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Negisho K, Shibru S, Matros A, Pillen K, Ordon F, Wehner G. Association Mapping of Drought Tolerance Indices in Ethiopian Durum Wheat ( Triticum turgidum ssp. durum). FRONTIERS IN PLANT SCIENCE 2022; 13:838088. [PMID: 35693182 PMCID: PMC9178276 DOI: 10.3389/fpls.2022.838088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Ethiopia is a major producer of durum wheat in sub-Saharan Africa. However, its production is prone to drought stress as it is fully dependent on rain, which is erratic and unpredictable. This study aimed to detect marker-trait associations (MTAs) and quantitative trait loci (QTLs) related to indices. Six drought tolerance indices, i.e., drought susceptibility index (DSI), geometric mean productivity (GMP), relative drought index (RDI), stress tolerance index (STI), tolerance index (TOL), and yield stability index (YSI) were calculated from least-square means (lsmeans) of grain yield (GY) and traits significantly (p < 0.001) correlated with grain yield (GY) under field drought stress (FDS) and field non-stress (FNS) conditions. GY, days to grain filling (DGF), soil plant analysis development (SPAD) chlorophyll meter, seeds per spike (SPS), harvest index (HI), and thousand kernel weight (TKW) were used to calculate DSI, GMP, RDI, STI, TOL, and YSI drought indices. Accessions, DW084, DW082, DZ004, C037, and DW092 were selected as the top five drought-tolerant based on DSI, RDI, TOL, and YSI combined ranking. Similarly, C010, DW033, DW080, DW124-2, and C011 were selected as stable accessions based on GMP and STI combined ranking. A total of 184 MTAs were detected linked with drought indices at -log10p ≥ 4.0,79 of which were significant at a false discovery rate (FDR) of 5%. Based on the linkage disequilibrium (LD, r 2 ≥ 0.2), six of the MTAs with a positive effect on GY-GMP were detected on chromosomes 2B, 3B, 4A, 5B, and 6B, explaining 14.72, 10.07, 26.61, 21.16, 21.91, and 22.21% of the phenotypic variance, respectively. The 184 MTAs were clustered into 102 QTLs. Chromosomes 1A, 2B, and 7A are QTL hotspots with 11 QTLs each. These chromosomes play a key role in drought tolerance and respective QTL may be exploited by marker-assisted selection for improving drought stress tolerance in wheat.
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Affiliation(s)
- Kefyalew Negisho
- National Agricultural Biotechnology Research Center, Ethiopian Institute of Agricultural Research (EIAR), Holeta, Ethiopia
| | - Surafel Shibru
- Melkassa Research Center, Ethiopian Institute of Agricultural Research (EIAR), Melkassa, Ethiopia
| | - Andrea Matros
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin Luther University, Halle, Germany
| | - Frank Ordon
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Gwendolin Wehner
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
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2
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Singh V, Johansson P, Ekedahl E, Lin YL, Hammarsten O, Westerlund F. Quantification of single-strand DNA lesions caused by the topoisomerase II poison etoposide using single DNA molecule imaging. Biochem Biophys Res Commun 2022; 594:57-62. [DOI: 10.1016/j.bbrc.2022.01.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/11/2022] [Indexed: 11/02/2022]
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3
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Swan RL, Cowell IG, Austin CA. Mechanisms to repair stalled Topoisomerase II-DNA covalent complexes. Mol Pharmacol 2021; 101:24-32. [PMID: 34689119 DOI: 10.1124/molpharm.121.000374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/11/2021] [Indexed: 11/22/2022] Open
Abstract
