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Plasmodium Ape1 is a multifunctional enzyme in mitochondrial base excision repair and is required for efficient transition from liver to blood stage infection. DNA Repair (Amst) 2021; 101:103098. [PMID: 33743509 DOI: 10.1016/j.dnarep.2021.103098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/01/2021] [Accepted: 03/09/2021] [Indexed: 02/02/2023]
Abstract
The malaria parasite has a single mitochondrion which carries multiple tandem repeats of its 6 kb genome encoding three proteins of the electron transport chain. There is little information about DNA repair mechanisms for mitochondrial genome maintenance in Plasmodium spp. Of the two AP-endonucleases of the BER pathway encoded in the parasite nuclear genome, the EndoIV homolog PfApn1 has been identified as a mitochondrial protein with restricted functions. We explored the targeting and biochemical properties of the ExoIII homolog PfApe1. PfApe1 localized in the mitochondrion and exhibited AP-site cleavage, 3'-5' exonuclease, 3'-phosphatase, nucleotide incision repair (NIR) and RNA cleavage activities indicating a wider functional role than PfApn1. The parasite enzyme differed from human APE1 in possessing a large, disordered N-terminal extension. Molecular modelling revealed conservation of structural domains but variations in DNA-interacting residues and an insertion in the α-8 loop suggested differences with APE1. Unlike APE1, where AP-site cleavage and NIR activities could be mutually exclusive based on pH and Mg2+ ion concentration, PfApe1 was optimally active under similar conditions suggesting that it can function both as an AP-endonuclease in BER and directly cleave damaged bases in NIR under similar physiological conditions. To investigate the role of Ape1 in malaria life cycle, we disrupted the gene by double-cross-over homologous recombination. Ape1 knockout (KO) P. berghei parasites showed normal development of blood and mosquito stages. However, inoculation of mice with Ape1 KO salivary gland sporozoites revealed a reduced capacity to initiate blood stage infection. Ape1 KO parasites underwent normal liver stage development until merozoites egressed from hepatocytes. Our results indicated that the delay in pre-patent period was due to the inability of Ape1 KO merosomes to infect erythrocytes efficiently.
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Tiwari A, Kuldeep J, Siddiqi MI, Habib S. Plasmodium falciparumApn1 homolog is a mitochondrial base excision repair protein with restricted enzymatic functions. FEBS J 2019; 287:589-606. [DOI: 10.1111/febs.15032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/18/2019] [Accepted: 08/02/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Anupama Tiwari
- Division of Molecular and Structural Biology CSIR‐Central Drug Research Institute Lucknow India
| | - Jitendra Kuldeep
- Division of Molecular and Structural Biology CSIR‐Central Drug Research Institute Lucknow India
| | - Mohammad Imran Siddiqi
- Division of Molecular and Structural Biology CSIR‐Central Drug Research Institute Lucknow India
| | - Saman Habib
- Division of Molecular and Structural Biology CSIR‐Central Drug Research Institute Lucknow India
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3
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Characterization of biochemical properties of an apurinic/apyrimidinic endonuclease from Helicobacter pylori. PLoS One 2018; 13:e0202232. [PMID: 30110394 PMCID: PMC6093668 DOI: 10.1371/journal.pone.0202232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/30/2018] [Indexed: 01/08/2023] Open
Abstract
Apurinic/apyrimidinic (AP) endonucleases play critical roles in the repair of abasic sites and strand breaks in DNA. Complete genome sequences of Helicobacter pylori reveal that this bacterial specie has a single AP endonuclease. An H. pylori homolog of Xth (HpXth) is a member of exonuclease III family, which is represented by Escherichia coli Xth. Currently, it remains unknown whether this single AP endonuclease has DNA repair activities similar to those of its counterpart in E. coli and other bacteria. We report that HpXth possesses efficient AP site cleavage, 3’-repair phosphodiesterase, and 3’-phosphatase activities but not the nucleotide incision repair function. Optimal reaction conditions for HpXth’s AP endonuclease activity are low ionic strength, high Mg2+ concentration, pH in the range 7–8, and temperature 30 °C. The kinetic parameters measured under steady-state conditions showed that HpXth removes the AP site, 3’-blocking sugar-phosphate, and 3’-terminal phosphate in DNA strand breaks with good efficiency (kcat/KM = 1240, 44, and 5,4 μM–1·min–1, respectively), similar to that of E. coli Xth. As expected, the presence of HpXth protein in AP endonuclease—deficient E. coli xth nfo strain significantly reduced the sensitivity to an alkylating agent and H2O2. Mutation of active site residue D144 in HpXth predicted to be essential for catalysis resulted in a complete loss of enzyme activities. Several important structural features of HpXth were uncovered by homology modeling and phylogenetic analysis. Our data show the DNA substrate specificity of H. pylori AP endonuclease and suggest that HpXth counteracts the genotoxic effects of DNA damage generated by endogenous and host-imposed factors.
