1
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Maurya P, Rawat RS, Gupta S, Krishna S, Siddiqi MI, Sashidhara KV, Banerjee D. Synergy between human DNA ligase I and topoisomerase 1 unveils new therapeutic strategy for the management of colorectal cancer. J Biomol Struct Dyn 2024:1-16. [PMID: 38179981 DOI: 10.1080/07391102.2023.2297817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024]
Abstract
DNA topoisomerase 1 (Topo 1) is a pivotal player in various DNA processes, including replication, repair, and transcription. It serves as a target for anticancer drugs like camptothecin and its derivatives (Topotecan and SN-38/Irinotecan). However, the emergence of drug resistance and the associated adverse effects, such as alopecia, anemia, dyspnea, fever, chills, and painful or difficult urination, pose significant challenges in Topo 1-targeted therapy, necessitating urgent attention. Human DNA Ligase 1 (hLig I), recognized primarily for its role in DNA replication and repair of DNA breaks, intriguingly exhibits a DNA relaxation activity akin to Topo 1. This raised the hypothesis that hLig I might compensate for Topo 1 inhibition, contributing to resistance against Topo 1 inhibitors. To explore this hypothesis, we assessed the efficacy of hLig I inhibition alone and in combination with Topo 1 in cancer cells. As anticipated, the overexpression of hLig I was observed after Topo 1 inhibition in colorectal cancer cells, affirming our hypothesis. Previously identified as an inhibitor of hLig I's DNA relaxation activity, compound 27 (C 27), when combined with Topotecan, demonstrated a synergistic antiproliferative effect on colorectal cancer cells. Notably, cells with downregulated hLig I (via siRNA, inhibitors, or genetic manipulation) exhibited significantly heightened sensitivity to Topotecan. This observation strongly supports the concept that hLig I contribute to resistance against clinically relevant Topo 1 inhibitors in colorectal cancers. In conclusion, our findings offer evidence for the synergistic impact of combining hLig I inhibitors with Topotecan in the treatment of colorectal cancers, providing a promising strategy to overcome resistance to Topo 1 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pooja Maurya
- Cancer Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
- Jawaharlal Nehru University, New Delhi, India
| | - Rohit Singh Rawat
- Cancer Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
- Jawaharlal Nehru University, New Delhi, India
| | - Sampa Gupta
- Jawaharlal Nehru University, New Delhi, India
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Shagun Krishna
- Jawaharlal Nehru University, New Delhi, India
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohammad Imran Siddiqi
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Koneni V Sashidhara
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Dibyendu Banerjee
- Cancer Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
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2
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G4-interacting proteins endangering genomic stability at G4 DNA-forming sites. Biochem Soc Trans 2023; 51:403-413. [PMID: 36629511 PMCID: PMC10018705 DOI: 10.1042/bst20221018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/09/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
In guanine-rich DNA strands, base-base interactions among guanines allow the conformational shift from the B-form DNA to the non-canonical quadruplex or G4 structure. The functional significance of G4 DNA in vivo is largely dependent on the interaction with protein factors, many of which contain the arginine-glycine-glycine or RGG repeat and other consensus G4-binding motifs. These G4-interacting proteins can significantly modulate the effect of G4 DNA structure on genome maintenance, either preventing or aggravating G4-assoicated genome instability. While the role of helicases in resolving G4 DNA structure has been extensively discussed, identification and characterization of protein factors contributing to elevation in G4-associated genome instability has been relatively sparse. In this minireview, we will particularly highlight recent discoveries regarding how interaction between certain G4-binding proteins and G4 DNA could exacerbate genome instability potentiated by G4 DNA-forming sequences.