DNA topoisomerases regulate the topological state of DNA, relaxing DNA supercoils and resolving catenanes and knots that result from biological processes such as transcription and replication. DNA topoisomerase II (TOP2) enzymes achieve this by binding DNA and introducing an enzyme-bridged DNA double-strand break (DSB) where each protomer of the dimeric enzyme is covalently attached to the 5' end of the cleaved DNA via an active site tyrosine phosphodiester linkage. The enzyme then passes a second DNA duplex though the DNA break, before religation and release of the enzyme. However, this activity is potentially hazardous to the cell, as failure to complete religation leads to persistent TOP2 protein-DNA covalent complexes which are cytotoxic. Indeed, this property of topoisomerase has been exploited in cancer therapy in the form of topoisomerase poisons which block the religation stage of the reaction cycle, leading to an accumulation of topoisomerase-DNA adducts. A number of parallel cellular processes have been identified that lead to removal of these covalent TOP2-DNA complexes facilitating repair of the resulting protein-free DSB by standard DNA repair pathways. These pathways presumably arose to repair spontaneous stalled or poisoned TOP2-DNA complexes, but understanding their mechanisms also has implications for cancer therapy, particularly resistance to anti-cancer TOP2 poisons and the genotoxic side effects of these drugs. Here we review recent progress in the understanding of the processing to TOP2 DNA covalent complexes., The basic components and mechanisms plus the additional layer of complexity posed by the post-translational modifications that modulate these pathways. Significance Statement Multiple pathways have been reported for removal and repair of TOP2-DNA covalent complexes to ensure the timely and efficient repair of TOP2-DNA covalent adducts to protect the genome. Post-translational modifications such as ubiquitination and SUMOylation are involved in the regulation of TOP2-DNA complex repair. Small molecule inhibitors of these post translational modifications may help to improve outcomes of TOP2 poison chemotherapy, for example by increasing TOP2 poison cytotoxicity and reducing genotoxicity, but this remains to be determined.
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Affiliation(s)
- Rebecca L Swan
- Biosciences Institute, Newcastle University, United Kingdom
| | - Ian G Cowell
- Institute for Cell and Molecular Biosciences, Newcastle University, United Kingdom
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4
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Tsuda M, Kitamasu K, Hosokawa S, Nakano T, Ide H. Repair of trapped topoisomerase II covalent cleavage complexes: Novel proteasome-independent mechanisms. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:170-184. [PMID: 31608820 DOI: 10.1080/15257770.2019.1674332] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Topoisomerase II (TOP2) resolves topologically entwined duplex DNA. It generates a transient DNA double-strand break intermediate, known as TOP2 cleavage complex (TOP2cc) that contains a covalent link between TOP2 and the 5'-terminus of the incised DNA duplex. Etoposide, a frontline anticancer drug, freezes the intermediate and forms irreversible TOP2ccs. Tyrosyl-DNA phosphodiesterase 2 (TDP2) is thought to repair irreversible TOP2ccs by hydrolyzing the phosphodiester bond between TOP2 and DNA after the proteasomal degradation of trapped TOP2ccs. However, the functional cooperation between TOP2 and proteasome in the repair of trapped TOP2ccs in vivo remains unknown. In this study, we analyze the repair of etoposide-induced TOP2ccs in wild-type and TDP2-deficient (TDP2-/-) TK6 cells in the absence and presence of MG132, a potent proteasome inhibitor. The results suggested that TOP2ccs were repaired by proteasome-dependent and proteasome-independent pathways. Both proteasome-dependent and proteasome-independent pathways were further subdivided into TDP2-dependent and TDP2-independent pathways, indicating that four pathways operate in the repair of TOP2ccs. In cell survival assays, MG132 increased the etoposide sensitivity of TDP2-/- cells, supporting the TDP2-independent and proteasome-dependent pathway among these multiple repair pathways. We also demonstrated that TDP2 released TOP2 from DNA that contained etoposide-induced TOP2cc without proteolytic degradation in vitro. Taken together, the present findings uncover novel proteasome-independent mechanisms for the repair of TOP2ccs.
