Prereplicative repair of oxidized bases in the human genome is mediated by NEIL1 DNA glycosylase together with replication proteins

Base oxidation by endogenous and environmentally induced reactive oxygen species preferentially occurs in replicating single-stranded templates in mammalian genomes, warranting prereplicative repair of the mutagenic base lesions. It is not clear how such lesions (which, unlike bulky adducts, do not block replication) are recognized for repair. Furthermore, strand breaks caused by base excision from ssDNA by DNA glycosylases, including Nei-like (NEIL) 1, would generate double-strand breaks during replication, which are not experimentally observed. NEIL1, whose deficiency causes a mutator phenotype and is activated during the S phase, is present in the DNA replication complex isolated from human cells, with enhanced association with DNA in S-phase cells and colocalization with replication foci containing DNA replication proteins. Furthermore, NEIL1 binds to 5-hydroxyuracil, the oxidative deamination product of C, in replication protein A-coated ssDNA template and inhibits DNA synthesis by DNA polymerase δ. We postulate that, upon encountering an oxidized base during replication, NEIL1 initiates prereplicative repair by acting as a “cowcatcher” and preventing nascent chain growth. Regression of the stalled replication fork, possibly mediated by annealing helicases, then allows lesion repair in the reannealed duplex. This model is supported by our observations that NEIL1, whose deficiency slows nascent chain growth in oxidatively stressed cells, is stimulated by replication proteins in vitro. Furthermore, deficiency of the closely related NEIL2 alone does not affect chain elongation, but combined NEIL1/2 deficiency further inhibits DNA replication. These results support a mechanism of NEIL1-mediated prereplicative repair of oxidized bases in the replicating strand, with NEIL2 providing a backup function.Several dozen oxidatively modified, and mostly mutagenic, bases are induced in the genomes of aerobic organisms by endogenous and environmentally induced reactive oxygen species (ROS) (1, 2). For example, 5-hydroxyuracil (5-OHU), a predominant lesion generated by oxidative deamination of C, is mutagenic because of its mispairing with A (3). The bases in the single-stranded (ss) replicating DNA template are particularly prone to oxidation (4); the lack of their repair before replication could fix the mutations. The bulky base adducts if formed in the template strand would block replication and trigger DNA damage-response signaling. In contrast, oxidized bases with minor modifications, which are continuously formed in much higher abundance than the bulky adducts, would mostly allow replication. This raises the question of how these bases are marked for repair before replication to avoid mutagenic consequences. Oxidized base repair in mammalian genomes occurs primarily via the base excision repair (BER) pathway which is initiated with lesion base excision mediated by one of five major DNA glycosylases belonging to the Nth or Nei families, with distinct structural features and reaction mechanisms (1). Nei-like (NEIL) 1 and NEIL2 DNA glycosylases (5, 6) of the Nei family (which also contains the less characterized NEIL3; ref. 7) are distinct from NTH1 and OGG1 of the Nth family because the NEILs can excise damaged bases from ssDNA substrates (8). Furthermore, NEIL1 is activated during the S phase (5). Our earlier studies also showed that NEIL1 functionally interacts with many DNA replication proteins including sliding clamp proliferating cell nuclear antigen (PCNA), flap endonuclease 1 (FEN-1), and Werner RecQ helicase (WRN) via its disordered C-terminal segment (9–12). Importantly, mammalian ssDNA-binding replication protein A (RPA), essential for DNA replication and most other DNA transactions, inhibits NEIL1 or NEIL2 activity with primer-template DNA substrates mimicking the replication fork, presumably to prevent double-strand break formation (13). Although they collectively implicate NEIL1 in the repair of replicating DNA, those observations did not provide direct evidence for NEIL1’s role in prereplicative repair, nor did they address whether NEIL1 is unique for this function. In this report, we document that NEIL1 binds to the lesion base in an RPA-coated ssDNA template in vitro, without excising the lesion and cleaving the DNA strand, and blocks primer elongation by the replicative DNA polymerase δ (Polδ). This strongly suggests that the replication complex at the lesion site is stalled in vivo in the presence of NEIL1, which provides the signal for repair of lesions in the template strand before replication.     

