Exonuclease III and endonuclease IV remove 3' blocks from DNA synthesis primers in H2O2-damaged Escherichia coli.

Demple, Bruce; Johnson, Arlen; Fung, David Dang

doi:10.1073/pnas.83.20.7731

Cited by 246 publications

(163 citation statements)

References 31 publications

(24 reference statements)

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“…It is also active as a 3′ exonuclease/phosphatase and produces 3′ OH terminus at strand breaks with 3′ blocks. Another endonuclease, endonuclease IV (Nfo), was subsequently discovered in E. coli whose activities as AP site-specific endonuclease and 3′ end cleaning phosphodiesterase are very similar to that of Xth except that Nfo lacks 3′ exonuclease activity and does not require Mg 2+ for catalysis [90,91]. Subsequently APEs were characterized in a variety of organisms ranging from bacteria to yeast, C. elegans and mammals.…”

Section: Ap-endonuclease (Ape) a Ubiquitous Repair Protein With Dualmentioning

confidence: 99%

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

2008

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Base excision repair (BER) is an evolutionarily conserved process for maintaining genomic integrity by eliminating several dozen damaged (oxidized or alkylated) or inappropriate bases that are generated endogenously or induced by genotoxicants, predominantly, reactive oxygen species (ROS). BER involves 4-5 steps starting with base excision by a DNA glycosylase, followed by a common pathway usually involving an AP-endonuclease (APE) to generate 3′ OH terminus at the damage site, followed by repair synthesis with a DNA polymerase and nick sealing by a DNA ligase. This pathway is also responsible for repairing DNA single-strand breaks with blocked termini directly generated by ROS. Nearly all glycosylases, far fewer than their substrate lesions particularly for oxidized bases, have broad and overlapping substrate range, and could serve as back-up enzymes in vivo. In contrast, mammalian cells encode only one APE, APE1, unlike two APEs in lower organisms. In spite of overall similarity, BER with distinct subpathways in the mammals is more complex than in E. coli. The glycosylases form complexes with downstream proteins to carry out efficient repair via distinct subpathways one of which, responsible for repair of strand breaks with 3′ phosphate termini generated by the NEIL family glycosylases or by ROS, requires the phosphatase activity of polynucleotide kinase instead of APE1. Different complexes may utilize distinct DNA polymerases and ligases. Mammalian glycosylases have nonconserved extensions at one of the termini, dispensable for enzymatic activity but needed for interaction with other BER and non-BER proteins for complex formation and organelle targeting. The mammalian enzymes are sometimes covalently modified which may affect activity and complex formation. The focus of this review is on the early steps in mammalian BER for oxidized damage.

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Section: Ap-endonuclease (Ape) a Ubiquitous Repair Protein With Dualmentioning

confidence: 99%

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

2008

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“…While the reaction that these proteins catalyze is identical, they differ dramatically in both tertiary structure and mechanisms of catalysis (9). Whereas exonuclease III displays a fourlayered R, -sandwich fold and employs a single readily dissociatable magnesium ion (9, 10), endonuclease IV is an R 8 8 TIM barrel that utilizes three tightly bound zinc ions (9,11).In addition to their APE activities, both exonuclease III and endonuclease IV (and their respective homologues) possess an array of 3′ processing activities (within the general categories of 3′-phosphatase and 3′-phosphodiesterase) responsible for removing phosphate and ribose fragments, produced both by oxidative damage and the AP lyase activity described above, to generate polymerase-usable 3′-hydroxyl termini (7,(12)(13)(14)(15). APEs from both families are also capable of acting as 3′ f 5′ exonucleases at nicks (16,17); because this activity is most efficient for nicks containing a 3′ mismatched base pair, it is speculated to enhance the fidelity of DNA repair by providing, in trans, the proofreading activity that is typically absent in repair polymerases (16).…”

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confidence: 99%

Contributions of an Endonuclease IV Homologue to DNA Repair in the African Swine Fever Virus

