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Gelin A, Redrejo-Rodríguez M, Laval J, Fedorova OS, Saparbaev M, Ishchenko AA. Genetic and biochemical characterization of human AP endonuclease 1 mutants deficient in nucleotide incision repair activity. PLoS One 2010; 5:e12241. [PMID: 20808930 PMCID: PMC2923195 DOI: 10.1371/journal.pone.0012241] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Accepted: 07/25/2010] [Indexed: 11/19/2022] Open
Abstract
Background Human apurinic/apyrimidinic endonuclease 1 (APE1) is a key DNA repair enzyme involved in both base excision repair (BER) and nucleotide incision repair (NIR) pathways. In the BER pathway, APE1 cleaves DNA at AP sites and 3′-blocking moieties generated by DNA glycosylases. In the NIR pathway, APE1 incises DNA 5′ to a number of oxidatively damaged bases. At present, physiological relevance of the NIR pathway is fairly well established in E. coli, but has yet to be elucidated in human cells. Methodology/Principal Finding We identified amino acid residues in the APE1 protein that affect its function in either the BER or NIR pathway. Biochemical characterization of APE1 carrying single K98A, R185A, D308A and double K98A/R185A amino acid substitutions revealed that all mutants exhibited greatly reduced NIR and 3′→5′ exonuclease activities, but were capable of performing BER functions to some extent. Expression of the APE1 mutants deficient in the NIR and exonuclease activities reduced the sensitivity of AP endonuclease-deficient E. coli xth nfo strain to an alkylating agent, methylmethanesulfonate, suggesting that our APE1 mutants are able to repair AP sites. Finally, the human NIR pathway was fully reconstituted in vitro using the purified APE1, human flap endonuclease 1, DNA polymerase β and DNA ligase I proteins, thus establishing the minimal set of proteins required for a functional NIR pathway in human cells. Conclusion/Significance Taken together, these data further substantiate the role of NIR as a distinct and separable function of APE1 that is essential for processing of potentially lethal oxidative DNA lesions.
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Affiliation(s)
- Aurore Gelin
- CNRS UMR8126, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Modesto Redrejo-Rodríguez
- CNRS UMR8200 Groupe «Réparation de l′ADN», Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Jacques Laval
- CNRS UMR8200 Groupe «Réparation de l′ADN», Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Olga S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Murat Saparbaev
- CNRS UMR8200 Groupe «Réparation de l′ADN», Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Alexander A. Ishchenko
- CNRS UMR8200 Groupe «Réparation de l′ADN», Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
- * E-mail:
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Bürstenbinder K, Waduwara I, Schoor S, Moffatt BA, Wirtz M, Minocha SC, Oppermann Y, Bouchereau A, Hell R, Sauter M. Inhibition of 5'-methylthioadenosine metabolism in the Yang cycle alters polyamine levels, and impairs seedling growth and reproduction in Arabidopsis. Plant J 2010; 62:977-88. [PMID: 20345605 DOI: 10.1111/j.1365-313x.2010.04211.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The methionine or Yang cycle recycles Met from 5'-methylthioadenosine (MTA) which is produced from S-adenosyl-L-methionine (SAM) as a by-product of ethylene, polyamines, and nicotianamine (NA) synthesis. MTA nucleosidase is encoded by two genes in Arabidopsis thaliana, MTN1 and MTN2. Analysis of T-DNA insertion mutants and of wt revealed that MTN1 provides approximately 80% of the total MTN activity. Severe knock down of MTN enzyme activity in the mtn1-1 and mtn1-2 allelic lines resulted in accumulation of SAM/dSAM (decarboxylated SAM) and of MTA in seedlings grown on MTA as sulfur source. While ethylene and NA synthesis were not altered in mtn1-1 and mtn1-2 seedlings grown on MTA, putrescine and spermine were elevated. By contrast, mtn2-1 and mtn2-2 seedlings with near wt enzyme activity had wt levels of SAM/dSAM, MTA, and polyamines. In addition to the metabolic phenotypes, mtn1-1 and mtn1-2 seedlings were growth retarded, while seedlings of wt, mtn2-1, and mtn2-2 showed normal growth on 500 microm MTA. The double knock down mutant mtn1-1/mtn2-1 was sterile. In conclusion, the data presented identify MTA as a crucial metabolite that acts as a regulatory link between the Yang cycle and polyamine biosynthesis and identifies MTA nucleosidase as a crucial enzyme of the Yang cycle.
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Affiliation(s)
- Katharina Bürstenbinder
- Physiologie und Entwicklungsbiologie der Pflanzen, Botanisches Institut, Universität Kiel, Am Botanischen Garten 5, 24118 Kiel, Germany
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Jaruga P, Xiao Y, Vartanian V, Lloyd RS, Dizdaroglu M. Evidence for the involvement of DNA repair enzyme NEIL1 in nucleotide excision repair of (5'R)- and (5'S)-8,5'-cyclo-2'-deoxyadenosines. Biochemistry 2010; 49:1053-5. [PMID: 20067321 PMCID: PMC2817919 DOI: 10.1021/bi902161f] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 01/11/2010] [Indexed: 01/30/2023]
Abstract
The DNA repair enzyme NEIL1 is a DNA glycosylase that is involved in the first step of base excision repair (BER) of oxidatively induced DNA damage. NEIL1 exhibits a strong preference for excision of 4,6-diamino-5-formamidopyrimidine (FapyAde) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyGua) from DNA with no specificity for 8-hydroxyguanine (8-OH-Gua). In this study, we report on the significant accumulation of (5'R)-8,5'-cyclo-2'-deoxyadenosine (R-cdA) and (5'S)-8,5'-cyclo-2'-deoxyadenosine (S-cdA) in liver DNA of neil1(-/-) mice that were not exposed to exogenous oxidative stress, while no accumulation of these lesions was observed in liver DNA from control or ogg1(-/-) mice. Significant accumulation of FapyGua was detected in liver DNA of both neil1(-/-) and ogg1(-/-) mice, while 8-OH-Gua accumulated in ogg1(-/-) only. Since R-cdA and S-cdA contain an 8,5'-covalent bond between the base and sugar moieties, they cannot be repaired by BER. There is evidence that these lesions are repaired by nucleotide excision repair (NER). Since the accumulation of R-cdA and S-cdA in neil1(-/-) mice strongly points to the failure of their repair, these data suggest that NEIL1 is involved in NER of R-cdA and S-cdA. Further studies aimed at elucidating the mechanism of action of NEIL1 in NER are warranted.
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Affiliation(s)
- Pawel Jaruga
- Chemical Science and Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899
- Department of Clinical Biochemistry, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Yan Xiao
- Chemical Science and Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899
| | - Vladimir Vartanian
- Center for Research on Occupational and Environmental Toxicology, Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon 97239
| | - R. Stephen Lloyd
- Center for Research on Occupational and Environmental Toxicology, Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon 97239
| | - Miral Dizdaroglu
- Chemical Science and Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899
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Pal A, Tewari-Singh N, Gu M, Agarwal C, Huang J, Day BJ, White CW, Agarwal R. Sulfur mustard analog induces oxidative stress and activates signaling cascades in the skin of SKH-1 hairless mice. Free Radic Biol Med 2009; 47:1640-51. [PMID: 19761830 PMCID: PMC2801552 DOI: 10.1016/j.freeradbiomed.2009.09.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 08/20/2009] [Accepted: 09/09/2009] [Indexed: 12/16/2022]
Abstract
A monofunctional analog of the chemical warfare agent sulfur mustard (HD), 2-chloroethyl ethyl sulfide (CEES), induces tissue damage similar to HD. Herein we studied the molecular mechanisms associated with CEES-induced skin inflammation and toxicity in SKH-1 hairless mice. Topical CEES exposure caused an increase in oxidative stress as observed by enhanced 4-hydroxynonenal and 5,5-dimethyl-2-(8-octanoic acid)-1-pyrroline N-oxide protein adduct formation and an increase in protein oxidation. The CEES-induced increase in the formation of 8-oxo-2-deoxyguanosine indicated DNA oxidation. CEES exposure instigated an increase in the phosphorylation of mitogen-activated protein kinases (MAPKs; ERK1/2, JNK, and p38). After CEES exposure, a significant increase in the phosphorylation of Akt at Ser473 and Thr308 was observed as well as upregulation of its upstream effector, PDK1, in mouse skin tissue. Subsequently, CEES exposure caused activation of AP-1 family proteins and the NF-kappaB pathway, including phosphorylation and degradation of IkappaBalpha in addition to phosphorylation of the NF-kappaB essential modulator. Collectively, our results indicate that CEES induces oxidative stress and the activation of the transcription factors AP-1 and NF-kappaB via upstream signaling pathways including MAPKs and Akt in SKH-1 hairless mouse skin. These novel molecular targets could be supportive in the development of prophylactic and therapeutic interventions against HD-related skin injury.
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Affiliation(s)
- Arttatrana Pal
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Colorado at Denver, Aurora, CO 80045, USA
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Upadhyaya P, Hecht SS. Identification of adducts formed in the reactions of 5'-acetoxy-N'-nitrosonornicotine with deoxyadenosine, thymidine, and DNA. Chem Res Toxicol 2008; 21:2164-71. [PMID: 18821782 PMCID: PMC2646895 DOI: 10.1021/tx8002559] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
N'-Nitrosonornicotine (NNN) is the most prevalent of the carcinogenic tobacco-specific nitrosamines found in all tobacco products. Previous studies have demonstrated that cytochrome P450-mediated 5'-hydroxylation of NNN is a major metabolic pathway leading to mutagenic products, but to date, DNA adducts formed by this pathway have been only partially characterized, and there have been no studies reported on adducts formed with bases other than dGuo. Because adducts with dAdo and dThd have been identified in the DNA of the livers of rats treated with the structurally related carcinogen N-nitrosopyrrolidine, we investigated dAdo and dThd adduct formation from 5'-acetoxyNNN (3), a stable precursor to 5'-hydroxyNNN (2). Reaction of 3 with dAdo gave diastereomeric products, which were identified by their spectral properties and LC-ESI-MS/MS-SRM analysis as N(6)-[5-(3-pyridyl)tetrahydrofuran-2-yl]dAdo (9). This adduct was further characterized by NaBH(3)CN reduction to N(6)-[4-hydroxy-4-(3-pyridyl)but-1-yl]dAdo (17). A second dAdo adduct was identified, after NaBH(3)CN treatment, as 6-[2-(3-pyridyl)pyrrolidin-1-yl]purine-2'-deoxyriboside (18). Reaction of 3 with dThd, followed by NaBH(3)CN reduction, gave O(2)-[4-(3-pyridyl)-4-hydroxybut-1-yl]thymidine (11). Adducts 9, 11, 17, and 18 were all identified by LC-ESI-MS/MS-SRM comparison to synthetic standards. The reaction of 3 with calf thymus DNA was then investigated. The DNA was enzymatically hydrolyzed to deoxyribonucleosides, and the resulting mixture was treated with NaBH(3)CN and analyzed by LC-ESI-MS/MS-SRM. Adducts 11, 17, and 18, as well as the previously identified dGuo adducts, were identified. The results of this study provide a more comprehensive picture of DNA adduct formation by the quantitatively important 5'-hydroxylation pathway of NNN and will facilitate investigation of the presence of these adducts in laboratory animals treated with NNN or in people who use tobacco products.
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Affiliation(s)
- Pramod Upadhyaya
- Masonic Cancer Center, University of Minnesota Minneapolis, MN 55455
| | - Stephen S. Hecht
- Masonic Cancer Center, University of Minnesota Minneapolis, MN 55455
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Simmonds HA, Sahota A, Potter CF, Perrett D, Hugh-Jones K, Watson JG. Purine metabolism in adenosine deaminase deficiency. Ciba Found Symp 2008:255-62. [PMID: 387357 DOI: 10.1002/9780470720516.ch16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Deoxyadenosine was identified in the urine of a second child with almost undetectable levels of adenosine deaminase (ADA) in erythrocyte lysates. Deoxyadenosine excretion thus appears to be characteristic of ADA deficiency: the acid lability of deoxyadenosine (responsible for the frequent confusion of this abnormal urinary metabolite with adenine) may be used in screening for this defect by isotachophoresis. The deoxynucleotides dATP, dADP and dAMP found initially in the child's erythrocytes (in comparable amounts to ATP, ADP and AMP) disappeared after a successful marrow graft from an unrelated donor, as did the urinary deoxy metabolites. Erythrocyte ADA activity decreased after the marrow graft but was still greater than 10% of normal congruent to 10 weeks after the last red cell transfusion.