Differential modulation of chemosensitivity to alkylating agents and platinum compounds by DNA repair modulators in human lung cancer cell lines

Purpose: Modulation of DNA repair represents one strategy to overcome cellular drug resistance to alkylating agents and platinum compounds. The effects of different known DNA repair modulators such as O ⁶-benzylguanine (6 μg/ml), fludarabine (25 ng/ml), aphidicolin (8.5 ng/ml), pentoxifylline (1.4 μg/ml) and methoxamine (12.4 μg/ml) on the cytotoxicity of mafosfamide, chlorambucil, 1,3-bis-(2-chloroethyl)-1-nitrosourea (BCNU), cisplatin and carboplatin were tested in human lung cancer cell lines. Methods: Chemosensitivity of the human adenocarcinoma cell line MOR/P and the cisplatin-resistant subline MOR/CPR as well as the large-cell lung cancer cell line L23/P and its cisplatin-resistant counterpart L23/CPR were evaluated by the MTT colorimetric assay. Results: O ⁶-benzylguanine, an inhibitor of O ⁶-alkylguanine-DNA alkyltransferase, significantly sensitised MOR/P and MOR/CPR cells to the cytotoxic effect of BCNU. Fludarabine, methoxamine and aphidicolin did not change the chemosensitivity of the parental and cisplatin-resistant cell lines to any cytotoxic drug tested. Interestingly, O ⁶-benzylguanine enhanced the chemoresistance of parental and cisplatin-resistant cell lines to platinum compounds. Also, pentoxifylline increased resistance of the MOR cell lines to mafosfamide. Conclusions: Modulation of DNA repair elicits not only chemosensitisation but may also enhance cellular resistance to DNA-affine drugs. Received: 17 August 1999 / Accepted: 19 November 1999     

DNA修复相关蛋白与肺癌顺铂耐药的关系

目的研究DNA修复相关蛋白ERCC1、BRCA1和hMLH1与肺癌顺铂耐药的关系。方法应用免疫组化链霉素抗生物素蛋白——过氧化物酶连接法检测60例肺癌组织中ERCC1、BRCA1和hMLH1蛋白的表达,分析其与临床病理特征和顺铂耐药的关系及3种DNA修复蛋白的相关性。结果60例肺癌组织ERCC1、BRCA1、hMLH1蛋白的阳性表达率分别为30％、25％、68．3％。顺铂化疗耐药组ERCC1、BRCA1蛋白阳性表达率明显高于化疗敏感组（P〈0．05）。BRCA1和hMLH1蛋白的表达具有相关性（P〈0．05）。结论ERCC1、BRCA1蛋白的表达与肺癌顺铂耐药有关,可能成为预测肺癌顺铂敏感性的指标。     

Single-molecule imaging reveals the mechanism of Exo1 regulation by single-stranded DNA binding proteins