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Valenzuela L, Sepúlveda S, Ponce I, Galanti N, Cabrera G. The overexpression of TcAP1 endonuclease confers resistance to infective Trypanosoma cruzi trypomastigotes against oxidative DNA damage. J Cell Biochem 2018; 119:5985-5995. [PMID: 29575156 DOI: 10.1002/jcb.26795] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/20/2018] [Indexed: 01/22/2023]
Abstract
Trypanosoma cruzi, the causative agent of Chagas' disease survives to DNA damage generated by ROS/RNS inside to their different hosts. In recent eukaryotes, oxidative DNA damage is repaired mainly by the Base Excision Repair (BER) pathway, being essential the apurinic/apyrimidinic endonuclease activity. Using a pTREX-gfp vector, the nucleotide sequence that encodes T. cruzi AP endonuclease TcAP1 (orthologue of human APE1) and a putative TcAP1 dominant negative (TcAP1DN), were transfectedand expressed in T. cruzi epimastigotes. TcAP1-GFP and TcAP1DN-GFP were expressed in those modified epimastigotes and found in the parasite nucleus. The endonucleases were purified under native conditions and the AP endonuclease activity was evaluated. While TcAP1 presents the expected AP endonuclease activity TcAP1DN does not. Moreover, TcAP1DN partially inhibits in vitro TcAP1 enzymatic activity. Transfected epimastigotes expressing TcAP1-GFP and TcAP1DN-GFP were differentiated to infective trypomastigotes. The infective parasites maintained both proteins (TcAP1-GFP and TcAP1DN-GFP) in the nucleus. The overexpression of TcAP1-GFP in epimastigotes and trypomastigotes increases the viability of both parasite forms when exposed to oxidative stress while the expression of TcAP1DN-GFP did not show any in vivo inhibitory effect, suggesting that endogenous TcAP1 constitutive expression overcomes the TcAP1DN inhibitory activity. Our results show that TcAP1 is important for trypomastigote survival under oxidative conditions similar to those found in infected mammalian cells, then increasing its permanence in the infected cells and the possibility of development of Chagas disease.
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Affiliation(s)
- Lucía Valenzuela
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Universidad de Chile, Santiago, Chile
| | - Soía Sepúlveda
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Iván Ponce
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Norbel Galanti
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Gonzalo Cabrera
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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5
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Verissimo-Villela E, Kitahara-Oliveira MY, Reis ABDBD, Albano RM, Da-Cruz AM, Bello AR. Functional complementation of Leishmania (Leishmania) amazonensis AP endonuclease gene (lamap) in Escherichia coli mutant strains challenged with DNA damage agents. Mem Inst Oswaldo Cruz 2017; 111:349-54. [PMID: 27223868 PMCID: PMC4878305 DOI: 10.1590/0074-02760150412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 04/09/2016] [Indexed: 01/25/2023] Open
Abstract
During its life cycle Leishmania spp. face several stress conditions
that can cause DNA damages. Base Excision Repair plays an important role in DNA
maintenance and it is one of the most conserved mechanisms in all living organisms.
DNA repair in trypanosomatids has been reported only for Old World
Leishmania species. Here the AP endonuclease from
Leishmania (L.) amazonensis was cloned, expressed in
Escherichia coli mutants defective on the DNA repair machinery,
that were submitted to different stress conditions, showing ability to survive in
comparison to the triple null mutant parental strain BW535. Phylogenetic and multiple
sequence analyses also confirmed that LAMAP belongs to the AP endonuclease class of
proteins.