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Abstract
Acylfulvenes (AFs) are a class of antitumor agents that exert their cytotoxic effects by forming covalent adducts with biomolecules, including DNA and proteins; clinical trials are ongoing for (-)-(hydroxymethyl)AF. Recently, depurinating DNA adducts N3-AF-deoxyadenosine (dAdo) and N7-AF-deoxyguanosine (dGuo) were identified from reactions of the parent compound, AF, with calf thymus DNA in the presence of the reductase enzyme alkenal/one oxidoreductase (AOR) and cofactor NADPH. We report here the development of a structure-specific quantitative analytical method for evaluating levels of the major base adduct N3-AF-adenine (Ade), which results from depurination of N3-AF-dAdo, and its utilization to further probe the relationship between AOR-mediated bioactivation and adduct formation in a cell-free system. As an internal standard, the isotopomer N3-AF-Ade-d3 was synthesized, and electrospray-ionization mass spectrometry coupled with high-performance liquid chromatography (HPLC-ESI-MS/MS) was used to detect and quantitate the adduct. This method was validated and found to be accurate (R2>or=0.99) and precise (relative standard deviation 5.8-6.4%), with a limit of detection of 2 fmol. DNA samples, to which the stable-isotope-labeled internal standard was added, were subjected to neutral thermal hydrolysis yielding N3-AF-Ade. Adducts were isolated by a simple solid-liquid methanol extraction procedure, and adduct formation was examined in the presence of either high (1-3 micromol) or low (15 nmol) levels of DNA. Absolute amounts of N3-AF-Ade were measured in cell-free reaction mixtures containing varying levels of AOR as the only drug-activating enzyme. The increase in adduct formation (5-100 adducts per 10(5) DNA bases) over a range of enzyme concentrations (1-24 nM of AOR) showed saturation type behavior. This study reports a sensitive HPLC-ESI-MS/MS method for quantitation of the major DNA adduct induced by AF and illustrates a correlation between N3-AF-Ade formation and AOR-mediated enzymatic activation in a cell-free system, thus providing a template for further studies of drug toxicity in cells and in vivo.
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Affiliation(s)
- James F Neels
- Department of Medicinal Chemistry and The Cancer Center, University of Minnesota, Minneapolis 55455, USA
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Nair J, De Flora S, Izzotti A, Bartsch H. Lipid peroxidation-derived etheno-DNA adducts in human atherosclerotic lesions. Mutat Res 2007; 621:95-105. [PMID: 17412369 DOI: 10.1016/j.mrfmmm.2007.02.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Revised: 12/12/2006] [Accepted: 12/13/2006] [Indexed: 05/14/2023]
Abstract
Atherosclerosis and cancer are characterized by uncontrolled cell proliferation and share common risk factors, such as cigarette smoking, dietary habits and ageing. Growth of smooth muscle cells (SMCs) in atherosclerotic plaques may result from DNA damage, caused either by exogenous mutagens or by agents endogenously generated due to oxidative stress and lipid peroxidation (LPO). Hydroxy-2-nonenal (HNE), a major LPO product, binds covalently to cellular DNA to form the exocyclic etheno-DNA-base adducts, 1,N(6)-ethenodeoxyadenine (varepsilondA) and 3,N(4)-ethenodeoxycytosine (varepsilondC). By applying an ultrasensitive (32)P-postlabeling-immunoaffinity method, varepsilondA and varepsilondC were quantified in abdominal aorta SMCs from 13 atherosclerotic patients and 3 non-smoking subjects without atherosclerotic lesions. The levels of etheno-adducts ranged for varepsilondA from 2.3 to 39.6/10(8)dA and for varepsilondC from 10.7 to 157.7/10(8)dC, with a high correlation between varepsilondA and varepsilondC (r=0.84, P=0.0001). Etheno-adduct levels were higher in atherosclerotic smokers than in ex-smokers for both varepsilondA (means 15.2 versus 7.3, P=0.06) and varepsilondC (71.9 versus 51.6, not significant). varepsilondC levels were higher in either ex-smokers (P=0.03) or smokers (P=0.07) than in non-smokers. There was a poor correlation between either varepsilondA or varepsilondC and 8-hydroxy-2'-deoxyguanosine, whereas significant positive correlations were detected with the levels of several postlabeled bulky aromatic DNA adducts. In conclusion, two different types of DNA damage may be involved in atherosclerotic plaque formation and progression: (i) bulky aromatic compounds, to which aorta SMCs are chronically exposed in smokers, can either covalently bind to DNA, induce redox-cycling via quinone intermediates and/or activate local chronic inflammatory processes in the arterial wall; ii) this in turn leads to a self perpetuating generation of reactive oxygen species, LPO-products and increasing DNA-damage, as documented by the presence of high levels of miscoding etheno-DNA adducts in human aorta SMCs.
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Affiliation(s)
- Jagadeesan Nair
- Division of Toxicology and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
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Muguruma M, Unami A, Kanki M, Kuroiwa Y, Nishimura J, Dewa Y, Umemura T, Oishi Y, Mitsumori K. Possible involvement of oxidative stress in piperonyl butoxide induced hepatocarcinogenesis in rats. Toxicology 2007; 236:61-75. [PMID: 17498859 DOI: 10.1016/j.tox.2007.03.025] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Revised: 03/27/2007] [Accepted: 03/28/2007] [Indexed: 12/20/2022]
Abstract
To clarify the possible mechanism of non-genotoxic hepatocarcinogenesis induced by piperonyl butoxide (PBO), male F344 rats were administered an i.p. injection of N-diethylnitrosamine (DEN) to initiate hepatocarcinogenesis. Two weeks later, the rats were administered a PBO-containing (0, 1, or 2%) diet for 6 weeks and subjected to a two-third partial hepatectomy 1 week later. After sacrificing them on week 8, their livers were histopathologically examined and analyzed for gene expression using a microarray and real-time RT-PCR. Reactive oxygen species (ROS) products were also measured using liver microsomes. Hepatocytes exhibited centrilobular hypertrophy and increased glutathione S-transferase placental form (GST-P) positive foci formation. ROS products increased significantly in liver microsomes. In the microarray analysis, the expressions of genes related to metabolism and oxidative stress - NAD(P)H dehydrogenase, quinone 1 (Nqo1), UDP-glucuronosyltransferase (UDPGTR-2), glutathione peroxidase 2 (Gpx2), glutathione reductase (GRx) - multidrug resistance associated protein 3 (Abcc3), and solute carrier family 7 (cationic amino acid transporter, y+ system) member 5 (Slc7a5) were up-regulated in the PBO group in comparison to the 0% PBO group; this was confirmed by real-time RT-PCR. Additionally, a significant up-regulation of stress response related genes such as CYP1A1 was observed in PBO-treated groups in real-time RT-PCR. HPLC analysis revealed that the level of 8-OHdG in the 2% PBO group was significantly higher than that in the 0% PBO group. This suggests that PBO has the potential to generate ROS via metabolic pathways and induce oxidative stress, including oxidative DNA damage, resulting in the induction of hepatocellular tumors in rats.
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Affiliation(s)
- Masako Muguruma
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, Fuchu City, Tokyo 183-8509, Japan.
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Hermann JC, Marti-Arbona R, Fedorov AA, Fedorov E, Almo SC, Shoichet BK, Raushel FM. Structure-based activity prediction for an enzyme of unknown function. Nature 2007; 448:775-9. [PMID: 17603473 PMCID: PMC2254328 DOI: 10.1038/nature05981] [Citation(s) in RCA: 194] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Accepted: 06/07/2007] [Indexed: 01/09/2023]
Abstract
With many genomes sequenced, a pressing challenge in biology is predicting the function of the proteins that the genes encode. When proteins are unrelated to others of known activity, bioinformatics inference for function becomes problematic. It would thus be useful to interrogate protein structures for function directly. Here, we predict the function of an enzyme of unknown activity, Tm0936 from Thermotoga maritima, by docking high-energy intermediate forms of thousands of candidate metabolites. The docking hit list was dominated by adenine analogues, which appeared to undergo C6-deamination. Four of these, including 5-methylthioadenosine and S-adenosylhomocysteine (SAH), were tested as substrates, and three had substantial catalytic rate constants (10(5) M(-1 )s(-1)). The X-ray crystal structure of the complex between Tm0936 and the product resulting from the deamination of SAH, S-inosylhomocysteine, was determined, and it corresponded closely to the predicted structure. The deaminated products can be further metabolized by T. maritima in a previously uncharacterized SAH degradation pathway. Structure-based docking with high-energy forms of potential substrates may be a useful tool to annotate enzymes for function.
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Affiliation(s)
- Johannes C Hermann
- Department of Pharmaceutical Chemistry, University of California, San Francisco, MC 2550 1700 4th Street, San Francisco, California 94158-2330, USA
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Theruvathu JA, Jaruga P, Dizdaroglu M, Brooks PJ. The oxidatively induced DNA lesions 8,5'-cyclo-2'-deoxyadenosine and 8-hydroxy-2'-deoxyadenosine are strongly resistant to acid-induced hydrolysis of the glycosidic bond. Mech Ageing Dev 2007; 128:494-502. [PMID: 17692895 PMCID: PMC2430076 DOI: 10.1016/j.mad.2007.06.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Accepted: 06/21/2007] [Indexed: 12/27/2022]
Abstract
The 8,5'-cyclopurine-2'-deoxynucleosides (cPu) are unique oxidatively induced DNA lesions in that they are specifically repaired by NER. In the absence of NER, a possible mechanism for cPu removal is spontaneous glycosidic bond hydrolysis followed by enzymic processing. Such a mechanism could be significant if the glycosidic bond in cPu were substantially destabilized, as shown for other DNA lesions. Therefore, we investigated the stability of the glycosidic bond in a cPu, (5'S)-8,5'-cyclo-2'-deoxyadenosine (S-cdA) against acid hydrolysis. For comparison, we also studied 8-hydroxy-2'-deoxyadenosine (8-OH-dA). We found that the glycosidic bond in S-cdA is approximately 40-fold more resistant to glycosidic bond hydrolysis compared to dA. Interestingly, under the same conditions, the glycosidic bond in 8-OH-dA was even more stable than in S-cdA. These studies effectively rule out any mechanism for the removal of S-cdA or 8-OH-dA from DNA that requires spontaneous glycosidic bond hydrolysis, and further support the proposed role of cPu in the neurodegeneration observed in xeroderma pigmentosum patients who lack NER. Of broader significance, since NER does not function in non-transcribed DNA sequences of terminally differentiated cells, including neurons, cPu are expected to accumulate in such sequences even in individuals with normal NER, which could be important in the ageing process.
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Affiliation(s)
- Jacob A Theruvathu
- Section on Molecular Neurobiology, Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, 5625 Fishers Lane, Room 3S-32, MSC 9412, Bethesda, MD 20952-9412, USA
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Nyaga SG, Jaruga P, Lohani A, Dizdaroglu M, Evans MK. Accumulation of oxidatively induced DNA damage in human breast cancer cell lines following treatment with hydrogen peroxide. Cell Cycle 2007; 6:1472-8. [PMID: 17568196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
Breast cancer is a leading cause of cancer deaths in women. Although the causes of this disease are largely unknown, inefficient repair of oxidatively induced DNA lesions has been thought to play a major role in the transformation of normal breast tissue to malignant breast tissue. Previous studies have revealed higher levels of 8-hydroxyguanine in malignant breast tissue compared to non-malignant breast tissue. Furthermore, some breast cancer cell lines have greatly reduced capacity to repair this lesion suggesting that oxidatively induced DNA lesions may be elevated in breast cancer cells. We used liquid chromatography/mass spectrometry and gas chromatography/mass spectrometry to measure the levels of 8-hydroxy-2'-deoxyadenosine, (5'S)-8,5'-cyclo-2'-deoxyadenosine, 2,6-diamino-4-hydroxy-5-formamidopyrimidine, and 4,6-diamino-5-formamidopyrimidine in MCF-7 and HCC1937 breast cancer cell lines before and after exposure to H(2)O(2) followed by a DNA repair period. We show that H(2)O(2)-treated HCC1937 and MCF-7 cell lines accumulate significantly higher levels of these lesions than the untreated cells despite a 1 h repair period. In contrast, the four lesions did not accumulate to any significant level in H(2)O(2)-treated non-malignant cell lines, AG11134 and HCC1937BL. Furthermore, MCF-7 and HCC1937 cell lines were deficient in the excision repair of all the four lesions studied. These results suggest that oxidatively induced DNA damage and its repair may be critical in the etiology of breast cancer.