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Affiliation(s)
- Masataka Tsuda
- Program of Mathematical and Life Sciences, Department of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kaito Kitamasu
- Program of Mathematical and Life Sciences, Department of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Seiji Hosokawa
- Program of Mathematical and Life Sciences, Department of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Toshiaki Nakano
- DNA Damage Chemistry Research Group, Institute for Quantum Life Science, National Institutes of Quantum and Radiological Science and Technology, Kizugawa-shi, Japan
| | - Hiroshi Ide
- Program of Mathematical and Life Sciences, Department of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
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5
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Wang W, Daley JM, Kwon Y, Xue X, Krasner DS, Miller AS, Nguyen KA, Williamson EA, Shim EY, Lee SE, Hromas R, Sung P. A DNA nick at Ku-blocked double-strand break ends serves as an entry site for exonuclease 1 (Exo1) or Sgs1-Dna2 in long-range DNA end resection. J Biol Chem 2018; 293:17061-17069. [PMID: 30224356 DOI: 10.1074/jbc.ra118.004769] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/10/2018] [Indexed: 12/14/2022] Open
Abstract
The repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) is initiated by nucleolytic resection of the DNA break ends. The current model, being based primarily on genetic analyses in Saccharomyces cerevisiae and companion biochemical reconstitution studies, posits that end resection proceeds in two distinct stages. Specifically, the initiation of resection is mediated by the nuclease activity of the Mre11-Rad50-Xrs2 (MRX) complex in conjunction with its cofactor Sae2, and long-range resection is carried out by exonuclease 1 (Exo1) or the Sgs1-Top3-Rmi1-Dna2 ensemble. Using fully reconstituted systems, we show here that DNA with ends occluded by the DNA end-joining factor Ku70-Ku80 becomes a suitable substrate for long-range 5'-3' resection when a nick is introduced at a locale proximal to one of the Ku-bound DNA ends. We also show that Sgs1 can unwind duplex DNA harboring a nick, in a manner dependent on a species-specific interaction with the ssDNA-binding factor replication protein A (RPA). These biochemical systems and results will be valuable for guiding future endeavors directed at delineating the mechanistic intricacy of DNA end resection in eukaryotes.
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Affiliation(s)
- Weibin Wang
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520 and
| | - James M Daley
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520 and
| | - Youngho Kwon
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520 and.,Departments of Biochemistry and Structural Biology
| | - Xiaoyu Xue
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520 and
| | - Danielle S Krasner
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520 and
| | - Adam S Miller
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520 and
| | - Kevin A Nguyen
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520 and
| | | | | | - Sang Eun Lee
- Radiation Oncology, and.,Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas 78229
| | | | - Patrick Sung
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520 and .,Departments of Biochemistry and Structural Biology
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6
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Effect of TDP2 on the Level of TOP2-DNA Complexes and SUMOylated TOP2-DNA Complexes. Int J Mol Sci 2018; 19:ijms19072056. [PMID: 30011940 PMCID: PMC6073685 DOI: 10.3390/ijms19072056] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/05/2018] [Accepted: 07/11/2018] [Indexed: 11/19/2022] Open
Abstract
DNA topoisomerase II (TOP2) activity involves a normally transient double-strand break intermediate in which the enzyme is coupled to DNA via a 5′-phosphotyrosyl bond. However, etoposide and other topoisomerase drugs poison the enzyme by stabilising this enzyme-bridged break, resulting in the accumulation of TOP2-DNA covalent complexes with cytotoxic consequences. The phosphotyrosyl diesterase TDP2 appears to be required for efficient repair of this unusual type of DNA damage and can remove 5′-tyrosine adducts from a double-stranded oligonucleotide substrate. Here, we adapt the trapped in agarose DNA immunostaining (TARDIS) assay to investigate the role of TDP2 in the removal of TOP2-DNA complexes in vitro and in cells. We report that TDP2 alone does not remove TOP2-DNA complexes from genomic DNA in vitro and that depletion of TDP2 in cells does not slow the removal of TOP2-DNA complexes. Thus, if TDP2 is involved in repairing TOP2 adducts, there must be one or more prior steps in which the protein-DNA complex is processed before TDP2 removes the remaining 5′ tyrosine DNA adducts. While this is partly achieved through the degradation of TOP2 adducts by the proteasome, a proteasome-independent mechanism has also been described involving the SUMOylation of TOP2 by the ZATT E3 SUMO ligase. The TARDIS assay was also adapted to measure the effect of TDP2 knockdown on levels of SUMOylated TOP2-DNA complexes, which together with levels of double strand breaks were unaffected in K562 cells following etoposide exposure and proteasomal inhibition.