Lamarche

Tsai

2006

Biochemistry

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: We recently demonstrated that African swine fever virus DNA polymerase X (Pol X) is extremely error-prone during single-nucleotide gap-filling and that the downstream ASFV DNA ligase seals 3′ mismatched nicks with high efficiency. To further assess the credence of our hypothesis that these proteins may promote viral diversification by functioning within the context of an aberrant DNA repair pathway, herein we characterize the third protein expected to function in this system, a putative AP endonuclease (APE). Assays of the purified protein using oligonucleotide substrates unequivocally establish canonical APE activity, 3′-phosphatase and 3′-phosphodiesterase activities (in the context of a singlenucleotide gap), 3′ f 5′ exonuclease activity (in the context of a nick), and nucleotide incision repair activity against 5,6-dihydrothymine. The 3′ f 5′ exonuclease activity is shown to be highly dependent upon the identity of the nascent 3′ base pair and to be inhibited when 2-deoxyribose-5-phosphate, rather than phosphate, constitutes the 5′ moiety of the nick. ASFV APE retains activity when assayed in the presence of EDTA but is inactivated by incubation with 1,10-phenanthroline in the absence of a substrate, suggesting that it is an endonuclease IV homologue possessing intrinsic metal cofactors. The activities of ASFV APE, when considered alongside those of Pol X and ASFV DNA ligase, provide an enhanced understanding of (i) the types of damage that are likely to be sustained by the viral genome and (ii) the mechanisms by which the minimalist ASFV DNA repair pathway, consisting of just these three proteins, contributes to the fitness of the virus.Apurinic/apyrimidinic (AP) 1 sites, generated either by DNA glycosylase-mediated or spontaneous base loss, can be both mutagenic (1, 2) and cytotoxic (3) and are among the most abundant types of damage found in DNA (4). Although they can be processed by AP lyases, which cleave 3′ to the lesion by a -elimination mechanism to generate a single-nucleotide gap flanked by 5′-phosphate and a 3′-polymerase-blocking R, -unsaturated aldehyde (5-7), AP sites are likely to be processed predominantly by AP endonucleases (8), which catalyze hydrolysis of the sugarphosphate backbone 5′ of the lesion to generate a singlenucleotide gap flanked by a polymerase-usable 3′-hydroxyl and 5′-2-deoxyribose-5-phosphate (5′-dRP) (7). Two families of APEs have been identified to date; these consist of proteins with homology to Escherichia coli exonuclease III 2 and proteins with homology to E. coli endonuclease IV. While the reaction that these proteins catalyze is identical, they differ dramatically in both tertiary structure and mechanisms of catalysis (9). Whereas exonuclease III displays a fourlayered R, -sandwich fold and employs a single readily dissociatable magnesium ion (9, 10), endonuclease IV is an R 8 8 TIM barrel that utilizes three tightly bound zinc ions (9,11).In addition to their APE activities, both exonuclease III and endonuclease IV (and their respective homologues) pos...

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“…The ability of NL1Tc to repair 3Ј-terminal damage in DNA has also been demonstrated using two distinct activity assays similar to those reported for AP repair enzymes (13,14): a 3Ј-phosphodiesterase assay that directly measures the removal of terminal phosphoglycolate and a 3Ј-phosphatase assay that directly measures the removal of terminal phosphate. It has been demonstrated that 3Ј-phosphatase and 3Ј-phosphodiesterase activities are essential for the repair of the oxidative damage that causes 3Ј-blocking ends (11). The results obtained showed that NL1Tc efficiently repairs oxidative damage that includes 3Ј-phosphatase-blocked termini but only a small amount of the damage that includes 3Ј-phosphoglycolate-blocked termini.…”

Section: Discussionmentioning

confidence: 57%

“…The 3Ј-phosphatase and 3Ј-phosphodiesterase activities have been described to contribute to the repair of oxidative DNA damage (11). In the present paper we have analyzed whether those enzymatic activities are present in the recombinant protein NL1Tc.…”

mentioning

confidence: 99%

The L1Tc, Long Interspersed Nucleotide Element from Trypanosoma cruzi, Encodes a Protein with 3′-Phosphatase and 3′-Phosphodiesterase Enzymatic Activities

Olivares

Thomas

Alonso

et al. 1999

Journal of Biological Chemistry

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The presence of a long interspersed nucleotide element, named L1Tc, which is actively transcribed in the parasite Trypanosoma cruzi, has been recently described. The open reading frame 1 of this element encodes the NL1Tc protein, which has apurinic/apyrimidinic endonuclease activity and is probably implicated in the first stage of the transposition of the element. In the present paper we show that NL1Tc effectively removes 3 -blocking groups (3 -phosphate and 3 -phosphoglycolate) from damaged DNA substrates. Thus, both 3 -phosphatase and 3 -phosphodiesterase activities are present in NL1Tc. We propose that these enzymatic activities would allow the 3 -blocking ends to function as targets for the insertion of L1Tc element, in addition to the apurinic/apyrimidinic sites previously described. The potential biological function of the NL1Tc protein has also been evidenced by its ability to repair the DNA damage induced by the methyl methanesulfonate alkylating or oxidative agents such as hydrogen peroxide and t-butyl hydroperoxide in Escherichia coli (xth and xth, nfo) mutants.

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Exonuclease III and endonuclease IV remove 3' blocks from DNA synthesis primers in H2O2-damaged Escherichia coli.

Abstract: Escherichia coli deficient in exonuclease III (xth gene mutants) are known to be hypersensitive to hydrogen peroxide. We now show that such mutants accumulate many more DNA single-strand breaks than do wild-type bacteria upon exposure to H202.

Cited by 246 publications

References 31 publications

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

Contributions of an Endonuclease IV Homologue to DNA Repair in the African Swine Fever Virus

The L1Tc, Long Interspersed Nucleotide Element from Trypanosoma cruzi, Encodes a Protein with 3′-Phosphatase and 3′-Phosphodiesterase Enzymatic Activities

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