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Affiliation(s)
- Erika Verissimo-Villela
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Milene Yoko Kitahara-Oliveira
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Ana Beatriz de Bragança Dos Reis
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Rodolpho Mattos Albano
- Laboratório de Genoma, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Alda Maria Da-Cruz
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Alexandre Ribeiro Bello
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
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Akishev Z, Taipakova S, Joldybayeva B, Zutterling C, Smekenov I, Ishchenko AA, Zharkov DO, Bissenbaev AK, Saparbaev M. The major Arabidopsis thaliana apurinic/apyrimidinic endonuclease, ARP is involved in the plant nucleotide incision repair pathway. DNA Repair (Amst) 2016; 48:30-42. [PMID: 27836324 DOI: 10.1016/j.dnarep.2016.10.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 10/25/2016] [Accepted: 10/26/2016] [Indexed: 11/18/2022]
Abstract
Apurinic/apyrimidinic (AP) endonucleases are important DNA repair enzymes involved in two overlapping pathways: DNA glycosylase-initiated base excision (BER) and AP endonuclease-initiated nucleotide incision repair (NIR). In the BER pathway, AP endonucleases cleave DNA at AP sites and 3'-blocking moieties generated by DNA glycosylases, whereas in NIR, the same AP endonucleases incise DNA 5' to a wide variety of oxidized bases. The flowering plant Arabidopsis thaliana contains three genes encoding homologues of major human AP endonuclease 1 (APE1): Arp, Ape1L and Ape2. It has been shown that all three proteins contain AP site cleavage and 3'-repair phosphodiesterase activities; however, it was not known whether the plant AP endonucleases contain the NIR activity. Here, we report that ARP proteins from Arabidopsis and common wheat (Triticum aestivum) contain NIR and 3'→5' exonuclease activities in addition to their AP endonuclease and 3'-repair phosphodiesterase functions. The steady-state kinetic parameters of reactions indicate that Arabidopsis ARP cleaves oligonucleotide duplexes containing α-anomeric 2'-deoxyadenosine (αdA) and 5,6-dihydrouridine (DHU) with efficiencies (kcat/KM=134 and 7.3 μM-1·min-1, respectively) comparable to those of the human counterpart. However, the ARP-catalyzed 3'-repair phosphodiesterase and 3'→5' exonuclease activities (kcat/KM=314 and 34 μM-1·min-1, respectively) were about 10-fold less efficient as compared to those of APE1. Interestingly, homozygous A. thaliana arp-/- mutant exhibited high sensitivity to methyl methanesulfonate and tert-butyl hydroperoxide, but not to H2O2, suggesting that ARP is a major plant AP endonuclease that removes abasic sites and specific types of oxidative DNA base damage. Taken together, these data establish the presence of the NIR pathway in plants and suggest its possible role in the repair of DNA damage generated by oxidative stress.
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Affiliation(s)
- Zhiger Akishev
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - Sabira Taipakova
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - Botagoz Joldybayeva
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - Caroline Zutterling
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Izat Smekenov
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - Alexander A Ishchenko
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Dmitry O Zharkov
- Novosibirsk State University, Novosibirsk 630090, Russia; SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Amangeldy K Bissenbaev
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan.
| | - Murat Saparbaev
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France.
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7
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Feng Z, Kochanek S, Close D, Wang L, Srinivasan A, Almehizia AA, Iyer P, Xie XQ, Johnston PA, Gold B. Design and activity of AP endonuclease-1 inhibitors. J Chem Biol 2015; 8:79-93. [PMID: 26101550 DOI: 10.1007/s12154-015-0131-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 03/25/2015] [Indexed: 12/12/2022] Open
Abstract
Apurinic/apyrimidinic endonuclease-1/redox effector factor-1 (APE-1) is a critical component of base excision repair that excises abasic lesions created enzymatically by the action of DNA glycosylases on modified bases and non-enzymatically by hydrolytic depurination/depyrimidination of nucleobases. Many anticancer drugs generate DNA adducts that are processed by base excision repair, and tumor resistance is frequently associated with enhanced APE-1 expression. Accordingly, APE-1 is a potential therapeutic target to treat cancer. Using computational approaches and the high resolution structure of APE-1, we developed a 5-point pharmacophore model for APE-1 small molecule inhibitors. One of the nM APE-1 inhibitors (AJAY-4) that was identified based on this model exhibited an overall median growth inhibition (GI50) of 4.19 μM in the NCI-60 cell line panel. The mechanism of action is shown to be related to the buildup of abasic sites that cause PARP activation and PARP cleavage, and the activation of caspase-3 and caspase-7, which is consistent with cell death by apoptosis. In a drug combination growth inhibition screen conducted in 10 randomly selected NCI-60 cell lines and with 20 clinically used non-genotoxic anticancer drugs, a synergy was flagged in the SK-MEL-5 melanoma cell line exposed to combinations of vemurafenib, which targets melanoma cells with V600E mutated BRAF, and AJAY-4, our most potent APE-1 inhibitor. The synergy between AJAY-4 and vemurafenib was not observed in cell lines expressing wild-type B-Raf protein. This synergistic combination may provide a solution to the resistance that develops in tumors treated with B-Raf-targeting drugs.
