text Add to dashboard Cite

Erroneous replication of lesions in DNA by DNA polymerases leads to elevated mutagenesis. To understand the molecular basis of DNA damage-induced mutagenesis, we have determined the x-ray structures of the Y-family polymerase, Dpo4, in complex with a DNA substrate containing a bulky DNA lesion and incoming nucleotides. The DNA lesion is derived from an environmentally widespread carcinogenic polycyclic aromatic hydrocarbon, benzo[ a ]pyrene (BP). The potent carcinogen BP is metabolized to diol epoxides that form covalent adducts with cellular DNA. In the present study, the major BP diol epoxide adduct in DNA, BP- N 2 -deoxyguanosine (BP–dG), was placed at a template–primer junction. Three ternary complexes reveal replication blockage, extension past a mismatched lesion, and a −1 frameshift mutation. In the productive structures, the bulky adduct is flipped/looped out of the DNA helix into a structural gap between the little finger and core domains. Sequestering of the hydrophobic BP adduct in this new substrate-binding site permits the DNA to exhibit normal geometry for primer extension. Extrusion of the lesion by template misalignment allows the base 5′ to the adduct to serve as the template, resulting in a −1 frameshift. Subsequent strand realignment produces a mismatched base opposite the lesion. These structural observations, in combination with replication and mutagenesis data, suggest a model in which the additional substrate-binding site stabilizes the extrahelical nucleotide for lesion bypass and generation of base substitutions and −1 frameshift mutations.

show abstract

“…Y-family DNA polymerases are involved in the mutagenic bypass of BP adducts (1,3,(13)(14)(15). There are multiple Y-family DNA polymerases in cells.…”

Section: Biochemistrymentioning

confidence: 99%

A structural gap in Dpo4 supports mutagenic bypass of a major benzo[ a ]pyrene dG adduct in DNA through template misalignment

Bauer

Xing²,

Yagi³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

139

View full text Add to dashboard Cite

show abstract

“…The minor-groove lesion positioning is suggested to be relevant to other Y family DNA polymerases of the DinB branch, including the human homolog Pol κ [22]. The DinB polymerases seem to have a special role in bypassing N 2 -dG lesions [38], with higher efficiency and accuracy than other DNA polymerases in cellular [39] and in vitro environments [40,41].…”

Section: Dpo4 Produces Mismatch and Frameshift Mutations At Bp-derivementioning

confidence: 98%

Lesion processing: high-fidelity versus lesion-bypass DNA polymerases

Broyde¹,

Wang²,

Rechkoblit³

et al. 2008

Trends in Biochemical Sciences

Self Cite

View full text Add to dashboard Cite

When a high-fidelity DNA polymerase encounters certain DNA-damage sites, its progress can be stalled and one or more lesion-bypass polymerases are recruited to transit the lesion. Here, we consider two representative types of lesions: (i) 7,8-dihydro-8-oxogua-nine (8-oxoG), a small, highly prevalent lesion caused by oxidative damage; and (ii) bulky lesions derived from the environmental pre-carcinogen benzo [a]pyrene, in the high-fidelity DNA polymerase Bacillus fragment (BF) from Bacillus stearothermophilus and in the lesion-bypass DNA polymerase IV (Dpo4) from Sulfolobus solfataricus. The tight fit of the BF polymerase around the nascent base pair contrasts with the more spacious, solvent-exposed active site of Dpo4, and these differences in architecture result in distinctions in their respective functions: one-step versus stepwise polymerase translocation, mutagenic versus accurate bypass of 8-oxoG, and polymerase stalling versus mutagenic bypass at bulky benzo[a]pyrene-derived lesions. Lesions and DNA polymerasesUntil 1999, it was widely understood that bacteria have three DNA polymerases and mammals have five [1]. In 1999, however, an entirely new category of polymerases was discovered in prokaryotes and eukaryotes [2-4] -the lesion-bypass DNA polymerases. The function of lesion-bypass polymerases is to replicate past lesion-containing DNA templates in a process called translesion synthesis [5][6][7]. Now at least 16 DNA polymerases are known in eukaryotes [8] and five in bacteria [9]. Furthermore, since 1999, crystal structures of DNA polymerases, including those containing lesions, have provided new structural insights into the mechanistic aspects of translesion synthesis and polymerase stalling associated with DNA lesions. For a review of the structures and mechanisms of DNA polymerases up to the year 2005, see Ref.[10].Here, we discuss the structural and functional features of representative high-fidelity and lesion-bypass DNA polymerases (Box 1) and how these features affect the processing of certain forms of DNA damage. The lesions considered are derived from reactions of intermediates produced by endogenous sources or from the metabolic activation of environmental genotoxic

show abstract

“…Such bypass DNA synthesis sometimes occurs with insertion of a base complementary to the adducted base, but in many cases synthesis is with an incorrect base leading to a mutation. For example, Pol was accurate in bypassing a B[a]P DE-dG adduct (51,52), but Pol was error-prone (47,53). A crystal structure of Pol with unadducted DNA showed the templating base in a synconformation with Hoogsteen base pairing to the incoming dNTP (54).…”