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7
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Allen B, Pezone A, Porcellini A, Muller MT, Masternak MM. Non-homologous end joining induced alterations in DNA methylation: A source of permanent epigenetic change. Oncotarget 2018; 8:40359-40372. [PMID: 28423717 PMCID: PMC5522286 DOI: 10.18632/oncotarget.16122] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/07/2017] [Indexed: 01/11/2023] Open
Abstract
In addition to genetic mutations, epigenetic revision plays a major role in the development and progression of cancer; specifically, inappropriate DNA methylation or demethylation of CpG residues may alter the expression of genes that promote tumorigenesis. We hypothesize that DNA repair, specifically the repair of DNA double strand breaks (DSB) by Non-Homologous End Joining (NHEJ) may play a role in this process. Using a GFP reporter system inserted into the genome of HeLa cells, we are able to induce targeted DNA damage that enables the cells, after successfully undergoing NHEJ repair, to express WT GFP. These GFP+ cells were segregated into two expression classes, one with robust expression (Bright) and the other with reduced expression (Dim). Using a DNA hypomethylating drug (AzadC) we demonstrated that the different GFP expression levels was due to differential methylation statuses of CpGs in regions on either side of the break site. Deep sequencing analysis of this area in sorted Bright and Dim populations revealed a collection of different epi-alleles that display patterns of DNA methylation following repair by NHEJ. These patterns differ between Bright and Dim cells which are hypo- and hypermethylated, respectively, and between the post-repair populations and the original, uncut cells. These data suggest that NHEJ repair facilitates a rewrite of the methylation landscape in repaired genes, elucidating a potential source for the altered methylation patterns seen in cancer cells, and understanding the mechanism by which this occurs could provide new therapeutic targets for preventing this process from contributing to tumorigenesis.
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Affiliation(s)
- Brittany Allen
- College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Antonio Pezone
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, Napoli, Italy
| | | | - Mark T Muller
- Epigenetics Division, TopoGEN, Inc., Buena Vista, CO, USA
| | - Michal M Masternak
- College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA.,Department of Head and Neck Surgery, The Greater Poland Cancer Centre, Poznan, Poland, Europe
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8
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Paudyal SC, Li S, Yan H, Hunter T, You Z. Dna2 initiates resection at clean DNA double-strand breaks. Nucleic Acids Res 2017; 45:11766-11781. [PMID: 28981724 PMCID: PMC5714177 DOI: 10.1093/nar/gkx830] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/30/2017] [Accepted: 09/06/2017] [Indexed: 02/07/2023] Open
Abstract
Nucleolytic resection of DNA double-strand breaks (DSBs) is essential for both checkpoint activation and homology-mediated repair; however, the precise mechanism of resection, especially the initiation step, remains incompletely understood. Resection of blocked ends with protein or chemical adducts is believed to be initiated by the MRN complex in conjunction with CtIP through internal cleavage of the 5' strand DNA. However, it is not clear whether resection of clean DSBs with free ends is also initiated by the same mechanism. Using the Xenopus nuclear extract system, here we show that the Dna2 nuclease directly initiates the resection of clean DSBs by cleaving the 5' strand DNA ∼10-20 nucleotides away from the ends. In the absence of Dna2, MRN together with CtIP mediate an alternative resection initiation pathway where the nuclease activity of MRN apparently directly cleaves the 5' strand DNA at more distal sites. MRN also facilitates resection initiation by promoting the recruitment of Dna2 and CtIP to the DNA substrate. The ssDNA-binding protein RPA promotes both Dna2- and CtIP-MRN-dependent resection initiation, but a RPA mutant can distinguish between these pathways. Our results strongly suggest that resection of blocked and clean DSBs is initiated via distinct mechanisms.