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Affiliation(s)
- Zhiwei Feng
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - Stanton Kochanek
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - David Close
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - LiRong Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - Ajay Srinivasan
- Malaria Vaccine Development Program, New Delhi, 110067 India
| | | | - Prema Iyer
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - Paul A Johnston
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - Barry Gold
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA
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8
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Khanam T, Shukla A, Rai N, Ramachandran R. Critical determinants for substrate recognition and catalysis in the M. tuberculosis class II AP-endonuclease/3'-5' exonuclease III. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:505-16. [PMID: 25748880 DOI: 10.1016/j.bbapap.2015.02.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/02/2015] [Accepted: 02/25/2015] [Indexed: 01/13/2023]
Abstract
The Mycobacterium tuberculosis AP-endonuclease/3'-5' exodeoxyribonuclease (MtbXthA) is an important player in DNA base excision repair (BER). We demonstrate that the enzyme has robust apurinic/apyrimidinic (AP) endonuclease activity, 3'-5' exonuclease, phosphatase, and phosphodiesterase activities. The enzyme functions as an AP-endonuclease at high ionic environments, while the 3'-5'-exonuclease activity is predominant at low ionic environments. Our molecular modelling and mutational experiments show that E57 and D251 are critical for catalysis. Although nicked DNA and gapped DNA are fair substrates of MtbXthA, the gap-size did not affect the excision activity and furthermore, a substrate with a recessed 3'-end is preferred. To understand the determinants of abasic-site recognition, we examined the possible roles of (i) the base opposite the abasic site, (ii) the abasic ribose ring itself, (iii) local distortions in the AP-site, and (iv) conserved residues located near the active site. Our experiments demonstrate that the first three determinants do not play a role in MtbXthA, and in fact the enzyme exhibits robust endonucleolytic activity against single-stranded AP DNA also. Regarding the fourth determinant, it is known that the catalytic-site of AP endonucleases is surrounded by conserved aromatic residues and intriguingly, the exact residues that are directly involved in abasic site recognition vary with the individual proteins. We therefore, used a combination of mutational analysis, kinetic assays, and structure-based modelling, to identify that Y237, supported by Y137, mediates the formation of the MtbXthA-AP-DNA complex and AP-site incision.
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Affiliation(s)
- Taran Khanam
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, Uttar Pradesh 226031, India
| | - Ankita Shukla
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, Uttar Pradesh 226031, India
| | - Niyati Rai
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, Uttar Pradesh 226031, India
| | - Ravishankar Ramachandran
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, Uttar Pradesh 226031, India.
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9
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Tschoeke DA, Nunes GL, Jardim R, Lima J, Dumaresq AS, Gomes MR, de Mattos Pereira L, Loureiro DR, Stoco PH, de Matos Guedes HL, de Miranda AB, Ruiz J, Pitaluga A, Silva FP, Probst CM, Dickens NJ, Mottram JC, Grisard EC, Dávila AM. The Comparative Genomics and Phylogenomics of Leishmania amazonensis Parasite. Evol Bioinform Online 2014; 10:131-53. [PMID: 25336895 PMCID: PMC4182287 DOI: 10.4137/ebo.s13759] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 02/21/2014] [Accepted: 02/25/2014] [Indexed: 12/20/2022] Open
Abstract
Leishmaniasis is an infectious disease caused by Leishmania species. Leishmania amazonensis is a New World Leishmania species belonging to the Mexicana complex, which is able to cause all types of leishmaniasis infections. The L. amazonensis reference strain MHOM/BR/1973/M2269 was sequenced identifying 8,802 codifying sequences (CDS), most of them of hypothetical function. Comparative analysis using six Leishmania species showed a core set of 7,016 orthologs. L. amazonensis and Leishmania mexicana share the largest number of distinct orthologs, while Leishmania braziliensis presented the largest number of inparalogs. Additionally, phylogenomic analysis confirmed the taxonomic position for L. amazonensis within the “Mexicana complex”, reinforcing understanding of the split of New and Old World Leishmania. Potential non-homologous isofunctional enzymes (NISE) were identified between L. amazonensis and Homo sapiens that could provide new drug targets for development.