Section: Discussionmentioning

confidence: 99%

Structure of DNA polymerase β with a benzo[ c ]phenanthrene diol epoxide-adducted template exhibits mutagenic features

Batra

Shock

Prasad

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

We have determined the crystal structure of the human base excision repair enzyme DNA polymerase ␤ (Pol ␤) in complex with a 1-nt gapped DNA substrate containing a template N 2 -guanine adduct of the tumorigenic (؊)-benzo[c]phenanthrene 4R,3S-diol 2S,1R-epoxide in the gap. Nucleotide insertion opposite this adduct favors incorrect purine nucleotides over the correct dCMP and hence can be mutagenic. The structure reveals that the phenanthrene ring system is stacked with the base pair immediately 3 to the modified guanine, thereby occluding the normal binding site for the correct incoming nucleoside triphosphate. The modified guanine base is displaced downstream and prevents the polymerase from achieving the catalytically competent closed conformation. The incoming nucleotide binding pocket is distorted, and the adducted deoxyguanosine is in a syn conformation, exposing its Hoogsteen edge, which can hydrogen-bond with dATP or dGTP. In a reconstituted base excision repair system, repair of a deaminated cytosine (i.e., uracil) opposite the adducted guanine was dramatically decreased at the Pol ␤ insertion step, but not blocked. The efficiency of gap-filling dCMP insertion opposite the adduct was diminished by >6 orders of magnitude compared with an unadducted templating guanine. In contrast, significant misinsertion of purine nucleotides (but not dTMP) opposite the adducted guanine was observed. Pol ␤ also misinserts a purine nucleotide opposite the adduct with ungapped DNA and exhibits limited bypass DNA synthesis. These results indicate that Pol ␤-dependent base excision repair of uracil opposite, or replication through, this bulky DNA adduct can be mutagenic.DNA adduct ͉ DNA repair ͉ fidelity ͉ mutagenesis P olycyclic aromatic hydrocarbons (PAHs) such as benzo- , and the adduct derived from trans-opening of the epoxide ring by the exocyclic 2-amino group of guanine in DNA, which is the subject of the present investigation.Bulky PAH-derived lesions can persist in human tissues when cellular repair enzymes fail to correct these lesions (13). The presence of these lesions in the genome blocks replicative DNA polymerases. If these lesions are not repaired, they must be bypassed for replication to continue. Bypass DNA synthesis occurs when a translesional DNA polymerase is recruited to the site of DNA damage and inserts a nucleotide opposite the adduct. DNA synthesis can be error-free or error-prone. The resulting base pair is then extended by either the same DNA polymerase or an auxiliary polymerase. Because replication of these adducts is known to result in mutations (14-16), mutagenic bypass provides a mechanism for adduct-induced tumor initiation and progression.Several DNA repair mechanisms protect cells from the deleterious effects of DNA lesions. For example, bulky DNA adducts such as PAH adducts and the formamidopyrimidine adduct of aflatoxin are primarily repaired by nucleotide excision repair (17, 18), although some unstable B[a]P DE adducts might promote depurination and elicit the base excision repair (BER...

show abstract

trans-Lesion Synthesis Past Bulky Benzo[a]pyrene Diol Epoxide N2-dG and N6-dA Lesions Catalyzed by DNA Bypass Polymerases

Cited by 186 publications

References 66 publications

A structural gap in Dpo4 supports mutagenic bypass of a major benzo[ a ]pyrene dG adduct in DNA through template misalignment

A structural gap in Dpo4 supports mutagenic bypass of a major benzo[ a ]pyrene dG adduct in DNA through template misalignment

Lesion processing: high-fidelity versus lesion-bypass DNA polymerases

Structure of DNA polymerase β with a benzo[ c ]phenanthrene diol epoxide-adducted template exhibits mutagenic features

Contact Info

Product

Resources

About