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Affiliation(s)
- Sharad C. Paudyal
- Department of Cell Biology and Physiology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Shan Li
- Department of Cell Biology and Physiology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Hong Yan
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Tony Hunter
- Salk Institute, 10010 N Torrey Pines Road, La Jolla, CA 92037, USA
| | - Zhongsheng You
- Department of Cell Biology and Physiology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
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9
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Jia PP, Junaid M, Ma YB, Ahmad F, Jia YF, Li WG, Pei DS. Role of human DNA2 (hDNA2) as a potential target for cancer and other diseases: A systematic review. DNA Repair (Amst) 2017; 59:9-19. [PMID: 28903076 DOI: 10.1016/j.dnarep.2017.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/29/2017] [Accepted: 09/01/2017] [Indexed: 11/28/2022]
Abstract
DNA nuclease/helicase 2 (DNA2), a multi-functional protein protecting the high fidelity of genomic transmission, plays critical roles in DNA replication and repair processes. In the maturation of Okazaki fragments, DNA2 acts synergistically with other enzymes to cleave the DNA-RNA primer flaps via different pathways. DNA2 is also involved in the stability of mitochondrial DNA and the maintenance of telomeres. Moreover, DNA2 potentially participates in controlling the cell cycle by repairing the DNA replication faults at main checkpoints. In addition, previous evidences demonstrated that DNA2 also functions in the repair process of DNA damages, such as base excision repair (BER). Currently, large studies revealed the structures and functions of DNA2 in prokaryotes and unicellular eukaryotes, such as bacteria and yeast. However, the studies that highlighted the functions of human DNA2 (hDNA2) and the relationships with other multifunctional proteins are still elusive, and more precise investigations are immensely needed. Therefore, this review mainly encompasses the key functions of DNA2 in human cells with various aspects, especially focusing on the genome integrity, and also generalizes the recent insights to the mechanisms related to the occurrence of cancer and other diseases potentially linked to the mutations in DNA2.
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Affiliation(s)
- Pan-Pan Jia
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 401122, China; College of Life Science, Henan Normal University, Xinxiang 453007, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Muhammad Junaid
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 401122, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan-Bo Ma
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 401122, China
| | - Farooq Ahmad
- Sustainable Development Study Centre, GC University Lahore, Pakistan
| | - Yong-Fang Jia
- College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Wei-Guo Li
- College of Life Science, Henan Normal University, Xinxiang 453007, China.
| | - De-Sheng Pei
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 401122, China.
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10
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Pawłowska E, Szczepanska J, Blasiak J. DNA2-An Important Player in DNA Damage Response or Just Another DNA Maintenance Protein? Int J Mol Sci 2017; 18:ijms18071562. [PMID: 28718810 PMCID: PMC5536050 DOI: 10.3390/ijms18071562] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 02/01/2023] Open
Abstract
The human DNA2 (DNA replication helicase/nuclease 2) protein is expressed in both the nucleus and mitochondria, where it displays ATPase-dependent nuclease and helicase activities. DNA2 plays an important role in the removing of long flaps in DNA replication and long-patch base excision repair (LP-BER), interacting with the replication protein A (RPA) and the flap endonuclease 1 (FEN1). DNA2 can promote the restart of arrested replication fork along with Werner syndrome ATP-dependent helicase (WRN) and Bloom syndrome protein (BLM). In mitochondria, DNA2 can facilitate primer removal during strand-displacement replication. DNA2 is involved in DNA double strand (DSB) repair, in which it is complexed with BLM, RPA and MRN for DNA strand resection required for homologous recombination repair. DNA2 can be a major protein involved in the repair of complex DNA damage containing a DSB and a 5' adduct resulting from a chemical group bound to DNA 5' ends, created by ionizing radiation and several anticancer drugs, including etoposide, mitoxantrone and some anthracyclines. The role of DNA2 in telomere end maintenance and cell cycle regulation suggests its more general role in keeping genomic stability, which is impaired in cancer. Therefore DNA2 can be an attractive target in cancer therapy. This is supported by enhanced expression of DNA2 in many cancer cell lines with oncogene activation and premalignant cells. Therefore, DNA2 can be considered as a potential marker, useful in cancer therapy. DNA2, along with PARP1 inhibition, may be considered as a potential target for inducing synthetic lethality, a concept of killing tumor cells by targeting two essential genes.
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Affiliation(s)
- Elzbieta Pawłowska
- Department of Orthodontics, Medical University of Lodz, 92-216 Lodz, Poland.
| | - Joanna Szczepanska
- Department of Pediatric Dentistry, Medical University of Lodz, 92-216 Lodz, Poland.
| | - Janusz Blasiak
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland.