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Affiliation(s)
- Diogo A Tschoeke
- Pólo de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (Fiocruz/IOC), Rio de Janeiro, RJ, Brazil. ; Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Gisele L Nunes
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Rodrigo Jardim
- Pólo de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (Fiocruz/IOC), Rio de Janeiro, RJ, Brazil. ; Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Joana Lima
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Aline Sr Dumaresq
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Monete R Gomes
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Leandro de Mattos Pereira
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Daniel R Loureiro
- Pólo de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (Fiocruz/IOC), Rio de Janeiro, RJ, Brazil
| | - Patricia H Stoco
- Laboratório de Protozoologia, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Herbert Leonel de Matos Guedes
- Laboratório de Inflamação Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. ; Wellcome Trust Centre for Molecular Parasitology, Institute of Immunity, Infection and Inflammation, College of MVLS, University of Glasgow, Glasgow, UK
| | - Antonio Basilio de Miranda
- Pólo de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (Fiocruz/IOC), Rio de Janeiro, RJ, Brazil. ; Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Jeronimo Ruiz
- Pólo de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (Fiocruz/IOC), Rio de Janeiro, RJ, Brazil. ; Instituto René Rachou (Fiocruz/IRR), Belo Horizonte, MG, Brazil
| | - André Pitaluga
- Laboratório de Biologia Molecular de Parasitas e Vetores, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Floriano P Silva
- Pólo de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (Fiocruz/IOC), Rio de Janeiro, RJ, Brazil. ; Laboratório de Bioquímica de Proteínas e Peptídeos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Christian M Probst
- Pólo de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (Fiocruz/IOC), Rio de Janeiro, RJ, Brazil. ; Instituto Carlos Chagas (Fiocruz/ICC), Curitiba, PR, Brazil
| | - Nicholas J Dickens
- Wellcome Trust Centre for Molecular Parasitology, Institute of Immunity, Infection and Inflammation, College of MVLS, University of Glasgow, Glasgow, UK
| | - Jeremy C Mottram
- Wellcome Trust Centre for Molecular Parasitology, Institute of Immunity, Infection and Inflammation, College of MVLS, University of Glasgow, Glasgow, UK
| | - Edmundo C Grisard
- Laboratório de Protozoologia, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Alberto Mr Dávila
- Pólo de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (Fiocruz/IOC), Rio de Janeiro, RJ, Brazil. ; Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
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10
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DNA repair pathways in trypanosomatids: from DNA repair to drug resistance. Microbiol Mol Biol Rev 2014; 78:40-73. [PMID: 24600040 DOI: 10.1128/mmbr.00045-13] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
All living organisms are continuously faced with endogenous or exogenous stress conditions affecting genome stability. DNA repair pathways act as a defense mechanism, which is essential to maintain DNA integrity. There is much to learn about the regulation and functions of these mechanisms, not only in human cells but also equally in divergent organisms. In trypanosomatids, DNA repair pathways protect the genome against mutations but also act as an adaptive mechanism to promote drug resistance. In this review, we scrutinize the molecular mechanisms and DNA repair pathways which are conserved in trypanosomatids. The recent advances made by the genome consortiums reveal the complete genomic sequences of several pathogens. Therefore, using bioinformatics and genomic sequences, we analyze the conservation of DNA repair proteins and their key protein motifs in trypanosomatids. We thus present a comprehensive view of DNA repair processes in trypanosomatids at the crossroads of DNA repair and drug resistance.
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11
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Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis. Proc Natl Acad Sci U S A 2012; 109:16852-7. [PMID: 23035246 DOI: 10.1073/pnas.1206563109] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Base excision repair (BER) is a highly conserved DNA repair pathway throughout all kingdoms from bacteria to humans. Whereas several enzymes are required to complete the multistep repair process of damaged bases, apurinic-apyrimidic (AP) endonucleases play an essential role in enabling the repair process by recognizing intermediary abasic sites cleaving the phosphodiester backbone 5' to the abasic site. Despite extensive study, there is no structure of a bacterial AP endonuclease bound to substrate DNA. Furthermore, the structural mechanism for AP-site cleavage is incomplete. Here we report a detailed structural and biochemical study of the AP endonuclease from Neisseria meningitidis that has allowed us to capture structural intermediates providing more complete snapshots of the catalytic mechanism. Our data reveal subtle differences in AP-site recognition and kinetics between the human and bacterial enzymes that may reflect different evolutionary pressures.