Exonuclease 1 (Exo1) is a 5′→3′ exonuclease and 5′-flap endonuclease that plays a critical role in multiple eukaryotic DNA repair pathways. Exo1 processing at DNA nicks and double-strand breaks creates long stretches of single-stranded DNA, which are rapidly bound by replication protein A (RPA) and other single-stranded DNA binding proteins (SSBs). Here, we use single-molecule fluorescence imaging and quantitative cell biology approaches to reveal the interplay between Exo1 and SSBs. Both human and yeast Exo1 are processive nucleases on their own. RPA rapidly strips Exo1 from DNA, and this activity is dependent on at least three RPA-encoded single-stranded DNA binding domains. Furthermore, we show that ablation of RPA in human cells increases Exo1 recruitment to damage sites. In contrast, the sensor of single-stranded DNA complex 1—a recently identified human SSB that promotes DNA resection during homologous recombination—supports processive resection by Exo1. Although RPA rapidly turns over Exo1, multiple cycles of nuclease rebinding at the same DNA site can still support limited DNA processing. These results reveal the role of single-stranded DNA binding proteins in controlling Exo1-catalyzed resection with implications for how Exo1 is regulated during DNA repair in eukaryotic cells.All DNA maintenance processes require nucleases, which enzymatically cleave the phosphodiester bonds in nucleic acids. Exo1, a member of the Rad2 family of nucleases, participates in DNA mismatch repair (MMR), double-strand break (DSB) repair, nucleotide excision repair (NER), and telomere maintenance (1–3). Exo1 is the only nuclease implicated in MMR, where its 5ʹ to 3ʹ exonuclease activity is used to remove long tracts of mismatch-containing single-stranded DNA (ssDNA) (2, 4–7). In addition, functionally deficient Exo1 variants have been identified in familial colorectal cancers, and Exo1-null mice exhibit a significant increase in tumor development, decreased lifespan, and sterility (8, 9). Exo1 also promotes DSB repair via homologous recombination (HR) by processing the free DNA ends to generate kilobase-length ssDNA resection products (1, 10–12). The resulting ssDNA is paired with a homologous DNA sequence located on a sister chromatid, and the missing genetic information is then restored via DNA synthesis. The central role of Exo1 in DNA repair is highlighted by the large set of genetic interactions between Exo1 and nearly all other DNA maintenance and metabolism pathways (13).Exo1 generates long tracts of ssDNA in both MMR and DSB repair (3). This ssDNA is rapidly bound by replication protein A (RPA), a ubiquitous heterotrimeric protein that participates in all DNA transactions that generate ssDNA intermediates (14). RPA protects the ssDNA from degradation, participates in DNA damage response signaling, and acts as a loading platform for downstream DSB repair proteins (15–17). RPA also coordinates DNA resection by removing secondary ssDNA structures and by modulating the Bloom syndrome, RecQ helicase-like (BLM)/DNA2- and Exo1-dependent DNA resection pathways (18–21). Reconstitution of both the yeast and human BLM (Sgs1 in yeast)/DNA2-dependent resection reactions established that RPA stimulates DNA unwinding by BLM/Sgs1 and enforces a 5′-endonuclease polarity on DNA2 (20, 22). However, the effect of RPA on Exo1 remains unresolved. Independent studies using reconstituted yeast proteins reported that RPA could both inhibit (23) and stimulate yeast Exo1 (yExo1) (18). Similarly, human RPA has variously been reported to stimulate (19) or inhibit human Exo1 (hExo1) (4, 5, 21).In addition to RPA, human cells also encode SOSS1, a heterotrimeric ssDNA-binding complex that is essential for HR (24). SOSS1 consists of INTS3 (SOSSA), hSSB1 (SOSSB1), and C9orf80 (SOSSC) (24–26). SOSSB1 encodes a single ssDNA-binding domain that bears structural homology to Escherichia coli ssDNA-binding protein (SSB) (24). SOSS1 foci form rapidly after induction of DNA breaks, and ablation of SOSS1 severely reduces DNA resection, γH2AX foci formation, and HR at both ionizing radiation- and restriction endonuclease-induced DSBs (12, 24, 25, 27). In vitro, SOSS1 stimulates hExo1-mediated DNA resection and may help to load hExo1 at ss/dsDNA junctions (21). However, the functional relationship between SOSS1 and RPA during hExo1 resection remains unresolved.Here, we use high-throughput single-molecule DNA curtains and quantitative cell biology to reveal the interplay between human and yeast Exo1 and SSBs during DNA resection. We show that both human and yeast Exo1s are processive nucleases, but are rapidly stripped from DNA by RPA. RPA inhibition is dependent on its multiple DNA binding domains. Remarkably, SOSS1 and other SSBs with fewer than three DNA binding domains support long-range resection by hExo1. In human cells, depletion of RPA increases the rate of hExo1 recruitment to laser-induced DNA damage but reduces the extent of resection. In the presence of RPA, both human and yeast Exo1 can resect DNA using a distributive, multiple-turnover mechanism, potentially reconciling prior conflicting in vitro observations. Together, our work reveals the mechanistic basis for how RPA and SOSS1 differentially modulate hExo1 activity and highlights an additional, unexpected role for these SSBs in DNA resection. We anticipate that these findings will shed light on how Exo1 is regulated in multiple genome maintenance pathways.     