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Affiliation(s)
- Simon G Nyaga
- Laboratory of Cellular and Molecular Biology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
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Fleckenstein K, Zgonjanin L, Chen L, Rabbani Z, Jackson IL, Thrasher B, Kirkpatrick J, Foster WM, Vujaskovic Z. Temporal onset of hypoxia and oxidative stress after pulmonary irradiation. Int J Radiat Oncol Biol Phys 2007; 68:196-204. [PMID: 17448873 PMCID: PMC1939695 DOI: 10.1016/j.ijrobp.2006.12.056] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 12/26/2006] [Accepted: 12/27/2006] [Indexed: 11/17/2022]
Abstract
PURPOSE To investigate the temporal onset of hypoxia following irradiation, and to show how it relates to pulmonary vascular damage, macrophage accumulation, and the production of reactive oxygen species and cytokines. Our previous studies showed that tissue hypoxia in the lung after irradiation contributed to radiation-induced injury. METHODS AND MATERIALS Female Fisher 344 rats were irradiated to the right hemithorax with a single dose of 28 Gy. Serial studies were performed up to 20 weeks following irradiation. Radionuclide lung-perfusion studies were performed to detect changes in pulmonary vasculature. Immunohistochemical studies were conducted to study macrophages, tissue hypoxia (carbonic anhydrase-9 marker), oxidative stress (8-hydroxy-2'-deoxyguanosine), and the expression of profibrogenic (transforming growth factor-beta [TGF-beta]) and proangiogenic (vascular endothelial growth factor [VEGF]) cytokines. RESULTS Significant changes in lung perfusion along with tissue hypoxia were observed 3 days after irradiation. Significant oxidative stress was detected 1 week after radiation, whereas macrophages started to accumulate at 4 weeks. A significant increase in TGF-beta expression was seen within 1 day after radiation, and for VEGF at 2 weeks after radiation. Levels of hypoxia, oxidative stress, and both cytokines continued to rise with time after irradiation. The steepest increase correlated with vast macrophage accumulation. CONCLUSIONS Early changes in lung perfusion, among other factors initiate, the development of hypoxia and chronic oxidative stress after irradiation. Tissue hypoxia is associated with a significant increase in the activation of macrophages and their continuous production of reactive oxygen species, stimulating the production of fibrogenic and angiogenic cytokines, and maintaining the development of chronic radiation-induced lung injury.
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Affiliation(s)
- Katharina Fleckenstein
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
- Department of Radiation Oncology, Mannheim Medical Center, University of Heidelberg, Mannheim, Germany
| | - Larisa Zgonjanin
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Liguang Chen
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Zahid Rabbani
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Isabel L. Jackson
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Bradley Thrasher
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - John Kirkpatrick
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - W. Michael Foster
- Department of Pulmonary Medicine, Duke University Medical Center, Durham, NC, USA
| | - Zeljko Vujaskovic
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
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Nakata H, Amano M, Koh Y, Kodama E, Yang G, Bailey CM, Kohgo S, Hayakawa H, Matsuoka M, Anderson KS, Cheng YC, Mitsuya H. Activity against human immunodeficiency virus type 1, intracellular metabolism, and effects on human DNA polymerases of 4'-ethynyl-2-fluoro-2'-deoxyadenosine. Antimicrob Agents Chemother 2007; 51:2701-8. [PMID: 17548498 PMCID: PMC1932487 DOI: 10.1128/aac.00277-07] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We examined the intracytoplasmic anabolism and kinetics of antiviral activity against human immunodeficiency virus type 1 (HIV-1) of a nucleoside reverse transcriptase inhibitor, 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA), which has potent activity against wild-type and multidrug-resistant HIV-1 strains. When CEM cells were exposed to 0.1 microM [(3)H]EFdA or [(3)H]3'-azido-2',3'-dideoxythymidine (AZT) for 6 h, the intracellular EFdA-triphosphate (TP) level was 91.6 pmol/10(9) cells, while that of AZT was 396.5 pmol/10(9) cells. When CEM cells were exposed to 10 microM [(3)H]EFdA, the amount of EFdA-TP increased by 22-fold (2,090 pmol/10(9) cells), while the amount of [(3)H]AZT-TP increased only moderately by 2.4-fold (970 pmol/10(9) cells). The intracellular half-life values of EFdA-TP and AZT-TP were approximately 17 and approximately 3 h, respectively. When MT-4 cells were cultured with 0.01 microM EFdA for 24 h, thoroughly washed to remove EFdA, further cultured without EFdA for various periods of time, exposed to HIV-1(NL4-3), and cultured for an additional 5 days, the protection values were 75 and 47%, respectively, after 24 and 48 h with no drug incubation, while those with 1 microM AZT were 55 and 9.2%, respectively. The 50% inhibitory concentration values of EFdA-TP against human polymerases alpha, beta, and gamma were >100 microM, >100 microM, and 10 microM, respectively, while those of ddA-TP were >100 microM, 0.2 microM, and 0.2 microM, respectively. These data warrant further development of EFdA as a potential therapeutic agent for those patients who harbor wild-type HIV-1 and/or multidrug-resistant variants.
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Affiliation(s)
- Hirotomo Nakata
- Department of Infectious, Kumamoto University School of Medicine, 1-1-1 Honjo, Kumamoto, Japan
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Zhang J, Takeda M. Molecular characterization of MbADGF, a novel member of the adenosine deaminase-related growth factor in the cabbage armyworm, Mamestra brassicae: the functional roles in the midgut cell proliferation. Insect Mol Biol 2007; 16:351-60. [PMID: 17439545 DOI: 10.1111/j.1365-2583.2007.00732.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
To clarify the functional mechanism of the adenosine deaminase-related growth factor (ADGF) particularly in the regulation of insect development, the cDNA encoding a homologue of ADGF proteins was cloned from the cabbage armyworm, Mamestra brassicae, named MbADGF. The purified MbADGF recombinant protein stimulated cell proliferation in a dose-dependent manner of SES-MaBr-4 and NIAS-MaBr-93 cell lines that were derived from fat bodies and haemocytes of M. brassicae. The adenosine deaminase activity of MbADGF was detected using adenosine and 2'-deoxyadenosine as substrates. Northern analysis demonstrated that during the larval development the level of MbADGF in the midgut increased. In situ hybridization showed that MbADGF mRNA was expressed in midgut goblet cells and in the apical cytoplasm of columnar cells, which suggests that MbADGF protein may execute its adenosine deaminase activity at the apical cytoplasm of columnar cells to convert adenosine into inosine.
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Affiliation(s)
- J Zhang
- Division of Biofunctional Science, Graduate School of Science and Technology, Kobe University, Nada, Kobe, Japan.
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Abstract
Transition state theory suggests that enzymatic rate acceleration (kcat/knon) is related to the stabilization of the transition state for a given reaction. Chemically stable analogues of a transition state complex are predicted to convert catalytic energy into binding energy. Because transition state stabilization is a function of catalytic efficiency, differences in substrate specificity can be exploited in the design of tight-binding transition state analogue inhibitors. Coformycin and 2'-deoxycoformycin are natural product transition state analogue inhibitors of adenosine deaminases (ADAs). These compounds mimic the tetrahedral geometry of the ADA transition state and bind with picomolar dissociation constants to enzymes from bovine, human, and protozoan sources. The purine salvage pathway in malaria parasites is unique in that Plasmodium falciparum ADA (PfADA) catalyzes the deamination of both adenosine and 5'-methylthioadenosine. In contrast, neither human adenosine deaminase (HsADA) nor the bovine enzyme (BtADA) can deaminate 5'-methylthioadenosine. 5'-Methylthiocoformycin and 5'-methylthio-2'-deoxycoformycin were synthesized to be specific transition state mimics of the P. falciparum enzyme. These analogues inhibited PfADA with dissociation constants of 430 and 790 pM, respectively. Remarkably, they gave no detectable inhibition of the human and bovine enzymes. Adenosine deamination is involved in the essential pathway of purine salvage in P. falciparum, and prior studies have shown that inhibition of purine salvage results in parasite death. Inhibitors of HsADA are known to be toxic to humans, and the availability of parasite-specific ADA inhibitors may prevent this side-effect. The potent and P. falciparum-specific inhibitors described here have potential for development as antimalarials without inhibition of host ADA.
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Affiliation(s)
- Peter C. Tyler
- Carbohydrate Chemistry Team, Industrial Research Ltd., Lower Hutt, New Zealand
- *Corresponding authors: , telephone (718) 430-2813; fax (718) 430-8565
| | - Erika A. Taylor
- Department of Biochemistry, Albert Einstein College of Medicine at Yeshiva University, 1300 Morris Park Avenue, Bronx, New York, 10461, USA
| | | | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine at Yeshiva University, 1300 Morris Park Avenue, Bronx, New York, 10461, USA
- *Corresponding authors: , telephone (718) 430-2813; fax (718) 430-8565
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Ohtaki H, Takeda T, Dohi K, Yofu S, Nakamachi T, Satoh K, Hiraizumi Y, Miyaoka H, Matsunaga M, Shioda S. Increased mitochondrial DNA oxidative damage after transient middle cerebral artery occlusion in mice. Neurosci Res 2007; 58:349-55. [PMID: 17628732 DOI: 10.1016/j.neures.2007.04.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2007] [Revised: 04/04/2007] [Accepted: 04/10/2007] [Indexed: 11/28/2022]
Abstract
Oxidative stress and DNA oxidation play important roles in the induction of ischemic neuronal cell death. However, the subcellular source of oxidized DNA detected by 8-hydroxy-2'-deoxyguanosine (8-OHdG) after ischemia has not been clarified although it is known to increase in the brain after ischemia. One-hour transient ischemia of the middle cerebral artery was induced in mice utilizing an intraluminal filament. The occurrence of superoxide anion as an ethidium (Et) signal, 8-OHdG, cytochrome c release and neuronal cell death were examined using immunohistological and biochemical techniques in sham-operated control (0h) and 1, 3, 6, 24, or 96h after reperfusion. Et signals were prominent in the cortical neurons of ipsilateral hemisphere 3h after reperfusion. Strong 8-OHdG immunoreactivity was observed 3-6h after reperfusion. Immunoassays after cell fractionation revealed a significant increase of 8-OHdG in mitochondria 6h after reperfusion. Immunohistochemistry revealed that the 8-OHdG immunoreactivity colocalized with a neuronal marker, microfilament 200 and a mitochondrial marker, cytochrome oxidase subunit I. Cytochrome c rose in cytoplasm at 6h and TUNEL-positive neurons noted 6-24h after ischemia. The present results suggest the possibility that the mitochondrial damage including mitochondrial DNA oxidation might be responsible for the induction of ischemic neuronal cell death.