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3
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Takahashi DT, Gadelle D, Agama K, Kiselev E, Zhang H, Yab E, Petrella S, Forterre P, Pommier Y, Mayer C. Topoisomerase I (TOP1) dynamics: conformational transition from open to closed states. Nat Commun 2022; 13:59. [PMID: 35013228 PMCID: PMC8748870 DOI: 10.1038/s41467-021-27686-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 11/17/2021] [Indexed: 12/24/2022] Open
Abstract
Eukaryotic topoisomerases I (TOP1) are ubiquitous enzymes removing DNA torsional stress. However, there is little data concerning the three-dimensional structure of TOP1 in the absence of DNA, nor how the DNA molecule can enter/exit its closed conformation. Here, we solved the structure of thermostable archaeal Caldiarchaeum subterraneum CsTOP1 in an apo-form. The enzyme displays an open conformation resulting from one substantial rotation between the capping (CAP) and the catalytic (CAT) modules. The junction between these two modules is a five-residue loop, the hinge, whose flexibility permits the opening/closing of the enzyme and the entry of DNA. We identified a highly conserved tyrosine near the hinge as mediating the transition from the open to closed conformation upon DNA binding. Directed mutagenesis confirmed the importance of the hinge flexibility, and linked the enzyme dynamics with sensitivity to camptothecin, a TOP1 inhibitor targeting the TOP1 enzyme catalytic site in the closed conformation. Topoisomerase I (TOP1) relaxes both positive and negative supercoils by nicking DNA and after rotation of the broken DNA strand closes the nick. Here, the authors present the DNA free crystal structure of TOP1 from the hyperthermophilic archaeon Caldiarchaeum subterraneum in the open form and discuss the mechanism of how DNA enters the catalytic site of TOP1.
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Affiliation(s)
- Diane T Takahashi
- Institut de Biologie Integrative de la Cellule, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, Cedex, France. .,Institut Pasteur, Université de Paris, CNRS UMR 3528, Unité de Microbiologie Structurale, F-75015, Paris, France. .,Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR 7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, BP 10413, F-67412, Illkirch, France.
| | - Danièle Gadelle
- Institut de Biologie Integrative de la Cellule, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, Cedex, France
| | - Keli Agama
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA
| | - Evgeny Kiselev
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA
| | - Hongliang Zhang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA
| | - Emilie Yab
- Institut Pasteur, Université de Paris, CNRS UMR 3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Stephanie Petrella
- Institut Pasteur, Université de Paris, CNRS UMR 3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Patrick Forterre
- Institut de Biologie Integrative de la Cellule, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, Cedex, France
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA.
| | - Claudine Mayer
- Institut Pasteur, Université de Paris, CNRS UMR 3528, Unité de Microbiologie Structurale, F-75015, Paris, France.,Université de Paris, F-75013, Paris, France.,ICube-UMR7357, CSTB, Centre de Recherche en Biomédecine de Strasbourg, 67084, Strasbourg, France
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4
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Douglas C, Maciulyte V, Zohren J, Snell DM, Mahadevaiah SK, Ojarikre OA, Ellis PJI, Turner JMA. CRISPR-Cas9 effectors facilitate generation of single-sex litters and sex-specific phenotypes. Nat Commun 2021; 12:6926. [PMID: 34862376 PMCID: PMC8642469 DOI: 10.1038/s41467-021-27227-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/05/2021] [Indexed: 11/09/2022] Open
Abstract
Animals are essential genetic tools in scientific research and global resources in agriculture. In both arenas, a single sex is often required in surplus. The ethical and financial burden of producing and culling animals of the undesired sex is considerable. Using the mouse as a model, we develop a synthetic lethal, bicomponent CRISPR-Cas9 strategy that produces male- or female-only litters with one hundred percent efficiency. Strikingly, we observe a degree of litter size compensation relative to control matings, indicating that our system has the potential to increase the yield of the desired sex in comparison to standard breeding designs. The bicomponent system can also be repurposed to generate postnatal sex-specific phenotypes. Our approach, harnessing the technological applications of CRISPR-Cas9, may be applicable to other vertebrate species, and provides strides towards ethical improvements for laboratory research and agriculture.
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Affiliation(s)
- Charlotte Douglas
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - Valdone Maciulyte
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - Jasmin Zohren
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - Daniel M Snell
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | | | - Obah A Ojarikre
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | | | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK.
