Replication Inhibition and Miscoding Properties of DNA Templates Containing a Site-Specific <i>cis</i>-Thymine Glycol or Urea Residue

McNulty, John; Jerkovic, Bozidar; Bolton, Philip H.; Basu, Ashis K.

doi:10.1021/tx970225w

Cited by 84 publications

(78 citation statements)

References 41 publications

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“…Experiments with Klenow fragment suggest that the extension step of TLS is ratelimiting for Gh (35,58,59), Ua (60), and NI (61). Thus, it is possible that the requirement of pol V for bypass of these lesions reflects significant participation in extension rather than insertion.…”

Section: Discussionmentioning

confidence: 99%

DNA Polymerase V Allows Bypass of Toxic Guanine Oxidation Products in Vivo

Neeley

Delaney

Alekseyev

et al. 2007

Journal of Biological Chemistry

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Reactive oxygen and nitrogen radicals produced during metabolic processes, such as respiration and inflammation, combine with DNA to form many lesions primarily at guanine sites. Understanding the roles of the polymerases responsible for the processing of these products to mutations could illuminate molecular mechanisms that correlate oxidative stress with cancer. Using M13 viral genomes engineered to contain single DNA lesions and Escherichia coli strains with specific polymerase (pol) knockouts, we show that pol V is required for efficient bypass of structurally diverse, highly mutagenic guanine oxidation products in vivo. We also find that pol IV participates in the bypass of two spiroiminodihydantoin lesions. Furthermore, we report that one lesion, 5-guanidino-4-nitroimidazole, is a substrate for multiple SOS polymerases, whereby pol II is necessary for error-free replication and pol V for error-prone replication past this lesion. The results spotlight a major role for pol V and minor roles for pol II and pol IV in the mechanism of guanine oxidation mutagenesis.The genome is continually damaged by spontaneously generated and environmental chemical agents. Many of the lesions formed in DNA strongly inhibit replicative polymerases. If repair of these lesions fails or is not fast enough, cells can biochemically adapt to "tolerate" the toxic DNA lesions, as evidenced by replication of the damaged DNA (1). Human cells possess at least 15 DNA polymerases, including 5 that are referred to as translesion synthesis (TLS) 3 polymerases and are specifically involved in the replication of damaged DNA. Four of these enzymes, pol , pol , pol , and REV1, belong to the Y family of DNA polymerases, whereas pol belongs to the B family (2). Escherichia coli possess three polymerases, pol II, pol IV, and pol V, whose expression levels are up-regulated in response to DNA damage. Extensive research on the structure and function of these polymerases and their homologues suggests that these polymerases allow replication to progress in the presence of DNA lesions that are strongly inhibitory to the replicative polymerase, pol III (1). The presence of the three SOSinducible polymerases allows E. coli to be used as a model system for DNA replication past damage products.pol II (pol B) (3) is a B family DNA polymerase and has 3Ј 3 5Ј-exonuclease activity. Consequently, this enzyme replicates normal DNA with high fidelity and has an error rate less of than 10 Ϫ6 (4). pol II participates in error-free replication restart (5, 6) and can also carry out TLS past abasic sites (3, 7), 3,N 4 -ethenocytosine (8), and N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (9). pol IV (DinB) (10) and pol V (UmuD 2 ЈC) (11) are members of the Y family of DNA polymerases, which have less sterically restrictive active sites than normal replicative polymerases (12) and lack exonuclease activity (1). The error rates of these polymerases are much higher than the other E. coli polymerases and are on the order of 10 Ϫ4 to 10 Ϫ5 for pol IV (13) and 10 Ϫ3 to 10 Ϫ4...