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Affiliation(s)
- Hirokazu Ohtaki
- Department of Anatomy, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
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Chiron S, Barbati S, De Méo M, Botta A. In vitro synthesis of 1,N6-etheno-2'-deoxyadenosine and 1,N2-etheno-2'-deoxyguanosine by 2,4-dinitrophenol and 1,3-dinitropyrene in presence of a bacterial nitroreductase. Environ Toxicol 2007; 22:222-7. [PMID: 17366551 DOI: 10.1002/tox.20253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The formation of covalent nitro-PAH DNA adducts and nitro-PAH mediated oxidative lesions are two possible mechanisms for the initiation of nitro-PAH carcinogenesis. Sixty-minute incubation of 1,3-dinitropyrene (100 microM) or 1,4-dinitrophenol (100 microM) with a mixture of 150 microM NADH, 0.5 units of E. coli nitroreductase, 100 microM linoleic acid, 0.5 mM ferrous iron, and 100 microM 2'-deoxyadenosine (2'-dA) or 100 microM 2'-deoxyguanosine (2'-dG) were analyzed by liquid chromatography multistage mass spectrometry. Mixtures of 1,N(6)-etheno-2'-deoxyadenosine (epsilondA) plus 4-oxo-2-nonenal (4-ONE) and 1,N(2)-etheno-2'-deoxyguanosine (epsilondG) plus 4-ONE could be detected from 2'-dA and 2'-dG, respectively. Addition of 2% propanol inhibited the formation of etheno adducts. Analyses of disappearance kinetics of dA and dG showed that dG was more rapidly eliminated than does dA (t[1/2] = 23.3 min and 98.3 min for dG and dA, respectively). Curves of formation kinetics revealed that the peak of epsilondG was at 55.6 min while that of epsilondA was at 186.9 min. These peaks represented 1.43% and 1.25% of the original dG and dA, respectively. In both cases, the peaks were followed by rapid degradations of etheno adducts. The results, obtained in this system, do not allow any extrapolation to realistic cellular responses; nevertheless, these data questioned the validity of the use of unsubstituted etheno adducts as reliable oxidative stress and nitro-PAH exposure biomarkers.
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Affiliation(s)
- Serge Chiron
- Laboratoire Chimie et Environnement, Université de Provence, 3 Place Victor Hugo, 13331 Marseille Cedex 3, France
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Marietta C, Brooks PJ. Transcriptional bypass of bulky DNA lesions causes new mutant RNA transcripts in human cells. EMBO Rep 2007; 8:388-93. [PMID: 17363972 PMCID: PMC1852755 DOI: 10.1038/sj.embor.7400932] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 01/19/2007] [Accepted: 01/19/2007] [Indexed: 12/22/2022] Open
Abstract
Here, we characterize the mutant transcripts resulting from bypass of an 8,5'-cyclo-2'-deoxyadenosine (cyclo-dA) or cyclobutane pyrimidine dimer (CPD) by human RNA polymerase II (Pol II) in vivo. With the cyclo-dA lesion, we observed two new types of mutant transcripts. In the first type, the polymerase inserted uridine opposite the lesion and then misincorporated adenosine opposite the template deoxyadenosine downstream (5') of the lesion. The second type contained deletions of 7, 13 or 21 nucleotides (nt) after uridine incorporation opposite the lesion. The frequency of the different types of transcript from the cyclo-dA lesion in mutant human cell lines suggests that the Cockayne syndrome B protein affects the probability of deletion transcript formation. With the CPD-containing construct, we also detected rare transcripts containing 12 nt deletions. These results indicate that RNA pol II in living human cells can bypass helix-distorting DNA lesions that are substrates for nucleotide excision repair, resulting in transcriptional mutagenesis.
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Affiliation(s)
- Cheryl Marietta
- Section on Molecular Neurobiology, Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, 5625 Fishers Lane, Room 3S-32, MSC 9412, Bethesda, Maryland 20892, USA
| | - Philip J Brooks
- Section on Molecular Neurobiology, Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, 5625 Fishers Lane, Room 3S-32, MSC 9412, Bethesda, Maryland 20892, USA
- Tel: +1 301 496 7920; Fax: +1 301 480 2839; E-mail:
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Forkert PG, Kaufmann M, Black G, Bowers R, Chen H, Collins K, Sharma A, Jones G. Oxidation of vinyl carbamate and formation of 1,N6-ethenodeoxyadenosine in murine lung. Drug Metab Dispos 2007; 35:713-20. [PMID: 17296623 DOI: 10.1124/dmd.106.013805] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Vinyl carbamate (VC) is derived from ethyl carbamate, a carcinogen formed in fermentation of food and alcoholic products. We have undertaken studies to test the hypothesis that an epoxide generated from VC oxidation leads to formation of 1,N6-ethenodeoxyadenosine (epsilon dAS). We have developed approaches using liquid chromatography-mass spectrometry and liquid chromatography-tandem mass spectrometry for identification and quantitation of epsilon dAS. Scanning and fragment ion analyses confirmed the identity of epsilon dAS based on the molecular ion [M + H]+ m/z 276 and the specific fragment ion m/z 160. Chemical oxidation of VC in reactions containing 2'-deoxyadenosine produced epsilon dAS with 1H NMR, chromatographic, and mass spectral characteristics identical to those of the authentic epsilon dAS, suggesting DNA alkylation by the VC epoxide. Subsequent studies evaluated formation of epsilon dAS in incubations of murine lung microsomes or recombinant CYP2E1 with VC. The formation of epsilon dAS in incubations of lung microsomes or recombinant CYP2E1 with VC was dependent on protein concentrations, CYP2E1 enzyme levels, and incubation time. The rates of epsilon dAS formation were highly correlated with VC concentrations. Peak rates were produced by lung microsomes and recombinant CYP2E1 at 3.0 and 2.5 mM VC, respectively. In inhibitory studies, incubations of VC were performed using lung microsomes from mice treated with the CYP2E1 inhibitor diallyl sulfone (100 mg/kg, p.o.). Results from these studies showed significantly decreased epsilon dAS formation in microsomes incubated with VC, with an inhibition of 70% at 3.0 mM. These findings suggested that CYP2E1 is a major enzyme mediating VC oxidation, leading to the formation of a metabolite that alkylates DNA to form the epsilon dAS adduct.
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Affiliation(s)
- Poh-Gek Forkert
- Department of Anatomy and Cell Biology, Queen's University, Kingston, Ontario, Canada K7L 3N6.
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71
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Gong J, Vaidyanathan VG, Yu X, Kensler TW, Peterson LA, Sturla SJ. Depurinating acylfulvene-DNA adducts: characterizing cellular chemical reactions of a selective antitumor agent. J Am Chem Soc 2007; 129:2101-11. [PMID: 17256933 DOI: 10.1021/ja0665951] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acylfulvenes (AFs) are a class of semisynthetic agents with high toxicity toward certain tumor cells, and for one analogue, hydroxymethylacylfulvene (HMAF), clinical trials are in progress. DNA alkylation by AFs, mediated by bioreductive activation, is believed to contribute to cytotoxicity, but the structures and chemical properties of corresponding DNA adducts are unknown. This study provides the first structural characterization of AF-specific DNA adducts. In the presence of a reductive enzyme, alkenal/one oxidoreductase (AOR), AF selectively alkylates dAdo and dGuo in reactions with a monomeric nucleoside, as well as in reactions with naked or cellular DNA, with 3-alkyl-dAdo as the apparently most abundant AF-DNA adduct. Characterization of this adduct was facilitated by independent chemical synthesis of the corresponding 3-alkyl-Ade adduct. In addition, in naked or cellular DNA, evidence was obtained for the formation of an additional type of adduct resulting from direct conjugate addition of Ade to AF followed by hydrolytic cyclopropane ring-opening, indicating the potential for a competing reaction pathway involving direct DNA alkylation. The major AF-dAdo and AF-dGuo adducts are unstable under physiologically relevant conditions and depurinate to release an alkylated nucleobase in a process that has a half-life of 8.5 h for 3-alkyladenine and less than approximately 2 h for dGuo adducts. DNA alkylation further leads to single-stranded DNA cleavage, occurring exclusively at dGuo and dAdo sites, in a nonsequence-specific manner. In AF-treated cells that were transfected with either AOR or control vectors, the DNA adducts identified match those from in vitro studies. Moreover, a positive correlation was observed between DNA adduct levels and cell sensitivity to AF. The potential contributing roles of AOR-mediated bioactivation and adduct stability to the cytotoxicity of AF are discussed.
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Affiliation(s)
- Jiachang Gong
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Abstract
The oxidative metabolism of estrogens has been implicated in the development of breast cancer; yet, relatively little is known about the mechanism by which estrogens cause DNA damage and thereby initiate mammary carcinogenesis. To determine how the metabolism of the parent hormone 17beta-estradiol (E2) leads to the formation of DNA adducts, we used the recombinant, purified phase I enzyme, cytochrome P450 1B1 (CYP1B1), which is expressed in breast tissue, to oxidize E2 in the presence of 2'-deoxyguanosine or 2'-deoxyadenosine. We used both gas and liquid chromatography with tandem mass spectrometry to measure E2, the 2- and 4-catechol estrogens (2-OHE2, 4-OHE2), and the depurinating adducts 4-OHE(2)-1(alpha,beta)-N7-guanine (4-OHE2-N7-Gua) and 4-OHE(2)-1(alpha,beta)-N3-adenine (4-OHE2-N3-Ade). CYP1B1 oxidized E2 to the catechol 4-OHE2 and the labile quinone 4-hydroxyestradiol-quinone to produce 4-OHE2-N7-Gua and 4-OHE2-N3-Ade in a time- and concentration-dependent manner. Because the reactive quinones were produced as part of the CYP1B1-mediated oxidation reaction, the adduct formation followed Michaelis-Menten kinetics. Under the conditions of the assay, the 4-OHE2-N7-Gua adduct (Km, 4.6+/-0.7 micromol/L; kcat, 45+/-1.6/h) was produced 1.5 times more efficiently than the 4-OHE2-N3-Ade adduct (Km, 4.6+/-1.0 micromol/L; kcat, 30+/-1.5/h). The production of adducts was two to three orders of magnitude lower than the 4-OHE2 production. The results present direct proof of CYP1B1-mediated, E2-induced adduct formation and provide the experimental basis for future studies of estrogen carcinogenesis.
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Affiliation(s)
- Alexandra R Belous
- Department of Pathology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
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Palusa SG, Golovkin M, Shin SB, Richardson DN, Reddy ASN. Organ-specific, developmental, hormonal and stress regulation of expression of putative pectate lyase genes in Arabidopsis. New Phytol 2007; 174:537-550. [PMID: 17447910 DOI: 10.1111/j.1469-8137.2007.02033.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Pectate lyases catalyse the eliminative cleavage of de-esterified homogalacturonan in pectin, a major component of the primary cell walls in higher plants. In the completed genome of Arabidopsis, there are 26 genes (AtPLLs) that encode pectate lyase-like proteins. Here, we analysed the expression pattern of all AtPLLs in different organs, at different stages of seedling development and in response to various hormones and stresses. The expression of PLLs varied considerably in different organs, with no expression of some PLLs in vegetative organs. Interestingly, all PLL genes are expressed in flowers. Several PLLs are expressed highly in pollen, suggesting a role for these in pollen development and/or function. Analysis of expression of all PLL genes in seedlings treated with hormones, abiotic stresses and elicitors of defense responses revealed significant changes in the expression of some PLLs without affecting the other PLLs. The stability of transcripts of PLLs varied considerably among different genes. Our results indicate a complex regulation of expression of PLLs and involvement of PLLs in some of the hormonal and stress responses.
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Affiliation(s)
- Saiprasad Goud Palusa
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Maxim Golovkin
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Sung-Bong Shin
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Dale N Richardson
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Anireddy S N Reddy
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, CO 80523-1878, USA
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Brown KL, Li J, Zou X. NMR observations of 13C-enriched coenzyme B12 bound to the ribonucleotide reductase from Lactobacillus leichmannii. Inorg Chem 2006; 45:9172-4. [PMID: 17083212 PMCID: PMC2517903 DOI: 10.1021/ic061385a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 13C NMR resonance and one-bond 1H-13C coupling constants of coenzyme B12 enriched in 13C in the cobalt-bound carbon have been observed in the complex of the coenzyme with the B12-dependent ribonucleotide reductase from Lactobacillus leichmannii. Neither the 13C NMR chemical shift nor the 1H-13C coupling constants are significantly altered by binding of the coenzyme to the enzyme. The results suggest that ground-state Co-C bond distortion is not utilized by this enzyme to activate coenzyme B12 for C-Co bond homolysis.