DNA repair by the cryptic endonuclease activity of Mu transposase

Phage Mu transposes by two distinct pathways depending on the specific stage of its life cycle. A common θ strand transfer intermediate is resolved differentially in the two pathways. During lytic growth, the θ intermediate is resolved by replication of Mu initiated within the flanking target DNA; during integration of infecting Mu, it is resolved without replication, by removal and repair of DNA from a previous host that is still attached to the ends of the incoming Mu genome. We have discovered that the cryptic endonuclease activity reported for the isolated C-terminal domain of the transposase MuA [Wu Z, Chaconas G (1995) A novel DNA binding and nuclease activity in domain III of Mu transposase: Evidence for a catalytic region involved in donor cleavage. EMBO J 14:3835–3843], which is not observed in the full-length protein or in the assembled transpososome in vitro, is required in vivo for removal of the attached host DNA or “5′flap” after the infecting Mu genome has integrated into the E. coli chromosome. Efficient flap removal also requires the host protein ClpX, which is known to interact with the C-terminus of MuA to remodel the transpososome for replication. We hypothesize that ClpX constitutes part of a highly regulated mechanism that unmasks the cryptic nuclease activity of MuA specifically in the repair pathway.     

Schistosoma mansoni: gene expression of the nucleotide excision repair factor 2 (NEF2) during the parasite life cycle, and in adult worms after exposure to different DNA-damaging agents

DNA is often damaged by many environmental agents, which lead to the up-regulation of several genes involved in different repair pathways. Schistosoma mansoni has a complex life cycle, being exposed to a subset of DNA-damaging agents, such as those present in the environment and host immune response. Recently, studies showed that nucleotide excision repair (NER) is an indispensable mechanism for removing a broad spectrum of different DNA lesions. In the present report, we showed the gene expression of nucleotide excision repair factor 2 (NEF2) SmRad23 and SmRad4, in different developmental stages of S. mansoni, as well as the differential expression of these genes in S. mansoni adult worms treated with DNA-damaging agents. Furthermore, it was revealed the correlation of these genes with their orthologues in other eukaryotes. Our reports suggest that NER is an important repair pathway during the complex life cycle of S. mansoni.     

癌组织及外周血中CD44、PLCEl、甲基化Sept9基因及DNA错配修复蛋白表达水平与结直肠癌病理分期及预后的相关性分析

目的探讨癌组织及外周血中白细胞分化抗原分化簇第44号(CD44)、磷酯酶Cεl(PLCEl)、甲基化Sept9基因及DNA错配修复蛋白表达水平与结直肠癌病理分期及预后的相关性。方法将2013年3月至2015年5月在西宁市第二人民医院确诊为结直肠癌的56例患者设为观察组,将同期于我院体检的55名健康成年人设为对照组。比较两组甲基化Sept9基因、CD44、PLCEl及DNA错配修复蛋白表达情况,分析以上指标在结直肠癌患者中的临床分布特点并进行相关性检验,比较不同甲基化Sept9基因、CD44、PLCEl及DNA错配修复蛋白表达情况并分析其与结直肠癌患者的预后相关性。结果观察组甲基化Sept9基因及CD44表达阳性率、PLCEl表达阴性率、DNA错配修复蛋白表达缺失率高于对照组(P<0.05)。甲基化Sept9基因、PLCEl及DNA错配修复蛋白在不同肿瘤浸润深度、肿瘤大小、病理分期及有无淋巴结转移结直肠癌患者中的表达差异有统计学意义(P<0.05)。CD44在不同肿瘤浸润深度、病理分期及有无淋巴结转移结直肠癌患者中的表达差异有统计学意义(P<0.05)。PLCEl与结直肠癌的浸润深度、病理分期呈负相关(r=-0.367,P=0.045;r=-0.522,P=0.008);甲基化Sept9基因与浸润深度、病理分期、淋巴结转移呈正相关(r=0.715,P=0.026;r=0.471,P=0.032;r=0.453,P=0.010),CD44与浸润深度、病理分期、淋巴结转移呈正相关(r=0.349,P=0.007;r=0.591,P=0.022;r=0.452,P=0.027),DNA错配修复蛋白与病理分期﹑淋巴结转移呈负相关(r=-0.487,P=0.041;r=-0.551,P=0.030)。不同CD44、甲基化Sept9基因、PLCEl及DNA错配修复蛋白表达情况的结直肠癌患者3年生存率差异有统计学意义(P<0.05)。PLCEl、DNA错配修复蛋白与结直肠癌患者3年生存率呈正相关(r=0.574,P=0.041;r=0.478,P=0.037),甲基化Sept9基因与结直肠癌患者3年生存率呈负相关(r=-0.515,P=0.034)。结论CD44、PLCEl、甲基化Sept9基因及DNA错配修复蛋白均与结直肠癌的病理分期相关,其检测有助于了解疾病的恶性程度,评估患者预后。     