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Trypanosoma brucei AP endonuclease 1 has a major role in the repair of abasic sites and protection against DNA-damaging agents. DNA Repair (Amst) 2012; 11:53-64. [DOI: 10.1016/j.dnarep.2011.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 10/07/2011] [Accepted: 10/07/2011] [Indexed: 11/20/2022]
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13
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The Hus1 homologue of Leishmania major encodes a nuclear protein that participates in DNA damage response. Mol Biochem Parasitol 2011; 177:65-9. [DOI: 10.1016/j.molbiopara.2011.01.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 01/11/2011] [Accepted: 01/20/2011] [Indexed: 12/29/2022]
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14
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Onyango DO, Naguleswaran A, Delaplane S, Reed A, Kelley MR, Georgiadis MM, Sullivan WJ. Base excision repair apurinic/apyrimidinic endonucleases in apicomplexan parasite Toxoplasma gondii. DNA Repair (Amst) 2011; 10:466-75. [PMID: 21353648 DOI: 10.1016/j.dnarep.2011.01.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/20/2011] [Accepted: 01/25/2011] [Indexed: 10/18/2022]
Abstract
DNA repair is essential for cell viability and proliferation. In addition to reactive oxygen produced as a byproduct of their own metabolism, intracellular parasites also have to manage oxidative stress generated as a defense mechanism by the host. The spontaneous loss of DNA bases due to hydrolysis and oxidative DNA damage in intracellular parasites is great, but little is known about the type of DNA repair machineries that exist in these early-branching eukaryotes. However, it is clear, processes similar to DNA base excision repair (BER) must exist to rectify spontaneous and host-mediated damage in Toxoplasma gondii. Here we report that T. gondii, an opportunistic protozoan pathogen, possesses two apurinic/apyrimidinic (AP) endonucleases that function in DNA BER. We characterize the enzymatic activities of Toxoplasma exonuclease III (ExoIII, or Ape1) and endonuclease IV (EndoIV, or Apn1), designated TgAPE and TgAPN, respectively. Over-expression of TgAPN in Toxoplasma conferred protection from DNA damage, and viable knockouts of TgAPN were not obtainable. We generated an inducible TgAPN knockdown mutant using a ligand-controlled destabilization domain to establish that TgAPN is critical for Toxoplasma to recover from DNA damage. The importance of TgAPN and the fact that humans lack any observable APN family activity highlights TgAPN as a promising candidate for drug development to treat toxoplasmosis.
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Affiliation(s)
- David O Onyango
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, 46202, United States
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15
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Intrinsic apurinic/apyrimidinic (AP) endonuclease activity enables Bacillus subtilis DNA polymerase X to recognize, incise, and further repair abasic sites. Proc Natl Acad Sci U S A 2010; 107:19219-24. [PMID: 20974932 DOI: 10.1073/pnas.1013603107] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The N-glycosidic bond can be hydrolyzed spontaneously or by glycosylases during removal of damaged bases by the base excision repair pathway, leading to the formation of highly mutagenic apurinic/apyrimidinic (AP) sites. Organisms encode for evolutionarily conserved repair machinery, including specific AP endonucleases that cleave the DNA backbone 5' to the AP site to prime further DNA repair synthesis. We report on the DNA polymerase X from the bacterium Bacillus subtilis (PolX(Bs)) that, along with polymerization and 3'-5'-exonuclease activities, possesses an intrinsic AP-endonuclease activity. Both, AP-endonuclease and 3'-5'-exonuclease activities are genetically linked and governed by the same metal ligands located at the C-terminal polymerase and histidinol phosphatase domain of the polymerase. The different catalytic functions of PolX(Bs) enable it to perform recognition and incision at an AP site and further restoration (repair) of the original nucleotide in a standalone AP-endonuclease-independent way.
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Passos-Silva DG, Rajão MA, Nascimento de Aguiar PH, Vieira-da-Rocha JP, Machado CR, Furtado C. Overview of DNA Repair in Trypanosoma cruzi, Trypanosoma brucei, and Leishmania major. J Nucleic Acids 2010; 2010:840768. [PMID: 20976268 PMCID: PMC2952945 DOI: 10.4061/2010/840768] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 07/29/2010] [Accepted: 08/25/2010] [Indexed: 12/18/2022] Open
Abstract
A wide variety of DNA lesions arise due to environmental agents, normal cellular metabolism, or intrinsic weaknesses in the chemical bonds of DNA. Diverse cellular mechanisms have evolved to maintain genome stability, including mechanisms to repair damaged DNA, to avoid the incorporation of modified nucleotides, and to tolerate lesions (translesion synthesis). Studies of the mechanisms related to DNA metabolism in trypanosomatids have been very limited. Together with recent experimental studies, the genome sequencing of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, has revealed interesting features of the DNA repair mechanism in these protozoan parasites, which will be reviewed here.