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Affiliation(s)
- Kenneth L Brown
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, USA.
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Yoon M, Patwardhan A, Qiao C, Mansoorabadi SO, Menefee AL, Reed GH, Marsh ENG. Reaction of adenosylcobalamin-dependent glutamate mutase with 2-thiolglutarate. Biochemistry 2006; 45:11650-7. [PMID: 16981724 PMCID: PMC2517135 DOI: 10.1021/bi061067n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have investigated the reaction of glutamate mutase with the glutamate analogue, 2-thiolglutarate. In the standard assay, 2-thiolglutarate behaves as a competitive inhibitor with a Ki of 0.05 mM. However, rather than simply binding inertly at the active site, 2-thiolglutarate elicits cobalt-carbon bond homolysis and the formation of 5'-deoxyadenosine. The enzyme exhibits a complicated EPR spectrum in the presence of 2-thiolglutarate that is markedly different from any previously observed with the enzyme. The spectrum was simulated well by assuming that it arises from electron-electron spin coupling between a thioglycolyl radical and low-spin Co2+ in cob(II)alamin. Analysis of the zero-field splitting parameters obtained from the simulations places the organic radical approximately 10 A from the cobalt and at a tilt angle of approximately 70 degrees to the normal of the corrin ring. This orientation is in good agreement with that expected from the crystal structure of glutamate mutase complexed with the substrate. 2-Thiolglutarate appears to react in a manner analogous to that of glutamate by first forming a thiolglutaryl radical at C-4 that then undergoes fragmentation to produce acrylate and the sulfur-stabilized thioglycolyl radical. The thioglycolyl radical accumulates on the enzyme, suggesting it is too stable to undergo further steps in the mechanism at a detectable rate.
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Affiliation(s)
- Miri Yoon
- Departments of Chemistry and Biological Chemistry, University of Michigan, Ann Arbor, WI 48109−1055, USA
| | - Anjali Patwardhan
- Departments of Chemistry and Biological Chemistry, University of Michigan, Ann Arbor, WI 48109−1055, USA
| | - Chunhua Qiao
- Departments of Chemistry and Biological Chemistry, University of Michigan, Ann Arbor, WI 48109−1055, USA
| | | | - Ann L. Menefee
- Department of Biochemistry, University of Wisconsin, Madison, MI 53726−4087, USA
| | - George H. Reed
- Department of Biochemistry, University of Wisconsin, Madison, MI 53726−4087, USA
| | - E. Neil G. Marsh
- Departments of Chemistry and Biological Chemistry, University of Michigan, Ann Arbor, WI 48109−1055, USA
- Correspondence should be addressed to this author at: Department of Chemistry, University of Michigan, Ann Arbor, MI 48109−1055, USA Tel (734) 763 6096 FAX (734) 764 8815 e-mail
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Zang H, Chowdhury G, Angel KC, Harris TM, Guengerich FP. Translesion synthesis across polycyclic aromatic hydrocarbon diol epoxide adducts of deoxyadenosine by Sulfolobus solfataricus DNA polymerase Dpo4. Chem Res Toxicol 2006; 19:859-67. [PMID: 16780366 DOI: 10.1021/tx060056s] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanisms by which derivatives of polycyclic aromatic hydrocarbons (PAHs) cause mutations have been of considerable interest. Three different N(6)-adenyl PAH-diol epoxide oligonucleotide derivatives were studied with the archebacterial translesion DNA polymerase Sulfolobus solfataricus Dpo4. Steady-state kinetic analysis indicated insertion of all four dNTPs opposite each of the three N(6)-adenyl PAH adducts, with only slightly varying misincorporation efficiencies. Full-length extension of shorter primers paired with templates containing the N(6)-adenyl PAH derivatives proceeded to apparent completion at 45 degrees C in the presence of added dimethyl sulfoxide. Analysis of the products by high-performance liquid chromatography/collision-induced mass spectrometry indicated the presence of mixtures of products with each PAH adduct. These mixtures correspond to both error-free synthesis and mixtures of polymerization/realignment steps. With an unmodified template, only the expected A:T and G:C pairing was detected in the primer extension products under these conditions, with no frameshifts. These results demonstrate the complexity of polymerization opposite these bulky N(6)-adenyl PAH adducts, even with a single polymerase.
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Affiliation(s)
- Hong Zang
- Department of Biochemistry and Chemistry, Vanderbilt University, Nashville, Tennessee 37232-0146, USA
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77
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Lotierzo M, Raux E, Tse Sum Bui B, Goasdoue N, Libot F, Florentin D, Warren MJ, Marquet A. Biotin Synthase Mechanism: Mutagenesis of the YNHNLD Conserved Motif†,‡. Biochemistry 2006; 45:12274-81. [PMID: 17014080 DOI: 10.1021/bi060662m] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biotin synthase, a member of the "radical SAM" family, catalyzes the final step of the biotin biosynthetic pathway, namely, the insertion of a sulfur atom into dethiobiotin (DTB). The active form of the enzyme contains two iron-sulfur clusters, a [4Fe-4S](2+) cluster liganded by Cys-53, Cys-57, and Cys-60 and the S-adenosylmethionine (AdoMet or SAM) cosubstrate and a [2Fe-2S](2+) cluster liganded by Cys-97, Cys-128, Cys-188, and Arg-260. Single-point mutation of each of these six conserved cysteines produced inactive variants. In this work, mutants of other highly conserved residues from the Y(150)NHNLD motif are described. They have properties similar to those of the wild-type enzyme with respect to their cluster content and characteristics. For all of them, the as-isolated form, which contains an air-stable [2Fe-2S](2+) center, can additionally accommodate an air-sensitive [4Fe-4S](2+) center which is generated by incubation under anaerobic conditions with Fe(2+) and S(2-). Their spectroscopic properties are similar to those of the wild type. However, they are inactive, except the mutant H152A that exhibits a weak activity. We show that the mutants, inactive in producing biotin, are also unable to cleave AdoMet and to produce the deoxyadenosyl radical (AdoCH(2)(*)). In the case of H152A, a value of 5.5 +/- 0.4 is found for the 5'-deoxyadenosine (AdoCH(3)):biotin ratio, much higher than the value of 2.8 +/- 0.3 usually observed with the wild type. This reveals a greater contribution of the abortive process in which the AdoCH(2)(*) radical is quenched by hydrogen atoms from the protein or from some components of the system. Thus, in this case, the coupling between the production of AdoCH(2)(*) and its reaction with the hydrogen at C-6 and C-9 of DTB is less efficient than that in the wild type, probably because of geometry's perturbation within the active site.
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Affiliation(s)
- Manuela Lotierzo
- Université Pierre et Marie Curie-Paris 6, CNRS UMR 7613, (Synthèse, Structure et Fonction de Molécules Bioactives), FR2769, Case Courrier 182, 4 place Jussieu, 75005 Paris, France
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78
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Buis JM, Cheek J, Kalliri E, Broderick JB. Characterization of an Active Spore Photoproduct Lyase, a DNA Repair Enzyme in the Radical S-Adenosylmethionine Superfamily. J Biol Chem 2006; 281:25994-6003. [PMID: 16829680 DOI: 10.1074/jbc.m603931200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The major photoproduct in UV-irradiated Bacillus spore DNA is a unique thymine dimer called spore photoproduct (SP, 5-thyminyl-5,6-dihydrothymine). The enzyme spore photoproduct lyase (SP lyase) has been found to catalyze the repair of SP dimers to thymine monomers in a reaction that requires S-adenosylmethionine. We present here the first detailed characterization of catalytically active SP lyase, which has been anaerobically purified from overexpressing Escherichia coli. Anaerobically purified SP lyase is monomeric and is red-brown in color. The purified enzyme contains approximately 3.1 iron and 3.0 acid-labile S(2-) per protein and has a UV-visible spectrum characteristic of iron-sulfur proteins (410 nm (11.9 mM(-1) cm(-1)) and 450 nm (10.5 mM(-1) cm(-1))). The X-band EPR spectrum of the purified enzyme shows a nearly isotropic signal (g = 2.02) characteristic of a [3Fe-4S]1+ cluster; reduction of SP lyase with dithionite results in the appearance of a new EPR signal (g = 2.03, 1.93, and 1.89) with temperature dependence and g values consistent with its assignment to a [4Fe-4S]1+ cluster. The reduced purified enzyme is active in SP repair, with a specific activity of 0.33 micromol/min/mg. Only a catalytic amount of S-adenosylmethionine is required for DNA repair, and no irreversible cleavage of S-adenosylmethionine into methionine and 5'-deoxyadenosine is observed during the reaction. Label transfer from [5'-3H]S-adenosylmethionine to repaired thymine is observed, providing evidence to support a mechanism in which a 5'-deoxyadenosyl radical intermediate directly abstracts a hydrogen from SP C-6 to generate a substrate radical, and subsequent to radical-mediated beta-scission, a product thymine radical abstracts a hydrogen from 5'-deoxyadenosine to regenerate the 5'-deoxyadenosyl radical. Together, our results support a mechanism in which S-adenosylmethionine acts as a catalytic cofactor, not a substrate, in the DNA repair reaction.
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Affiliation(s)
- Jeffrey M Buis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
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79
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Smart DJ, Chipman JK, Hodges NJ. Activity of OGG1 variants in the repair of pro-oxidant-induced 8-oxo-2'-deoxyguanosine. DNA Repair (Amst) 2006; 5:1337-45. [PMID: 16861056 DOI: 10.1016/j.dnarep.2006.06.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Revised: 06/01/2006] [Accepted: 06/02/2006] [Indexed: 11/17/2022]
Abstract
Cells are continuously exposed to damaging reactive oxygen species (ROS), which are produced from both endogenous and exogenous sources. 8-Oxodeoxyguanosine (8-oxodG) is an abundant base lesion formed during oxidative stress which, if not repaired, can give rise to G:C-->T:A transversions in DNA. The 8-oxoguanine DNA glycosylase-1 (OGG1)-initiated base excision repair (BER) pathway operates to remove 8-oxodG lesions. Ogg1 deletion and polymorphism may result in a hypermutator phenotype and susceptibility to oxidative pathologies including cancer. Limited and conflicting evidence exists regarding the repair capacity of a prevalent human OGG1 (hOGG1) polymorphism, the Cys326-hOGG1 variant. The formamidopyrimidine DNA glycosylase (FPG)-modified comet assay was used to investigate the ability of sodium dichromate, potassium bromate and Ro19-8022 (+light) to induce DNA damage in mogg1(-/-) null (KO) and wild-type (WT) mouse embryonic fibroblasts (MEFs) and to assess hOGG1 variant-initiated BER capacities under conditions of oxidative stress. Treatment of WT MEFs with these pro-oxidant agents induced direct DNA strand breaks in a concentration-dependent manner, whereas, identical treatment of KO MEFs produced no effect. In contrast, KO MEFs accumulated significantly more FPG-sensitive sites than WT MEFs. Expression of hOGG1 in KO MEFs restored the WT phenotype in response to all pro-oxidants tested. The results suggest OGG1-initiated BER generates direct DNA strand breaks detected by the conventional comet assay, thus it is important that researchers do not interpret these as direct damage per se but rather a reflection of the repair process. The data also indicate Cys326-hOGG1-initiated BER is transiently impaired with respect to Ser326-hOGG1 (wild-type)- and Gly326-hOGG1 (artificial)-initiated BER following pro-oxidant treatment, possibly via hOGG1 cysteine 326 oxidation. This finding suggests the homozygous cys326/cys326 genotype may be classified as a biomarker of disease susceptibility, which is in support of a growing body of epidemiological evidence.