Neuroprotection by melatonin against ischemic neuronal injury associated with modulation of DNA damage and repair in the rat following a transient cerebral ischemia

In the present study, double fluorescence staining combined with confocal laser scanning microscopy analysis were used to examine the effects of melatonin on ischemia-induced neuronal DNA strand breaks and its possible mechanisms in a transient middle cerebral artery (MCA) occlusion model. Results showed that melatonin dose-dependently reduced infarct areas and decreased both DNA double and single strand breaks (DSB and SSB) and enhanced cell viability in the peri-ischemic brain regions. Furthermore, Bcl-2 induction in the ischemic brain was further enhanced by melatonin treatment. Double staining analysis indicated that the cells costained for Bcl-2 and TdT-mediated-deoxyuridine triphosphate (dUTP) nick-end labeling (TUNEL), a DSB marker, displayed a relative regular morphology compared with the cells only stained with TUNEL. Transient ischemia induced an expression of excision repair cross-complementing factor 6 (ERCC6) mRNA, a gene essential for the preferential repair of nuclear excision repair, in the injured neurons. Double labeling showed that ERCC6 only co-localized with proliferating cell nuclear antigen (PCNA), a member of the nuclear excision repair complex, but not with TUNEL. Melatonin further and statistical significantly up-regulated ERCC6 mRNA expression in the peri-ischemic region of rat brains. The results suggest that neuroprotection by melatonin against ischemic injury may be related to modulation of apoptosis and DNA repair capacity.     

Xeroderma pigmentosum patients from Germany: repair capacity of 45 XP fibroblast strains of the Mannheim XP Collection as measured by colony-forming ability and unscheduled DNA synthesis following treatment with methyl methanesulfonate and N-methyl-N-nitrosourea

Summary A total of 45 XP fibroblast strains from the Mannheim XP Collection (representatives of XP complementation groups A, C, D, E, F or G, I, and XP variants) were investigated for colony-forming ability (term: D₀ after treatment with up to ten doses of the methylating carcinogen MeSO₂OMe. As controls 16 fibroblast strains from normal donors were used. Except for 4 XP strains (1 from group C and 3 from group D) which, however, were borderline cases, none of the remaining 41 XP strains was found to be more sensitive than normal controls. This held true within the limits of an experimental accuracy (experimental variability of D₀ values) of ±7%. When weighted means were calculated for XP complementation groups and compared with that of normal donors at a significance level of 5%, no significant difference was detected. In contrast, after exposure of 6 XP group D strains to MeNOUr, a weighted mean D₀ value was obtained which was significantly decreasd by 27%. Unscheduled DNA synthesis (term: G₀ which serves as a measure of excision repair) after exposure to MeNOUr was quantitatively the same (exposure to MeNOUr was quantitatively the same (experimental varability: ±8%) both in the group of normal strains and in most of the XP complementation groups. Exceptions were group E and group F (or G) which had higher, and group I which had lower repair. Analogous G₀ values measured after exposure to MeSO₂OMe (experimental variability: ±13%), however, differed from that of the control strains: they were lower in XP complementation groups A, D, E, F (or G), and I. However, groups A, E, F (or G), and I including only 3 individual strains or less may be considered to be possibly ill-represented. Yet, group D including 11 XP strains did show reduction of the mean G₀ value by 35%. From this it is concluded that there are repair defects in XP group D strains with regrad to MeSO₂OMe-induced adducts. These defects seem to be small.Abbreviations XP xeroderma pigmentosum - MeSO₂OMe methyl methanesulfonate - MeNOUr N-methyl-N-nitrosourea - Me(NO)(NO₂)Gdn N-methyl-N-nitro-N-nitrosoguanidine - HEPES N-2-hydroxyethyl-piperazine-N-2-ethanesulfonic acid This work was supported by the Deutsche Forschungsgemeinschaft, SFB 136