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5
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Gonzalez-Klein Z, Cuevas-Zuviria B, Wangorsch A, Hernandez-Ramirez G, Pazos-Castro D, Oeo-Santos C, Romero-Sahagun A, Pacios LF, Tome-Amat J, Scheurer S, Diaz-Perales A, Garrido-Arandia M. The key to the allergenicity of lipid transfer protein (LTP) ligands: A structural characterization. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158928. [PMID: 33771708 DOI: 10.1016/j.bbalip.2021.158928] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/15/2021] [Accepted: 03/20/2021] [Indexed: 12/28/2022]
Abstract
Plant lipid transfer proteins are a large family that can be found in all land plants. They have a hydrophobic cavity that allows them to harbor lipids and facilitates their traffic between membranes. However, in humans, this plant protein family is responsible for the main food allergies in the Mediterranean area. Nevertheless, not only the protein itself but also its ligand is relevant for allergic sensitization. The main aim of the present work is to analyse the natural ligands carried by four allergenic LTPs (Tri a 14, Art v 3, Par j 2, and Ole e 7), compared with the previously identified ligand of Pru p 3 (CPT-PHS ligand), and clarify their role within the immunological reactions. Results showed that the ligands of the LTPs studied shared a chemical identity, in which the presence of a polar head was essential to the protein-ligand binding. This ligand was transported through a skin cellular model, and phosphorylated phytosphingosine could be detected as result of cell metabolism. Since sphingosine kinase 1 was overexpressed in keratinocytes incubated with the LTP-ligand complex, this enzyme might be responsible for the phosphorylation of the phytosphingosine fraction of the CPT-PHS ligand. This way, phytosphingosine-1-phosphate could be mimicking the role of the human inflammatory mediator sphingosine-1-phosphate, explaining why LTPs are associated with more severe allergic responses. In conclusion, this work contributes to the understanding of the chemical nature and behavior of lipid ligands carried by allergens, which would help to gain insight into their role during allergic sensitization.
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Affiliation(s)
- Zulema Gonzalez-Klein
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain.
| | - Bruno Cuevas-Zuviria
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain.
| | | | - Guadalupe Hernandez-Ramirez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain.
| | - Diego Pazos-Castro
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain.
| | - Carmen Oeo-Santos
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain; Cellular Degradation Systems Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Alejandro Romero-Sahagun
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain.
| | - Luis F Pacios
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain.
| | - Jaime Tome-Amat
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain.
| | | | - Araceli Diaz-Perales
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain.
| | - María Garrido-Arandia
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain.
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6
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Xia Q, Tian H, Li Y, Yu X, Zhang W, Wang Q. Biomimetic Synthesis of Iridoid Alkaloids as Novel Leads for Fungicidal and Insecticidal Agents. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:12577-12584. [PMID: 33125223 DOI: 10.1021/acs.jafc.0c04885] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Monoterpenoid alkaloids are well known for their broad and excellent biological activities, but their extremely low content and complex chemical structure limit their practical application. This study used the biosynthetic precursor genipin as a basic material to conduct a biomimetic synthesis of iridoid alkaloids. The structures of the iridoid alkaloids were characterized by 1H and 13C NMR spectroscopy and high-resolution mass spectrometry, and their fungicidal and insecticidal activities were evaluated. Bioassay results indicated that iridoid alkaloids possess good to excellent activities against phytopathogenic fungi, diamondback moth, bean aphid, and spider mite. Compound 3s had the most promising activity against three important phytopathogenic fungi Fusarium graminearum (LC50 value of 34.5 μg/mL with a 95% confidence interval of 33.4-35.5 μg/mL), Rhizoctonia solani (18 μg/mL, 15.7-20.8 μg/mL), and Botrytis cinerea (26 μg/mL, 22.4-30.4 μg/mL), thereby emerging as a potential new fungicidal lead. The structure-activity relationship research has shown that the electrical property and steric hindrance sizes of iridoid alkaloids apparently influence fungicidal activity. Moreover, compound 3n exhibited good insecticidal activity against diamondback moth with an LC50 (35.6 μg/mL, 95% confidence interval 19.0-66.6 μg/mL) comparable to that of the commercial insecticide rotenone (35.4 μg/mL, 95% confidence interval 22.2-56.4 μg/mL). This outcome indicates that this compound deserves further study as a potential lead for development of new insecticides.
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Affiliation(s)
- Qing Xia
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Hao Tian
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, People's Republic of China
| | - Yufei Li
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiang Yu
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Weihua Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Qingmin Wang
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, People's Republic of China
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7
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Soren BC, Dasari JB, Ottaviani A, Iacovelli F, Fiorani P. Topoisomerase IB: a relaxing enzyme for stressed DNA. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2020; 3:18-25. [PMID: 35582040 PMCID: PMC9094055 DOI: 10.20517/cdr.2019.106] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 11/12/2022]
Abstract
DNA topoisomerase I enzymes relieve the torsional strain in DNA; they are essential for fundamental molecular processes such as DNA replication, transcription, recombination, and chromosome condensation; and act by cleaving and then religating DNA strands. Over the past few decades, scientists have focused on the DNA topoisomerases biological functions and established a unique role of Type I DNA topoisomerases in regulating gene expression and DNA chromosome condensation. Moreover, the human enzyme is being investigated as a target for cancer chemotherapy. The active site tyrosine is responsible for initiating two transesterification reactions to cleave and then religate the DNA backbone, allowing the release of superhelical tension. The different steps of the catalytic mechanism are affected by various inhibitors; some of them prevent the interaction between the enzyme and the DNA while others act as poisons, leading to TopI-DNA lesions, breakage of DNA, and eventually cellular death. In this review, our goal is to provide an overview of mechanism of human topoisomerase IB action together with the different types of inhibitors and their effect on the enzyme functionality.