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Affiliation(s)
- Danielle Gomes Passos-Silva
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
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17
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Collaborative actions in anti-trypanosomatid chemotherapy with partners from disease endemic areas. Trends Parasitol 2010; 26:395-403. [DOI: 10.1016/j.pt.2010.04.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 04/28/2010] [Accepted: 04/29/2010] [Indexed: 11/22/2022]
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Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L, Ficner R. Crystal structure analysis of DNA uridine endonuclease Mth212 bound to DNA. J Mol Biol 2010; 399:604-17. [PMID: 20434457 DOI: 10.1016/j.jmb.2010.04.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 04/21/2010] [Indexed: 11/30/2022]
Abstract
The reliable repair of pre-mutagenic U/G mismatches that originated from hydrolytic cytosine deamination is crucial for the maintenance of the correct genomic information. In most organisms, any uracil base in DNA is attacked by uracil DNA glycosylases (UDGs), but at least in Methanothermobacter thermautotrophicus DeltaH, an alternative strategy has evolved. The exonuclease III homologue Mth212 from the thermophilic archaeon M. thermautotrophicus DeltaH exhibits a DNA uridine endonuclease activity in addition to the apyrimidinic/apurinic site endonuclease and 3'-->5'exonuclease functions. Mth212 alone compensates for the lack of a UDG in a single-step reaction thus substituting the two-step pathway that requires the consecutive action of UDG and apyrimidinic/apurinic site endonuclease. In order to gain deeper insight into the structural basis required for the specific uridine recognition by Mth212, we have characterized the enzyme by means of X-ray crystallography. Structures of Mth212 wild-type or mutant proteins either alone or in complex with DNA substrates and products have been determined to a resolution of up to 1.2 A, suggesting key residues for the uridine endonuclease activity. The insertion of the side chain of Arg209 into the DNA helical base stack resembles interactions observed in human UDG and seems to be crucial for the uridine recognition. In addition, Ser171, Asn153, and Lys125 in the substrate binding pocket appear to have important functions in the discrimination of aberrant uridine against naturally occurring thymidine and cytosine residues in double-stranded DNA.
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Affiliation(s)
- Kristina Lakomek
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, D-37077 Göttingen, Germany
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López-Camarillo C, Lopez-Casamichana M, Weber C, Guillen N, Orozco E, Marchat LA. DNA repair mechanisms in eukaryotes: Special focus in Entamoeba histolytica and related protozoan parasites. INFECTION GENETICS AND EVOLUTION 2009; 9:1051-6. [PMID: 19591963 DOI: 10.1016/j.meegid.2009.06.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 06/22/2009] [Accepted: 06/29/2009] [Indexed: 01/11/2023]
Abstract
Eukaryotic cell viability highly relies on genome stability and DNA integrity maintenance. The cellular response to DNA damage mainly consists of six biological conserved pathways known as homologous recombination repair (HRR), non-homologous end-joining (NHEJ), base excision repair (BER), mismatch repair (MMR), nucleotide excision repair (NER), and methyltransferase repair that operate in a concerted way to minimize genetic information loss due to a DNA lesion. Particularly, protozoan parasites survival depends on DNA repair mechanisms that constantly supervise chromosomes to correct damaged nucleotides generated by cytotoxic agents, host immune pressure or cellular processes. Here we reviewed the current knowledge about DNA repair mechanisms in the most relevant human protozoan pathogens. Additionally, we described the recent advances to understand DNA repair mechanisms in Entamoeba histolytica with special emphasis in the use of genomic approaches based on bioinformatic analysis of parasite genome sequence and microarrays technology.
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Affiliation(s)
- César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, México DF, Mexico.
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Castillo-Acosta VM, Ruiz-Pérez LM, Yang W, González-Pacanowska D, Vidal AE. Identification of a residue critical for the excision of 3'-blocking ends in apurinic/apyrimidinic endonucleases of the Xth family. Nucleic Acids Res 2009; 37:1829-42. [PMID: 19181704 PMCID: PMC2665217 DOI: 10.1093/nar/gkp021] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
DNA single-strand breaks containing 3'-blocking groups are generated from attack of the sugar backbone by reactive oxygen species or after base excision by DNA glycosylase/apurinic/apyrimidinic (AP) lyases. In human cells, APE1 excises sugar fragments that block the 3'-ends thus facilitating DNA repair synthesis. In Leishmania major, the causal agent of leishmaniasis, the APE1 homolog is the class II AP endonuclease LMAP. Expression of LMAP but not of APE1 reverts the hypersensitivity of a xth nfo repair-deficient Escherichia coli strain to the oxidative compound hydrogen peroxide (H(2)O(2)). To identify the residues specifically involved in the repair of oxidative DNA damage, we generated random mutations in the ape1 gene and selected those variants that conferred protection against H(2)O(2). Among the resistant clones, we isolated a mutant in the nuclease domain of APE1 (D70A) with an increased capacity to remove 3'-blocking ends in vitro. D70 of APE1 aligns with A138 of LMAP and mutation of the latter to aspartate significantly reduces its 3'-phosphodiesterase activity. Kinetic analysis shows a novel role of residue D70 in the excision rate of 3'-blocking ends. The functional and structural differences between the parasite and human enzymes probably reflect a divergent molecular evolution of their DNA repair responses to oxidative damage.