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Affiliation(s)
- D J Smart
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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80
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Abstract
Findings from epidemiologic studies have been important in evaluating risk of exposure to many contaminants in drinking water. In the case of bromate, a byproduct of ozone disinfection of water, it is unlikely that observational studies of populations exposed to bromate in drinking water will be as revealing as studies of other contaminants, unless risks are much higher than predicted from laboratory studies of rodents. Occupational exposure to bromate has occurred in the flour milling and baking industries, as well as in chemical production of potassium bromate, used as a flour additive. The feasibility of a cohort study of bromate-exposed workers should be evaluated by studying the conditions and levels of exposure in these occupational settings. Bromate exposure causes oxidative damage to guanine bases of DNA, producing 8-hydroxy-guanine (8-OH-Gua), which is excised by 8-oxoguanosine glycosylase (OGG1) and excreted in the urine. Polymorphic variants of OGG1 in human populations have been associated with elevated cancer risk. 8-OH-Gua and 8-hydroxy-deoxyguanosine (8-OHdG) have been used as biomarkers of oxidative damage in many human studies, and it would be feasible to employ these indicators in controlled clinical experimental settings to see if exposure to bromate in water at levels close to the maximum contaminant level influences urinary levels of excretion, and if so, to help quantify the level of oxidative damage. Such a study could fill an important data gap by providing human data to help estimate the carcinogenic risk from this exposure.
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Affiliation(s)
- Kenneth P Cantor
- Occupational & Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, 6120 Executive Plaza South, Bethesda, MD 20892, USA.
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81
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Conners R, Hooley E, Clarke AR, Thomas S, Brady RL. Recognition of Oxidatively Modified Bases within the Biotin-binding Site of Avidin. J Mol Biol 2006; 357:263-74. [PMID: 16413579 DOI: 10.1016/j.jmb.2005.12.054] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Revised: 12/14/2005] [Accepted: 12/15/2005] [Indexed: 11/23/2022]
Abstract
Oxidative damage of DNA results in the formation of many products, including 8-oxodeoxyguanosine, which has been used as a marker to quantify DNA damage. Earlier studies have demonstrated that avidin, a protein prevalent in egg-white and which has high affinity for the vitamin biotin, binds to 8-oxodeoxyguanosine and related bases. In this study, we have determined crystal structures of avidin in complex with 8-oxodeoxyguanosine and 8-oxodeoxyadenosine. In each case, the base is observed to bind within the biotin-binding site of avidin. However, the mode of association between the bases and the protein varies and, unlike in the avidin:biotin complex, complete ordering of the protein in this region does not accompany binding. Fluorescence studies indicate that in solution the individual bases, and a range of oligonucleotides, bind to avidin with micromolar affinity. Only one of the modes of binding observed is consistent with recognition of oxidised purines when incorporated within a DNA oligomer, and from this structure a model is proposed for the selective binding of avidin to DNA containing oxidatively damaged deoxyguanosine. These studies illustrate the molecular basis by which avidin might act as a marker of DNA damage, although the low levels of binding observed are inconsistent with the recognition of oxidised purines forming a major physiological role for avidin.
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Affiliation(s)
- Rebecca Conners
- Department of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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82
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Abstract
In Pseudomonas aeruginosa, cell-cell communication based on N-acyl-homoserine lactone (AHL) signal molecules (termed quorum sensing) is known to control the production of extracellular virulence factors. Hence, in pathogenic interactions with host organisms, the quorum-sensing (QS) machinery can confer a selective advantage on P. aeruginosa. However, as shown by transcriptomic and proteomic studies, many intracellular metabolic functions are also regulated by quorum sensing. Some of these serve to regenerate the AHL precursors methionine and S-adenosyl-methionine and to degrade adenosine via inosine and hypoxanthine. The fact that a significant percentage of clinical and environmental isolates of P. aeruginosa is defective for QS because of mutation in the major QS regulatory gene lasR, raises the question of whether the QS machinery can have a negative impact on the organism's fitness. In vitro, lasR mutants have a higher probability to escape lytic death in stationary phase under alkaline conditions than has the QS-proficient wild type. Similar selective forces might also operate in natural environments.
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Affiliation(s)
- Karin Heurlier
- Institute of Infection, Immunity, and Inflammation, Centre for Biomolecular Sciences, Nottingham University, Nottingham NG7 2RD, UK
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83
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Ishchenko AA, Deprez E, Maksimenko A, Brochon JC, Tauc P, Saparbaev MK. Uncoupling of the base excision and nucleotide incision repair pathways reveals their respective biological roles. Proc Natl Acad Sci U S A 2006; 103:2564-9. [PMID: 16473948 PMCID: PMC1413785 DOI: 10.1073/pnas.0508582103] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The multifunctional DNA repair enzymes apurinic/apyrimidinic (AP) endonucleases cleave DNA at AP sites and 3'-blocking moieties generated by DNA glycosylases in the base excision repair pathway. Alternatively, in the nucleotide incision repair (NIR) pathway, the same AP endonucleases incise DNA 5' of a number of oxidatively damaged bases. At present, the physiological relevance of latter function remains unclear. Here, we report genetic dissection of AP endonuclease functions in base excision repair and NIR pathways. Three mutants of Escherichia coli endonuclease IV (Nfo), carrying amino acid substitutions H69A, H109A, and G149D have been isolated. All mutants were proficient in the AP endonuclease and 3'-repair diesterase activities but deficient in the NIR. Analysis of metal content reveals that all three mutant proteins have lost one of their intrinsic zinc atoms. Expression of the nfo mutants in a repair-deficient strain of E. coli complemented its hypersensitivity to alkylation but not to oxidative DNA damage. The differential drug sensitivity of the mutants suggests that the NIR pathway removes lethal DNA lesions generated by oxidizing agents. To address the physiological relevance of the NIR pathway in human cells, we used the fluorescence quenching mechanism of molecular beacons. We show that in living cells a major human AP endonuclease, Ape1, incises DNA containing alpha-anomeric 2'-deoxyadenosine, indicating that the intracellular environment supports NIR activity. Our data establish that NIR is a distinct and separable function of AP endonucleases essential for handling lethal oxidative DNA lesions.
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Affiliation(s)
- Alexander A. Ishchenko
- Groupe Réparation de l’ADN, Unité Mixte de Recherche 8126, Centre National de la Recherche Scientifique, Institut Gustave Roussy, 94805 Villejuif Cedex, France
| | - Eric Deprez
- Laboratoire de Biotechnologie et Pharmacologie Génétique Appliquée, Unité Mixte de Recherche 8113, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Cachan, 94235 Cachan Cedex, France; and
| | - Andrei Maksimenko
- Laboratoire de Biotechnologie et Pharmacologie Génétique Appliquée, Unité Mixte de Recherche 8113, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Cachan, 94235 Cachan Cedex, France; and
- BioAlliance Pharma, 59, Boulevard du Général Martial Valin, 75015 Paris, France
| | - Jean-Claude Brochon
- Laboratoire de Biotechnologie et Pharmacologie Génétique Appliquée, Unité Mixte de Recherche 8113, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Cachan, 94235 Cachan Cedex, France; and
| | - Patrick Tauc
- Laboratoire de Biotechnologie et Pharmacologie Génétique Appliquée, Unité Mixte de Recherche 8113, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Cachan, 94235 Cachan Cedex, France; and
| | - Murat K. Saparbaev
- Groupe Réparation de l’ADN, Unité Mixte de Recherche 8126, Centre National de la Recherche Scientifique, Institut Gustave Roussy, 94805 Villejuif Cedex, France
- To whom correspondence should be addressed. E-mail:
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84
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Choudhary S, Doherty KM, Handy CJ, Sayer JM, Yagi H, Jerina DM, Brosh RM. Inhibition of Werner syndrome helicase activity by benzo[a]pyrene diol epoxide adducts can be overcome by replication protein A. J Biol Chem 2005; 281:6000-9. [PMID: 16380375 DOI: 10.1074/jbc.m510122200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
RecQ helicases are believed to function in repairing replication forks stalled by DNA damage and may also play a role in the intra-S-phase checkpoint, which delays the replication of damaged DNA, thus permitting repair to occur. Since little is known regarding the effects of DNA damage on RecQ helicases, and because the replication and recombination defects in Werner syndrome cells may reflect abnormal processing of damaged DNA associated with the replication fork, we examined the effects of specific bulky, covalent adducts at N(6) of deoxyadenosine (dA) or N(2) of deoxyguanosine (dG) on Werner (WRN) syndrome helicase activity. The adducts are derived from the optically active 7,8-diol 9,10-epoxide (DE) metabolites of the carcinogen benzo[a]pyrene (BaP). The results demonstrate that WRN helicase activity is inhibited in a strand-specific manner by BaP DE-dG adducts only when on the translocating strand. These adducts either occupy the minor groove without significant perturbation of DNA structure (trans adducts) or cause base displacement at the adduct site (cis adducts). In contrast, helicase activity is only mildly affected by intercalating BaP DE-dA adducts that locally perturb DNA double helical structure. This differs from our previous observation that intercalating dA adducts derived from benzo[c]phenanthrene (BcPh) DEs inhibit WRN activity in a strand- and stereospecific manner. Partial unwinding of the DNA helix at BaP DE-dA adduct sites may make such adducted DNAs more susceptible to the action of helicase than DNA containing the corresponding BcPh DE-dA adducts, which cause little or no destabilization of duplex DNA. The single-stranded DNA binding protein RPA, an auxiliary factor for WRN helicase, enabled the DNA unwinding enzyme to overcome inhibition by either the trans-R or cis-R BaP DE-dG adduct, suggesting that WRN and RPA may function together to unwind duplex DNA harboring specific covalent adducts that otherwise block WRN helicase acting alone.
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Affiliation(s)
- Saba Choudhary
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health/DHHS, Baltimore, MD 21224, USA
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85
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Nair J, Sinitsina O, Vasunina EA, Nevinsky GA, Laval J, Bartsch H. Age-dependent increase of etheno-DNA-adducts in liver and brain of ROS overproducing OXYS rats. Biochem Biophys Res Commun 2005; 336:478-82. [PMID: 16137653 DOI: 10.1016/j.bbrc.2005.08.114] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2005] [Accepted: 08/12/2005] [Indexed: 01/30/2023]
Abstract
Reactive oxygen species (ROS) and lipid peroxidation (LPO) play a role in aging and degenerative diseases. To correlate oxidative stress and LPO-derived DNA damage, we determined etheno-DNA-adducts in liver and brain from ROS overproducing OXYS rats in comparison with age-matched Wistar rats. Liver DNA samples from 3- and 15-month-old OXYS and Wistar rats were analyzed for 1,N6-ethenodeoxyadenosine (epsilondA) and 3,N4-ethenodeoxycytidine (epsilondC) by immunoaffinity/32P-postlabelling. While epsilondA and epsilondC levels were not different in young rats, adduct levels were significantly higher in old OXYS rats when compared to old Wistar or young OXYS rats. Frozen rat brain sections were analyzed for epsilondA by immunostaining of nuclei. Brains from old OXYS rats accumulated epsilondA more frequently than age-matched Wistar rats. Our results demonstrate increased LPO-induced DNA damage in organs of OXYS rats which correlates with their known shorter life-span and elevated frequency of chronic degenerative diseases.
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Affiliation(s)
- Jagadeesan Nair
- Division of Toxicology and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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86
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Byrns MC, Vu CC, Peterson LA. The formation of substituted 1,N6-etheno-2'-deoxyadenosine and 1,N2-etheno-2'-deoxyguanosine adducts by cis-2-butene-1,4-dial, a reactive metabolite of furan. Chem Res Toxicol 2005; 17:1607-13. [PMID: 15606136 DOI: 10.1021/tx049866z] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Furan is an environmental chemical that induces liver toxicity and tumor formation in rodents, leading to its classification as a probable human carcinogen. cis-2-Butene-1,4-dial, the metabolite considered responsible for furan's toxicological effects, is mutagenic in the Ames assay and reacts with 2'-deoxycytidine (dCyd), 2'-deoxyadenosine (dAdo), and 2'-deoxyguanosine (dGuo) to form previously characterized diastereomeric adducts. The initially formed dCyd adducts are stable to rearrangement, while the dAdo and dGuo adducts are unstable and rearrange to form secondary products. On the basis of UV absorbance, fluorescence, 1H NMR, and mass spectral data, the rearrangement product of the dAdo adduct was identified as the substituted etheno-dAdo adduct, 1''-[3-(2'-deoxy-beta-D-erythropentafuranosyl)-3H-imidazo[2,1-i]purin-8-yl]ethane-2''-al. The NMR characterization of the O-methyloxime derivative of the secondary dGuo adduct, along with mass spectral and UV data on the underivatized adduct, allowed for its structural assignment as the substituted etheno-dGuo compound, 3-(2'-deoxy-beta-D-erythropentafuranosyl)imidazo-7-(ethane-2''-al)[1,2-alpha]purine-9-one. The characterization of the primary and secondary products formed in the reaction of cis-2-butene-1,4-dial with nucleosides is important for understanding the mechanism of furan-induced carcinogenesis. These secondary adducts retain a reactive aldehyde with the potential to form cross-links and are likely to contribute significantly to furan's toxic and carcinogenic effects.