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Section: Discussionmentioning

confidence: 99%

DNA Polymerase V Allows Bypass of Toxic Guanine Oxidation Products in Vivo

Neeley

Delaney

Alekseyev

et al. 2007

Journal of Biological Chemistry

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“…5-Hydroxy-dC also deaminates to 5-hydroxy-deoxy-uracil, which codes as T. This provides an additional mechanism for the induction of C→T transitions. Thymidine glycol causes T→C mutations in vivo (30,31).…”

Section: Hydroxyl Radical-mediated Dna Damagementioning

confidence: 99%

Endogenous generation of reactive oxidants and electrophiles and their reactions with DNA and protein

Marnett¹,

Riggins²,

West³

2003

J. Clin. Invest.

392

281

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“…Because of the addition of hydroxyl groups at C5 and C6 in a Tg, the damaged base loses its aromatic character and becomes nonplanar (8)(9)(10). As a consequence, the C5 methyl group protrudes in an axial direction that prevents the base 5′ to the Tg lesion from stacking above it.…”

mentioning

confidence: 99%

Error-free replicative bypass of thymine glycol by the combined action of DNA polymerases κ and ζ in human cells

Yoon

Bhatia

Prakash

et al. 2010

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

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Thymine glycol (Tg) is the most common DNA lesion of thymine induced by interaction with reactive oxygen species. Because of the addition of hydroxyl groups at C5 and C6 in a Tg lesion, the damaged base loses its aromatic character and becomes nonplanar; consequently, the C5 methyl group protrudes in an axial direction and that prevents the stacking of the 5′ base above the Tg lesion. Because Tg presents a severe block to continued synthesis by replicative DNA polymerases, we determine here how human cells manage to replicate through this lesion. Using a duplex plasmid system where bidirectional replication ensues from an origin of replication, we show that translesion synthesis (TLS) makes a prominent contribution to Tg bypass and that it occurs in a predominantly error-free fashion. Also, we provide evidence that Polκ and Polζ function together in promoting error-free replication through the lesion, and based on structural and biochemical information, we propose a role for Polκ at the insertion step and of Polζ at the extension step of Tg bypass. We discuss the implications of these observations and suggest that human cells have adapted the TLS machinery to function in a much more error-free fashion than could have been predicted from the intrinsic catalytic efficiencies and fidelities of TLS polymerases.DNA polymerases kappa and zeta | error-free bypass of thymine glycol | replicative lesion bypass | thymine glycol bypass in humans T hymine glycol (Tg) is the most common oxidation product of thymine (1-3). Hydroxyl radicals, the principal DNA damaging species formed from aerobic respiration or from exposure to chemical oxidizing agents or ionizing radiation, interact directly with thymine primarily at the 5,6 double bond, generating a thymine glycol. Although Tg lesions in humans can be removed by base excision repair (BER) involving the action of the DNA glycosylase/AP lyase NTH1 or by nucleotide excision repair (NER) (4, 5), if the damaged base is not removed by these repair processes and goes through the replication fork, that presents a severe block to continued synthesis by eukaryotic replicative DNA polymerases (Pols) (6, 7).Because of the addition of hydroxyl groups at C5 and C6 in a Tg, the damaged base loses its aromatic character and becomes nonplanar (8-10). As a consequence, the C5 methyl group protrudes in an axial direction that prevents the base 5′ to the Tg lesion from stacking above it. Hence a Tg lesion presents a block not only for nucleotide (nt) insertion opposite it but also for the subsequent extension step. Steady-state kinetic analyses of Tg bypass by human translesion (TLS) Pols have indicated that Polη can insert an A opposite Tg with the same catalytic efficiency as for insertion of an A opposite undamaged T; moreover, Polη can also extend from the Tg:A base pair with only an ∼15-fold reduction in efficiency (7). However, Polη incorporates the wrong nts opposite Tg rather frequently as the misincorporation of G or a C residue occurs with only an ∼8-, and 20-fold reduction in effici...

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Replication Inhibition and Miscoding Properties of DNA Templates Containing a Site-Specific cis-Thymine Glycol or Urea Residue

Cited by 84 publications

References 41 publications

DNA Polymerase V Allows Bypass of Toxic Guanine Oxidation Products in Vivo

DNA Polymerase V Allows Bypass of Toxic Guanine Oxidation Products in Vivo

Endogenous generation of reactive oxidants and electrophiles and their reactions with DNA and protein

Error-free replicative bypass of thymine glycol by the combined action of DNA polymerases κ and ζ in human cells

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