Evidence for the Involvement of Nucleotide Excision Repair in the Removal of Abasic Sites in Yeast

Torres‐Ramos, Carlos A.; Johnson, Robert E.; Prakash, Louise; Prakash, Satya

doi:10.1128/mcb.20.10.3522-3528.2000

Cited by 77 publications

(62 citation statements)

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“…Because spontaneous depurination of 7meG would lead to the formation of abasic sites, we presume that the increase in the can1 r mutation frequency obtained in MMS-treated wild-type cells results from the mutagenic TLS that occurs opposite the abasic sites that happened to have escaped repair by the action of AP endonucleases or by nucleotide excision repair (46). In fact, the frequency of MMS-induced can1 r mutations rises greatly in the apn1⌬ apn2⌬ strain, which lacks both the AP endonucleases, and it rises even further in the apn1⌬ apn2⌬ rad14⌬ strain, which additionally lacks the nucleotide excision repair pathway (46). Also, since the elevated incidence of MMS-induced can1 r mutations in the apn1⌬ apn2⌬ strain is not affected by the rad30⌬ mutation, Pol does not contribute to TLS through the abasic sites in any significant way (8).…”

Section: Resultsmentioning

confidence: 99%

A Role for Yeast and Human Translesion Synthesis DNA Polymerases in Promoting Replication through 3-Methyl Adenine

Johnson

Prakash

et al. 2007

Molecular and Cellular Biology

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3-Methyl adenine (3meA), a minor-groove DNA lesion, presents a strong block to synthesis by replicative DNA polymerases (Pols). To elucidate the means by which replication through this DNA lesion is mediated in eukaryotic cells, here we carry out genetic studies in the yeast Saccharomyces cerevisiae treated with the alkylating agent methyl methanesulfonate. From the studies presented here, we infer that replication through the 3meA lesion in yeast cells can be mediated by the action of three Rad6-Rad18-dependent pathways that include translesion synthesis (TLS) by Pol or -and an Mms2-Ubc13-Rad5-dependent pathway which presumably operates via template switching. We also express human Pols and in yeast cells and show that they too can mediate replication through the 3meA lesion in yeast cells, indicating a high degree of evolutionary conservation of the mechanisms that control TLS in yeast and human cells. We discuss these results in the context of previous observations that have been made for the roles of Pols , , and in promoting replication through the minor-groove N 2 -dG adducts.Replicative DNA polymerase (Pols) are highly sensitive to geometric distortions in DNA; consequently, they are inhibited by the presence of DNA lesions in the template strand. A number of Pols that promote replication through DNA lesions exist in eukaryotes, and they are highly specialized for the roles they play in translesion synthesis (TLS) (40). For example, both yeast and human Pols are highly adept at promoting error-free replication through UV-induced cyclobutane pyrimidine dimers (CPDs) (15,20,50,52), and inactivation of Pol in humans causes the cancer-prone syndrome of the variant form of xeroderma pigmentosum (14,30).Although proficient replication through a DNA lesion such as a CPD can be accomplished by Pol alone, replication through many of the different lesions present in DNA requires the sequential action of two Pols, in which one polymerase inserts the nucleotide opposite the DNA lesion and another polymerase performs the subsequent extension reaction (40,41). Yeast Pol, comprised of the Rev3 catalytic and Rev7 accessory subunits (39), is highly specialized for performing the extension step of TLS (8,19,21,35). Although humans also have the Rev3 and Rev7 proteins, there is no biochemical information available on the role of human Pol in TLS.In addition to Pol, humans have Pols and , which belong to the Y family of Pols (40). Pol differs strikingly from Pols and and almost all other Pols in that it incorporates nucleotides opposite template purines with much higher efficiency and fidelity than opposite template pyrimidines (6,19,44,49). Moreover, even opposite template purines, Pol exhibits higher catalytic efficiency and fidelity opposite template A than opposite template G. The ternary crystal structures of Pol bound to template A or G and the correct incoming deoxynucleoside triphosphate have shown that the purine template adopts a syn conformation in the Pol active site and forms a Hoogsteen base pair with the incom...

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Section: Resultsmentioning

confidence: 99%

A Role for Yeast and Human Translesion Synthesis DNA Polymerases in Promoting Replication through 3-Methyl Adenine

Johnson

Prakash

et al. 2007

Molecular and Cellular Biology

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“…Synergism between NER and BER in the protection of alkylation damage has been observed in budding yeast (Xiao and Chow, 1998;Torres-Ramos et al, 2000) and mammalian cells (Plosky et al, 2002;Sitaram et al, 1997), even though the 3-meA DNA glycosylase-initiated BER plays a major role in the repair of MMS in these organisms. 3-meA and 7-meG were removed without strand bias from active genes of 3-meA DNA glycosylasedeficient mouse cells (Plosky et al, 2002).…”

Section: Discussionmentioning

confidence: 99%

Fission yeast homologs of human XPC and CSB, rhp41 and rhp26, are involved in transcription-coupled repair of methyl methanesulfonate-induced DNA damage

Kanamitsu

Ikeda

2011

Genes Genet. Syst.