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Affiliation(s)
- Michael C Byrns
- Division of Environmental Health Sciences and Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
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87
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Abstract
Ricin toxin A-chain (RTA) depurinates a single adenylate on a GAGA stem-loop region of eukaryotic 28S RNA, making it a potent toxin. Steady state rate analysis is used to establish the kinetic parameters for depurination of short RNA, DNA, and RNA-DNA hybrids of GAGA linear segments and stem-loop regions as substrates for RTA. Both stem and tetraloop structures are essential for action on RNA. For DNA stem-loop substrates, stem stability plays a small role in enhancing catalytic turnover but can enhance binding by up to 3 orders of magnitude. DNA sequences of d[GAGA] without stem-loop structures are found to be slow substrates for RTA. In contrast, equivalent RNA sequences exhibit no activity with RTA. Introduction of a deoxyadenosine at the depurination site of short RNA oligonucleotides restores catalytic function. NMR analysis indicates that the short, nonsubstrate GAGA is converted to substrate in GdAGA by the presence of a more flexible ribosyl group at the deoxyadenosine site. Conversion between C2'-endo and C2'-exo conformations at the deoxyadenosine site moves the 3'- and 5'-phosphorus atoms by 1.1 A, and the former is proposed to place them in a catalytically favorable configuration. The ability to use short RNA-DNA hybrids as substrates for RTA permits exploration of related structures to function as substrates and inhibitors.
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Affiliation(s)
- Tim K Amukele
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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88
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Keszler G, Virga S, Spasokoukotskaja T, Bauer PI, Sasvari-Szekely M, Staub M. Activation of deoxycytidine kinase by deoxyadenosine: implications in deoxyadenosine-mediated cytotoxicity. Arch Biochem Biophys 2005; 436:69-77. [PMID: 15752710 DOI: 10.1016/j.abb.2005.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2004] [Revised: 01/13/2005] [Indexed: 11/17/2022]
Abstract
The inborn deficiency of adenosine deaminase is characterised by accumulation of excess amounts of cytotoxic deoxyadenine nucleotides in lymphocytes. Formation of dATP requires phosphorylation of deoxyadenosine by deoxycytidine kinase (dCK), the main nucleoside salvage enzyme in lymphoid cells. Activation of dCK by a number of genotoxic agents including 2-chlorodeoxyadenosine, a deamination-resistant deoxyadenosine analogue, was found previously. Here, we show that deoxyadenosine itself is also a potent activator of dCK if its deamination was prevented by the adenosine deaminase inhibitor deoxycoformycin. In contrast, deoxycytidine was found to prevent stimulation of dCK by various drugs. The activated form of dCK was more resistant to tryptic digestion, indicating that dCK undergoes a substrate-independent conformational change upon activation. Elevated dCK activities were accompanied by decreased pyrimidine nucleotide levels whereas cytotoxic dATP pools were selectively enhanced. dCK activity was found to be downregulated by growth factor and MAP kinase signalling, providing a potential tool to slow the rate of dATP accumulation in adenosine deaminase deficiency.
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Affiliation(s)
- Gergely Keszler
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, P.O. Box 260, H-1444 Budapest, Hungary.
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89
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Dolezelova E, Zurovec M, Dolezal T, Simek P, Bryant PJ. The emerging role of adenosine deaminases in insects. Insect Biochem Mol Biol 2005; 35:381-389. [PMID: 15804573 DOI: 10.1016/j.ibmb.2004.12.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2004] [Revised: 11/10/2004] [Accepted: 12/21/2004] [Indexed: 05/24/2023]
Abstract
Adenosine deaminases catalyze the deamination of adenosine and deoxyadenosine into their respective inosine nucleosides. Recent sequencing of the genomes of several model organisms and human reveal that Metazoa usually have more than one adenosine deaminase gene. A deficiency in the gene encoding the major enzyme is lethal in mouse and Drosophila and leads to severe combined deficiency (SCID) in human. In these organisms, enzyme deficiency causes increased adenosine/deoxyadenosine concentration in body fluids and some organs. Elevated levels of adenosine and deoxyadenosine are toxic to certain mammalian and insect cells, and it was shown for human and mouse that it is a primary cause of pathophysiological effects. Data suggest that the major role of adenosine deaminases in various taxa is the protection of tissues against increased levels of adenosine and deoxyadenosine. This review also discusses potential roles of adenosine deaminases in Drosophila metamorphosis and the employment of a Drosophila model to study the cell-specific toxicity of elevated nucleoside levels.
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Affiliation(s)
- Eva Dolezelova
- Institute of Entomology, Czech Acad. Sci. and Faculty of Biology, University of South Bohemia, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
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90
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Abstract
A key step in the mechanism of all adenosylcobalamin-dependent enzymes is the abstraction of a hydrogen atom from the substrate by a 5'-deoxyadenosyl radical generated by homolytic fission of the coenzyme cobalt-carbon bond. We have investigated the isotope effects associated with this process for glutamate mutase reacting with deuterated glutamate. The kinetics of deuterium incorporation into 5'-deoxyadenosine (5'-dA) during the reaction were followed by rapid chemical quench, using HPLC and electrospray mass spectrometry to analyze the 5'-dA formed. The kinetics of 5'-dA formation are biphasic, comprising a rapid phase k(app) = 37 +/- 3 s(-)(1) and a slower phase k(app) = 0.9 +/- 0.4 s(-)(1). The mass spectral data clearly show that the faster phase is associated with the formation of monodeuterated 5'-dA whereas the slower phase is associated with the incorporation of a second and then a third deuterium into 5'-dA. This observation implies that a large inverse equilibrium secondary isotope effect is associated with the formation of 5'-dA from adenosylcobalamin. The primary deuterium kinetic isotope effects on V and V/K for the formation of 5'-dA were determined from time-based and competition experiments. (D)V = 2.4 +/-0.4 whereas (D)(V/K) = 10 +/- 0.4, implying that an isotopically insensitive step is partially rate-determining. The additional data provided by these experiments cause us to revise our interpretation of earlier UV-visible stopped-flow kinetic measurements of AdoCbl homolysis obtained with deuterated substrates.
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Affiliation(s)
- Mou-Chi Cheng
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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91
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Hori M, Fujikawa K, Kasai H, Harashima H, Kamiya H. Dual hydrolysis of diphosphate and triphosphate derivatives of oxidized deoxyadenosine by Orf17 (NtpA), a MutT-type enzyme. DNA Repair (Amst) 2005; 4:33-9. [PMID: 15533835 DOI: 10.1016/j.dnarep.2004.07.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2004] [Indexed: 10/26/2022]
Abstract
To determine whether the Orf17 (NtpA) protein of Escherichia coli, a MutT-type enzyme, functions as a hydrolyzing enzyme for a damaged deoxyribonucleotide, we purified the recombinant Orf17 protein and incubated it with oxidized deoxyribonucleotides. Of the deoxyribonucleoside 5'-triphosphates tested, 8-hydroxy-2'-deoxyadenosine 5'-triphosphate was hydrolyzed by this protein. Unexpectedly, the Orf17 protein degraded 8-hydroxy-2'-deoxyadenosine 5'-diphosphate 2.3-fold more efficiently than the corresponding triphosphate. Thus, this protein is the first MutT-type enzyme that hydrolyzes both the triphosphate and diphosphate derivatives of a deoxyribonucleoside, with similar efficiencies. These results suggest that the Orf17 protein may be involved in the hydrolysis of oxidized dATP and dADP.
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Affiliation(s)
- Mika Hori
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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92
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Olsen R, Molander P, Øvrebø S, Ellingsen DG, Thorud S, Thomassen Y, Lundanes E, Greibrokk T, Backman J, Sjöholm R, Kronberg L. Reaction of Glyoxal with 2‘-Deoxyguanosine, 2‘-Deoxyadenosine, 2‘-Deoxycytidine, Cytidine, Thymidine, and Calf Thymus DNA: Identification of DNA Adducts. Chem Res Toxicol 2005; 18:730-9. [PMID: 15833033 DOI: 10.1021/tx0496688] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glyoxal (ethanedial) is an increasingly used industrial chemical that has been found to be mutagenic in bacteria and mammalian cells. In this study, the reactions of glyoxal with 2'-deoxyguanosine, 2'-deoxyadenosine, 2'-deoxycytidine, cytidine, thymidine, and calf thymus DNA have been studied in aqueous buffered solutions. The nucleoside adducts were isolated by reversed-phase liquid chromatography and characterized by their UV absorbance and 1H and 13C NMR spectroscopic and mass spectrometric features. The reaction with 2'-deoxyguanosine gave one adduct, the previously known 3-(2'-deoxy-beta-D-erythro-pentofuranosyl)-5,6,7-trihydro-6,7-dihydroxyimidazo[1,2-a]purine-9-one adduct. The reaction of 2'-deoxyadenosine with glyoxal resulted in the formation of a previously not reported N6-(hydroxyacetyl)-2'-deoxyadenosine adduct. In the reaction of glyoxal with 2'-deoxycytidine and cytidine at neutral conditions and 37 degrees C, 5-hydroxyacetyl pyrimidine derivatives were obtained. When the cytidine reaction was performed at pH 4.5 and 50 degrees C, the 5-hydroxyacetyl derivative of uridine was formed through deamination of cytidine-glyoxal. Adducts in the thymidine reaction could not be detected. In the reaction of glyoxal with calf thymus DNA, the 2'-deoxyguanosine-glyoxal and 2'-deoxyadenosine-glyoxal adducts were obtained, the former being the major adduct.
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Affiliation(s)
- Raymond Olsen
- National Institute of Occupational Health, P.O. Box 8149 Dep., N-0033 Oslo, Norway
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93
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Lee JE, Singh V, Evans GB, Tyler PC, Furneaux RH, Cornell KA, Riscoe MK, Schramm VL, Howell PL. Structural rationale for the affinity of pico- and femtomolar transition state analogues of Escherichia coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase. J Biol Chem 2005; 280:18274-82. [PMID: 15746096 DOI: 10.1074/jbc.m414471200] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Immucillin and DADMe-Immucillin inhibitors are tight binding transition state mimics of purine nucleoside phosphorylases (PNP). 5'-Methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) is proposed to form a similar transition state structure as PNP. The companion paper describes modifications of the Immucillin and DADMe-Immucillin inhibitors to better match transition state features of MTAN and have led to 5'-thio aromatic substitutions that extend the inhibition constants to the femtomolar range (Singh, V., Evans, G. B., Lenz, D. H., Mason, J., Clinch, K., Mee, S., Painter, G. F., Tyler, P. C., Furneaux, R. H., Lee, J. E., Howell, P. L., and Schramm, V. L. (2005) J. Biol. Chem. 280, 18265-18273). 5'-Methylthio-Immucillin A (MT-ImmA) and 5'-methylthio-DADMe-Immucillin A (MT-DADMe-ImmA) exhibit slow-onset inhibition with K(i)(*) of 77 and 2 pm, respectively, and were selected for structural analysis as the parent compounds of each class of transition state analogue. The crystal structures of Escherichia coli MTAN complexed with MT-ImmA and MT-DADMe-ImmA were determined to 2.2 A resolution and compared with the existing MTAN inhibitor complexes. These MTAN-transition state complexes are among the tightest binding enzyme-ligand complexes ever described and analysis of their mode of binding provides extraordinary insight into the structural basis for their affinity. The MTAN-MT-ImmA complex reveals the presence of a new ion pair between the 4'-iminoribitol atom and the nucleophilic water (WAT3) that captures key features of the transition state. Similarly, in the MTAN-MT-DADMe-ImmA complex a favorable hydrogen bond or ion pair interaction between the cationic 1'-pyrrolidine atom and WAT3 is crucial for tight affinity. Distance analysis of the nucleophile and leaving group show that MT-ImmA is a mimic of an early transition state, while MT-DADMe-ImmA is a better mimic of the highly dissociated transition state of E. coli MTAN.