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Affiliation(s)
- Víctor M. Castillo-Acosta
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Avda. del Conocimiento s/n, 18100 Armilla (Granada), Spain and Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Luis M. Ruiz-Pérez
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Avda. del Conocimiento s/n, 18100 Armilla (Granada), Spain and Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Wei Yang
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Avda. del Conocimiento s/n, 18100 Armilla (Granada), Spain and Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Dolores González-Pacanowska
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Avda. del Conocimiento s/n, 18100 Armilla (Granada), Spain and Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Antonio E. Vidal
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Avda. del Conocimiento s/n, 18100 Armilla (Granada), Spain and Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
- *To whom correspondence should be addressed. Tel: +34 958 181621 (ext. 518); Fax: +34 958 181632;
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Schmiedel R, Kuettner EB, Keim A, Sträter N, Greiner-Stöffele T. Structure and function of the abasic site specificity pocket of an AP endonuclease from Archaeoglobus fulgidus. DNA Repair (Amst) 2008; 8:219-31. [PMID: 19015049 DOI: 10.1016/j.dnarep.2008.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Revised: 10/09/2008] [Accepted: 10/10/2008] [Indexed: 10/21/2022]
Abstract
The major AP endonuclease in Escherichia coli Exonuclease III (ExoIII) is frequently used in gene technology due to its strong exonucleolytic activity. A thermostabilized variant of ExoIII or a homologous enzyme from thermophilic organisms could be most useful for further applications. For this purpose we characterized a nuclease from the hyperthermophilic archaeon Archaeoglobus fulgidus (Af_Exo), which shares 33% overall sequence identity and 55% similarity to ExoIII. The gene coding for this thermostable enzyme was cloned and expressed in E. coli. The purified protein shows a strong Mg(2+)-dependent nicking activity at AP-sites, nicking of undamaged double-stranded (ds) DNA and a weak exonucleolytic activity. A V217G variant of the enzyme was crystallized with decamer ds-DNA molecule, and the three-dimensional structure was determined to 1.7A resolution. Besides our goal to find or produce a thermostable exonuclease, the structural and catalytic data of Af_Exo and a series of mutant proteins, based on the crystal structure, provide new insight into the mechanism of abasic site recognition and repair. Each of the hydrophobic residues Phe 200, Trp 215 and Val 217, forming a binding pocket for the abasic deoxyribose in Af_Exo, were mutated to glycine or serine. By expanding the size of the binding pocket the unspecific endonucleolytic activity is increased. Thus, size and flexibility of the mostly hydrophobic binding pocket have a significant influence on AP-site specificity. We suggest that its tight fitting to the flipped-out deoxyribose allows for a preferred competent binding of abasic sites. In a larger or more flexible pocket however, intact nucleotides more easily bind in a catalytically competent conformation, resulting in loss of specificity. Moreover, with mutations of Phe 200 and Trp 215 we induced a strong exonucleolytic activity on undamaged DNA.
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Affiliation(s)
- Ramona Schmiedel
- Institute of Biochemistry, Faculty of Biology, Pharmacy and Psychology, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
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Castillo-Acosta VM, Estévez AM, Vidal AE, Ruiz-Perez LM, González-Pacanowska D. Depletion of dimeric all-alpha dUTPase induces DNA strand breaks and impairs cell cycle progression in Trypanosoma brucei. Int J Biochem Cell Biol 2008; 40:2901-13. [PMID: 18656547 DOI: 10.1016/j.biocel.2008.06.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 06/20/2008] [Accepted: 06/24/2008] [Indexed: 11/17/2022]
Abstract
The enzyme deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) is responsible for the control of intracellular levels of dUTP thus controlling the incorporation of uracil into DNA during replication. Trypanosomes and certain eubacteria contain a dimeric dUTP-dUDPase belonging to the recently described superfamily of all-alpha NTP pyrophosphatases which bears no resemblance with typical eukaryotic trimeric dUTPases and presents unique properties regarding substrate specificity and product inhibition. While the biological trimeric enzymes have been studied in detail and the human enzyme has been proposed as a promising novel target for anticancer chemotherapeutic strategies, little is known regarding the biological function of dimeric proteins. Here, we show that in Trypanosoma brucei, the dimeric dUTPase is a nuclear enzyme and that down-regulation of activity by RNAi greatly reduces cell proliferation and increases the intracellular levels of dUTP. Defects in growth could be partially reverted by the addition of exogenous thymidine. dUTPase-depleted cells presented hypersensitivity to methotrexate, a drug that increases the intracellular pools of dUTP, and enhanced uracil-DNA glycosylase activity, the first step in base excision repair. The knockdown of activity produces numerous DNA strand breaks and defects in both S and G2/M progression. Multiple parasites with a single enlarged nucleus were visualized together with an enhanced population of anucleated cells. We conclude that dimeric dUTPases are strongly involved in the control of dUTP incorporation and that adequate levels of enzyme are indispensable for efficient cell cycle progression and DNA replication.
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Affiliation(s)
- Víctor M Castillo-Acosta
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, s/n 18100-Armilla, Granada, Spain
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