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Methyl methanesulfonate (MMS) methylates nitrogen atoms in purines, and predominantly produces 7-methylguanine and 3-methyladenine (3-meA). Previously, we showed that base excision repair (BER) and nucleotide excision repair (NER) synergistically function to repair MMS-induced DNA damage in the fission yeast Schizosaccharomyces pombe. Here, we studied the roles of NER components in repair of 3-meA and BER intermediates such as the AP site and single strand breaks. Mutants of rhp41 (XPC homolog) and rhp26 (CSB homolog) exhibited moderate sensitivity to MMS. Transcription of the fbp1 gene, which is induced by glucose starvation, was strongly inhibited by MMS damage in rhp41Δ and rhp26Δ strains but not in wild type and 3-meA DNA glycosylase-deficient cells. The results indicate that Rhp41p and Rhp26p are involved in transcriptioncoupled repair (TCR) of MMS-induced DNA damage. In the BER pathway of S. pombe, AP lyase activity of Nth1p mainly incises the AP site to generate a 3′-blocked end, which is in turn converted to 3′-OH by Apn2p. Deletion of rad16 or rhp26 in the nth1Δ strain greatly enhanced MMS sensitivity, suggesting that the AP site could also be corrected by TCR. Double mutant apn2Δ/rad16Δ exhibited hypersensitivity to MMS, implying that Rad16p provides a backup pathway for removal of the 3′-blocked end. Moreover, an rhp51Δ strain was extremely sensitive to MMS and double mutants of nth1Δ/rhp51Δ and apn2Δ/rhp51Δ increased the sensitivity, suggesting that homologous recombination is necessary for repair of three different types of lesions, 3-meA, AP sites and 3′-blocked ends.

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“…However, there is some evidence that in mammalian and yeast cells, NER can be involved partially in the repair of oxidative damage (Reardon et al, 1997;Torres-Ramos et al, 2000). It was shown that 8-oxoG can be repaired efficiently by a human cell extract, and some NER-deficient mutants exhibit deficiency in this repair.…”

Section: In Vitro Repair Synthesis Assay Monitors Ner and Ber Efficiementioning

confidence: 99%

Repair of Damaged DNA by Arabidopsis Cell Extract

Li¹,

Schuermann

Gallego³

et al. 2002

Plant Cell

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All living organisms have to protect the integrity of their genomes from a wide range of genotoxic stresses to which they are inevitably exposed. However, understanding of DNA repair in plants lags far behind such knowledge in bacteria, yeast, and mammals, partially as a result of the absence of efficient in vitro systems. Here, we report the experimental setup for an Arabidopsis in vitro repair synthesis assay. The repair of plasmid DNA treated with three different DNA-damaging agents, UV light, cisplatin, and methylene blue, after incubation with whole-cell extract was monitored. To validate the reliability of our assay, we analyzed the repair proficiency of plants depleted in AtRAD1 activity. The reduced repair of UV light-and cisplatin-damaged DNA confirmed the deficiency of these plants in nucleotide excision repair. Decreased repair of methylene blue-induced oxidative lesions, which are believed to be processed by the base excision repair machinery in mammalian cells, may indicate a possible involvement of AtRAD1 in the repair of oxidative damage. Differences in sensitivity to DNA polymerase inhibitors (aphidicolin and dideoxy TTP) between plant and human cell extracts were observed with this assay. INTRODUCTIONThe genomes of all living organisms are constantly subjected to a wide range of genotoxic stresses induced by environmental factors (e.g., UV-B irradiation, bacterial and fungal toxins) as well as by the intermediate products of normal cellular metabolism (e.g., alkylating and oxidizing agents). These can lead to the formation of different types of DNA damage, the persistence of which can block DNA replication and transcription or cause cell cycle arrest and apoptosis (Britt, 1999;Lindahl and Wood, 1999). Incorrect repair can result in heritable point mutations or gross rearrangements such as deletions and insertions. To keep the integrity of their genomes, all organisms have evolved protective mechanisms of repair of a broad variety of DNA lesions. According to the mode of action, the substrate specificity, and the size of the excised DNA fragment, these pathways generally have been classified as direct repair, base excision repair (BER), nucleotide excision repair (NER), and mismatch repair (reviewed by Friedberg, 1996;Sancar, 1996;Wood, 1996;Lindahl and Wood, 1999). These mechanisms were first described in bacteria and later characterized extensively in yeast and mammals (Sancar, 1996;Laat et al., 1999;Le Page et al., 2000;Memisoglu and Samson, 2000). Unfortunately, with the exception of light-dependent reversion of UV light-induced pyrimidine dimers by photolyases, very little is known about DNA repair pathways in plants (reviewed by Vonarx et al., 1998; Britt, 1999).To study different types of DNA repair mechanisms in vitro, the formation of pathway-specific DNA lesions is required. For the study of NER, we chose the following DNAdamaging agents: UV-C and cis -diamminedichloroplatinum II (cisplatin). Additionally, methylene blue-treated DNA was used to distinguish the relative contributions of ...

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Evidence for the Involvement of Nucleotide Excision Repair in the Removal of Abasic Sites in Yeast

Cited by 77 publications

References 46 publications

A Role for Yeast and Human Translesion Synthesis DNA Polymerases in Promoting Replication through 3-Methyl Adenine

A Role for Yeast and Human Translesion Synthesis DNA Polymerases in Promoting Replication through 3-Methyl Adenine

Fission yeast homologs of human XPC and CSB, rhp41 and rhp26, are involved in transcription-coupled repair of methyl methanesulfonate-induced DNA damage

Repair of Damaged DNA by Arabidopsis Cell Extract

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