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Affiliation(s)
- Jeffrey E Lee
- Structural Biology and Biochemistry, Research Institute, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
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94
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Loureiro APM, de Arruda Campos IP, Gomes OF, di Mascio P, Medeiros MHG. Structural characterization of diastereoisomeric ethano adducts derived from the reaction of 2'-deoxyguanosine with trans,trans-2,4-decadienal. Chem Res Toxicol 2005; 17:641-9. [PMID: 15144221 DOI: 10.1021/tx034225+] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Background levels of exocyclic DNA adducts have been detected in rodent and human tissues. Several studies have focused on bifunctional electrophiles generated from lipid peroxidation as one of the endogenous sources of these lesions. We have previously shown that the reaction of 2'-deoxyguanosine (dGuo) with trans,trans-2,4-decadienal (DDE), a highly cytotoxic aldehyde generated as a product of lipid peroxidation in cell membranes, results in the formation of a number of different base derivatives. Three of these derivatives have been fully characterized as 1,N(2)-etheno-2'-deoxyguanosine adducts. In the present work, four additional adducts, designated A3-A6, were isolated from in vitro reactions by reversed-phase HPLC and fully characterized on the basis of spectroscopic measurements. Adducts A3-A6 are four diastereoisomeric 1,N(2)-hydroxyethano-2'-deoxyguanosine derivatives possessing a carbon side chain with a double bond and a hydroxyl group. The systematic name of these adducts is 6-hydroxy-3-(2'-deoxy-beta-D-erythro-pentafuranosyl)-7-((E)-1-hydroxy-oct-2-enyl)-3,5,6,7-tetrahydro-imidazo[1,2-a]purin-9-one. The proposed reaction mechanism yielding adducts A3-A6 involves DDE epoxidation at C2, followed by nucleophilic addition of the exocyclic amino group of dGuo to the C1 of the aldehyde and cyclization, via nucleophilic attack, on the C2 epoxy group by N-1. The formation of adducts A1-A6 has been investigated in acidic, neutral, and basic pH in the presence of H(2)O(2) or tert-butyl hydroperoxide. Neutral conditions, in the presence of H(2)O(2), have favored the formation of adducts A1 and A2, with minor amounts of A3-A6, which were prevalent under basic conditions. These data indicate that DDE can modify DNA bases through different oxidative pathways involving its two double bonds. It is important to structurally characterize DNA base derivatives induced by alpha,beta-unsaturated aldehydes so that the genotoxic risks associated with the lipid peroxidation process can be assessed.
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Affiliation(s)
- Ana Paula M Loureiro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, CEP 05508-900, Sao Paulo, Brazil
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95
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Abstract
Increased levels of nucleic acid oxidation have been described as part of normal brain aging and have been demonstrated to occur in multiple neurological disorders. The basis for increased nucleic acid oxidation in each of these conditions is presently unknown. Proteasome inhibition occurs in a host of neurodegenerative conditions and likely contributes to increased levels of oxidative damage and neurotoxicity. In the present study we demonstrate for the first time the ability of proteasome inhibition to increase the level of nucleic acid oxidation in primary neuron and astrocyte cultures. Administration of proteasome inhibitors (MG262, MG115) at concentrations that do not induce neuron death in the first 24 h of treatment, dramatically increase the levels of 8-hydroxy-2'-deoxyguanosine (8-OHdG) and 8-hydroxyguanosine (8OHG) immunoreactivity in both cell types. Neurons underwent larger increases in nucleic acid oxidation compared to astrocyte cultures. While both DNA and RNA oxidation were observed following proteasome inhibition, RNA appeared to undergo a greater degree of oxidation than DNA. Both 18S and 28S ribosomal RNA were dramatically decreased following proteasome inhibition. Interestingly, an accumulation of unprocessed and/or cross-linked RNA species was observed following proteasome inhibition. Taken together, these data indicate the ability of proteasome inhibition to increase the levels of nucleic acid oxidation in both neurons and astrocytes, and suggest that proteasome inhibition may have deleterious effects on transcription and translation in both neurons and glia.
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Affiliation(s)
- Qunxing Ding
- Department of Anatomy and Neurobiology, University of Kentucky, Lexington, Kentucky, USA
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96
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Webb MR, Reid GP, Munasinghe VRN, Corrie JET. A series of related nucleotide analogues that aids optimization of fluorescence signals in probing the mechanism of P-loop ATPases, such as actomyosin. Biochemistry 2005; 43:14463-71. [PMID: 15533051 DOI: 10.1021/bi0486334] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have synthesized a set of ATP and ADP analogues that have a fluorophore linked to the nucleotide via the 3'-position of the ribose moiety. Combinations of three different coumarins are each attached via different length linkers. A linker based on propylenediamine increases the separation between the nucleotide and fluorophore relative to that of the previously reported ethylenediamine-linked coumarin nucleotides [Webb, M. R., and Corrie, J. E. T. (2001) Biophys. J. 81, 1562-1569]. A synthesis of 3'-amino-3'-deoxyATP is described using a combination of chemical and enzymatic procedures, mostly from published methods for synthesis of this compound but with some modifications that improved the convenience of the experimental procedures. This compound is used as a basis of a series of analogues with effectively a zero-length linker. Fluorescence properties of all these analogues are described, together with the kinetics of their interaction with rabbit skeletal myosin subfragment 1 in the presence and absence of actin. One particular analogue, deac-aminoATP [3'-(7-diethylaminocoumarin-3-carbonylamino)-3'-deoxyadenosine 5'-triphosphate], shows a 17-fold enhancement of fluorescence upon binding to this (skeletal) myosin II. As the diphosphate, it exhibits a large signal change upon dissociation from the actomyosin, with kinetics similar to those of natural ADP. The ability of this set of analogues to produce large signals indicated potential uses when scarce proteins are studied in small amounts.
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Affiliation(s)
- Martin R Webb
- National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom.
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97
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Abstract
We have synthesized the deoxyadenosine derivative tethering a phenyl group (X), which mimics the Watson-Crick A/T base pair. The RNA/DNA hybrid duplexes containing X in the middle of the DNA sequence showed a similar thermal stability regardless of the ribonucleotide species (A, G, C, or U) opposite to X, probably because of the phenyl group stacking inside of the duplex accompanied by the opposite ribonucleotide base flipped in an extrahelical position. The RNA strand hybridized with the DNA strand bearing X was cleaved on the 3'-side of the ribonucleotide opposite to X in the presence of MgCl2, and the RNA sequence to be cleaved was not restricted. The site-specific RNA hydrolysis suggests that the DNA strand bearing X has the advantage of the site-selective base flipping in the target sequence and the development of a "universal deoxyribozyme" to exclusively cleave a target RNA sequence.
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Affiliation(s)
- Shu-ichi Nakano
- Frontier Institute for Biomolecular Engineering Research and Department of Chemistry, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan
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98
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Sauter M, Cornell KA, Beszteri S, Rzewuski G. Functional analysis of methylthioribose kinase genes in plants. Plant Physiol 2004; 136:4061-71. [PMID: 15557090 PMCID: PMC535837 DOI: 10.1104/pp.104.053587] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Revised: 10/21/2004] [Accepted: 10/21/2004] [Indexed: 05/20/2023]
Abstract
Through a biochemical and a genetic approach, we have identified several plant genes encoding methylthioribose (MTR) kinase, an enzyme involved in recycling of methionine through the methylthioadenosine (MTA) cycle. OsMTK1, an MTR kinase from rice (Oryza sativa), is 48.6 kD in size and shows cooperative kinetics with a V(max) of 4.9 pmol/min and a K0.5 of 16.8 microm. MTR kinase genes are the first genes to be identified from the MTA cycle in plants. Insertional mutagenesis of the unique AtMTK gene in Arabidopsis (Arabidopsis thaliana) resulted in an inability of plants to grow on MTA as a supplemental sulfur source. MTK knock-out plants were not impaired in growth under standard conditions, indicating that the MTA cycle is a nonessential metabolic pathway in Arabidopsis when sulfur levels are replete. In rice, OsMTK genes were strongly up-regulated in shoots and roots when plants were exposed to sulfur starvation. Gene expression was largely unaffected by lack of nitrogen or iron in the nutrient solution, indicating that OsMTK regulation was linked specifically to sulfur metabolism.
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Affiliation(s)
- Margret Sauter
- Botanisches Institut, Universität Kiel, 24098 Kiel, Germany.
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99
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Abstract
8-oxo-7, 8-dihydrodeoxyguanosine (8-oxo-dG), one of the representative oxidative DNA lesions, frequently mispairs with the incoming dAMP during mammalian DNA replication. Mispaired dA is removed by post-replicative base excision repair (BER) initiated by adenine DNA glycosylase, MYH, creating an apurinic (AP) site. The subsequent mechanism ensuring a dC:8-oxo-dG pair, a substrate for 8-oxoguanine DNA glycosylase (OGG1), remains to be elucidated. At the nucleotide insertion step, none of the mammalian DNA polymerases examined exclusively inserted dC opposite 8-oxo-dG that was located in a gap. AP endonuclease 1, which possesses 3'-->5' exonuclease activity and potentially serves as a proofreader, did not discriminate dA from dC that was located opposite 8-oxo-dG. However, human DNA ligases I and III joined 3'-dA terminus much more efficiently than 3'-dC terminus when paired to 8-oxo-dG. In reconstituted short-patch BER, repair products contained only dA opposite 8-oxo-dG. These results indicate that human DNA ligases discriminate dC from dA and that MYH-initiated short-patch BER is futile and hence this BER must proceed to long-patch repair, even if it is initiated as short-patch repair, through strand displacement synthesis from the ligation-resistant dC terminus to generate the OGG1 substrate, dC:8-oxo-dG pair.
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Affiliation(s)
- Keiji Hashimoto
- Laboratory of Chemical Biology, Department of Pharmacological Sciences, State University of New York, Stony Brook, NY 11794-8651, USA
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100
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Ham AJL, Engelward BP, Koc H, Sangaiah R, Meira LB, Samson LD, Swenberg JA. New immunoaffinity-LC-MS/MS methodology reveals that Aag null mice are deficient in their ability to clear 1,N6-etheno-deoxyadenosine DNA lesions from lung and liver in vivo. DNA Repair (Amst) 2004; 3:257-65. [PMID: 15177041 DOI: 10.1016/j.dnarep.2003.11.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2003] [Accepted: 11/06/2003] [Indexed: 10/26/2022]
Abstract
The mouse alkyladenine DNA glycosylase (Aag) initiates base excision repair with a broad substrate range that includes the highly mutagenic exocyclic etheno DNA base adduct 1,N6-ethenodeoxyadenosine ((epsilon)dA). Previous attempts to determine the in vivo role of Aag in (epsilon)dA repair were complicated by technological difficulties in measuring low levels of (epsilon)dA in genomic DNA. Here we describe the development of a new method for (epsilon)dA detection in genomic DNA that couples an immunoaffinity purification with LC-MS/MS analysis and that utilizes an isotopically labeled internal standard. We go on to describe the application of this method to measuring the in vivo repair of (epsilon)dA base lesions in liver and lung tissue of wild type and Aag null mice. Our results demonstrate that while Aag clearly represents the major DNA repair enzyme for the in vivo removal (epsilon)dA bases, these lesions can also be eliminated from the genome via an alternative mechanism.
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Affiliation(s)
- Amy-Joan L Ham
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill 27599, USA
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