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11
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Sater AK, Moody SA. Using Xenopus to understand human disease and developmental disorders. Genesis 2017; 55. [PMID: 28095616 DOI: 10.1002/dvg.22997] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 11/14/2016] [Indexed: 02/03/2023]
Abstract
Model animals are crucial to biomedical research. Among the commonly used model animals, the amphibian, Xenopus, has had tremendous impact because of its unique experimental advantages, cost effectiveness, and close evolutionary relationship with mammals as a tetrapod. Over the past 50 years, the use of Xenopus has made possible many fundamental contributions to biomedicine, and it is a cornerstone of research in cell biology, developmental biology, evolutionary biology, immunology, molecular biology, neurobiology, and physiology. The prospects for Xenopus as an experimental system are excellent: Xenopus is uniquely well-suited for many contemporary approaches used to study fundamental biological and disease mechanisms. Moreover, recent advances in high throughput DNA sequencing, genome editing, proteomics, and pharmacological screening are easily applicable in Xenopus, enabling rapid functional genomics and human disease modeling at a systems level.
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Affiliation(s)
- Amy K Sater
- Department of Biology and Biochemistry, University of Houston, Houston, Texas
| | - Sally A Moody
- Department of Anatomy and Regenerative Biology, George Washington University School of Medicine and Health Sciences, Washington, District of Columbia
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12
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de Campos-Nebel M, Palmitelli M, González-Cid M. A flow cytometry-based method for a high-throughput analysis of drug-stabilized topoisomerase II cleavage complexes in human cells. Cytometry A 2016; 89:852-60. [PMID: 27517472 DOI: 10.1002/cyto.a.22919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/27/2016] [Accepted: 07/15/2016] [Indexed: 11/08/2022]
Abstract
Topoisomerase II (Top2) is an important target for anticancer therapy. A variety of drugs that poison Top2, including several epipodophyllotoxins, anthracyclines, and anthracenediones, are widely used in the clinic for both hematologic and solid tumors. The poisoning of Top2 involves the formation of a reaction intermediate Top2-DNA, termed Top2 cleavage complex (Top2cc), which is persistent in the presence of the drug and involves a 5' end of DNA covalently bound to a tyrosine from the enzyme through a phosphodiester group. Drug-induced Top2cc leads to Top2 linked-DNA breaks which are the major responsible for their cytotoxicity. While biochemical detection is very laborious, quantification of drug-induced Top2cc by immunofluorescence-based microscopy techniques is time consuming and requires extensive image segmentation for the analysis of a small population of cells. Here, we developed a flow cytometry-based method for the analysis of drug-induced Top2cc. This method allows a rapid analysis of a high number of cells in their cell cycle phase context. Moreover, it can be applied to almost any human cell type, including clinical samples. The methodology is useful for a high-throughput analysis of drugs that poison Top2, allowing not just the discrimination of the Top2 isoform that is targeted but also to track its removal. © 2016 International Society for Advancement of Cytometry.
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Affiliation(s)
- Marcelo de Campos-Nebel
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental (IMEX), Academia Nacional de Medicina, CONICET, Buenos Aires, Argentina.
| | - Micaela Palmitelli
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental (IMEX), Academia Nacional de Medicina, CONICET, Buenos Aires, Argentina
| | - Marcela González-Cid
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental (IMEX), Academia Nacional de Medicina, CONICET, Buenos Aires, Argentina
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13
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Yan H, Tammaro M, Liao S. Collision of Trapped Topoisomerase 2 with Transcription and Replication: Generation and Repair of DNA Double-Strand Breaks with 5' Adducts. Genes (Basel) 2016; 7:genes7070032. [PMID: 27376333 PMCID: PMC4962002 DOI: 10.3390/genes7070032] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/17/2016] [Accepted: 06/24/2016] [Indexed: 11/23/2022] Open
Abstract
Topoisomerase 2 (Top2) is an essential enzyme responsible for manipulating DNA topology during replication, transcription, chromosome organization and chromosome segregation. It acts by nicking both strands of DNA and then passes another DNA molecule through the break. The 5′ end of each nick is covalently linked to the tyrosine in the active center of each of the two subunits of Top2 (Top2cc). In this configuration, the two sides of the nicked DNA are held together by the strong protein-protein interactions between the two subunits of Top2, allowing the nicks to be faithfully resealed in situ. Top2ccs are normally transient, but can be trapped by cancer drugs, such as etoposide, and subsequently processed into DSBs in cells. If not properly repaired, these DSBs would lead to genome instability and cell death. Here, I review the current understanding of the mechanisms by which DSBs are induced by etoposide, the unique features of such DSBs and how they are repaired. Implications for the improvement of cancer therapy will be discussed.
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Affiliation(s)
- Hong Yan
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
| | - Margaret Tammaro
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
| | - Shuren Liao
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
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Liao S, Tammaro M, Yan H. The structure of ends determines the pathway choice and Mre11 nuclease dependency of DNA double-strand break repair. Nucleic Acids Res 2016; 44:5689-701. [PMID: 27084932 PMCID: PMC4937313 DOI: 10.1093/nar/gkw274] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/05/2016] [Indexed: 11/29/2022] Open
Abstract
The key event in the choice of repair pathways for DNA double-strand breaks (DSBs) is the initial processing of ends. Non-homologous end joining (NHEJ) involves limited processing, but homology-dependent repair (HDR) requires extensive resection of the 5′ strand. How cells decide if an end is channeled to resection or NHEJ is not well understood. We hypothesize that the structure of ends is a major determinant and tested this hypothesis with model DNA substrates in Xenopus egg extracts. While ends with normal nucleotides are efficiently channeled to NHEJ, ends with damaged nucleotides or bulky adducts are channeled to resection. Resection is dependent on Mre11, but its nuclease activity is critical only for ends with 5′ bulky adducts. CtIP is absolutely required for activating the nuclease-dependent mechanism of Mre11 but not the nuclease-independent mechanism. Together, these findings suggest that the structure of ends is a major determinant for the pathway choice of DSB repair and the Mre11 nuclease dependency of resection.
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Affiliation(s)
- Shuren Liao
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Margaret Tammaro
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Hong Yan
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
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John R, Ganeshan U, Singh BN, Kaul T, Reddy MK, Sopory SK, Rajam MV. Over-expression of Topoisomerase II Enhances Salt Stress Tolerance in Tobacco. FRONTIERS IN PLANT SCIENCE 2016; 7:1280. [PMID: 27630644 PMCID: PMC5006100 DOI: 10.3389/fpls.2016.01280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 08/11/2016] [Indexed: 05/09/2023]
Abstract
Topoisomerases are unique enzymes having an ability to remove or add DNA supercoils and untangle the snarled DNA. They can cut, shuffle, and religate DNA strands and remove the torsional stress during DNA replication, transcription or recombination events. In the present study, we over-expressed topoisomerase II (TopoII) in tobacco (Nicotiana tabaccum) and examined its role in growth and development as well as salt (NaCl) stress tolerance. Several putative transgenic plants were generated and the transgene integration and expression was confirmed by PCR and Southern blot analyses, and RT-PCR analysis respectively. Percent seed germination, shoot growth, and chlorophyll content revealed that transgenic lines over-expressing the NtTopoIIα-1 gene exhibited enhanced tolerance to salt (150 and 200 mM NaCl) stress. Moreover, over-expression of TopoII lead to the elevation in proline and glycine betaine levels in response to both concentrations of NaCl as compared to wild-type. In response to NaCl stress, TopoII over-expressing lines showed reduced lipid peroxidation derived malondialdehyde (MDA) generation. These results suggest that TopoII plays a pivotal role in salt stress tolerance in plants.
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Affiliation(s)
- Riffat John
- Plant Molecular Biology Laboratory, Department of Botany, University of KashmirSrinagar, India
- *Correspondence: Riffat John
| | - Uma Ganeshan
- Plant Polyamine, Transgenic and RNAi Laboratory, Department of Genetics, University of Delhi South CampusNew Delhi, India
| | - Badri N. Singh
- Plant Biology, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Tanushri Kaul
- Plant Biology, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Malireddy K. Reddy
- Plant Biology, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Sudhir K. Sopory
- Plant Biology, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Manchikatla V. Rajam
- Plant Polyamine, Transgenic and RNAi Laboratory, Department of Genetics, University of Delhi South CampusNew Delhi, India
- Manchikatla V. Rajam
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