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Affiliation(s)
- Bini Chhetri Soren
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Jagadish Babu Dasari
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy.,Present address: Department of Research and Application Development, Biogenex Life Sciences, Telangana 501510, India
| | - Alessio Ottaviani
- Institute of Translational Pharmacology, National Research Council, Rome 00133, Italy
| | - Federico Iacovelli
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Paola Fiorani
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy.,Institute of Translational Pharmacology, National Research Council, Rome 00133, Italy
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8
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Dasari JB, Soren BC, Ottaviani A, Tesauro C, Marino S, Messina B, Fiorani P. Swapping of The N-Terminal Domain of Human Topoisomerase 1B with the Corresponding Plasmodium Falciparum Counterpart Strongly Impairs Enzyme Activity. Rep Biochem Mol Biol 2020; 8:366-375. [PMID: 32582794 PMCID: PMC7275839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 06/03/2019] [Indexed: 06/11/2023]
Abstract
BACKGROUND DNA topoisomerases 1B are a class of ubiquitous enzyme that solves the topological problems associated with biological processes such as replication, transcription and recombination. Numerous sequence alignment of topoisomerase 1B from different species shows that the lengths of different domains as well as their amino acids sequences are quite different. In the present study a hybrid enzyme, generated by swapping the N-terminal of Plasmodium falciparum into the corresponding domain of the human, has been characterized. METHODS The chimeric enzyme was generated using different sets of PCR. The in vitro characterization was carried out using different DNA substrate including radio-labelled oligonucleotides. RESULTS The chimeric enzyme displayed slower relaxation activity, cleavage and re-ligation kinetics strongly perturbed when compared to the human enzyme. CONCLUSION These results indicate that the N-terminal domain has a crucial role in modulating topoisomerase activity in different species.
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Affiliation(s)
- Jagadish Babu Dasari
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133 Rome, Italy.
| | - Bini Chhetri Soren
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133 Rome, Italy.
| | - Alessio Ottaviani
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133 Rome, Italy.
- Institute of Translational Pharmacology, National Research Council, CNR, Via Del Fosso del Cavaliere 100, Rome 00133, Italy.
| | - Cinzia Tesauro
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133 Rome, Italy.
- Present address: Department of Molecular Biology and Genetics, University of Aarhus, C.F MøllersAllè 3, 8000 Aarhus C, Denmark.
| | - Simona Marino
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133 Rome, Italy.
| | - Beatrice Messina
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133 Rome, Italy.
| | - Paola Fiorani
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133 Rome, Italy.
- Institute of Translational Pharmacology, National Research Council, CNR, Via Del Fosso del Cavaliere 100, Rome 00133, Italy.
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9
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Wang Z, D'Annessa I, Tesauro C, Ottaviani A, Soren BC, Dasari JB, Messina B, Thareparambil A, Fiorani P. The human DNA topoisomerase I mutant Gly717Asp: Higher religation rate is not always associated with camptothecin resistance. Arch Biochem Biophys 2019; 663:165-172. [PMID: 30653963 DOI: 10.1016/j.abb.2019.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/07/2019] [Accepted: 01/09/2019] [Indexed: 11/15/2022]
Abstract
DNA topoisomerases are key enzyme responsible for modulating the topological state of the DNA by breaking and rejoining of DNA strand. Characterization of a Gly717Asp mutation in the human topoisomerase was performed using several catalytic assays. The mutant enzyme was shown to have comparable cleavage and fast religation rate as compared to the wild-type protein. Addition of the anticancer drug camptothecin significantly reduced the religation step. The simulative approaches and analysis of the cleavage/religation equilibrium indicate that the mutation is able to modify the architecture of the drug binding site, increasing the persistence of the drug for the enzyme-DNA covalent complex. Taken together these results indicate that the structure modification of the drug binding site is the key reason for the increasing CPT persistence and furthermore provide the possibility for new anti-cancer drug discovery.
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Affiliation(s)
- Zhenxing Wang
- Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ilda D'Annessa
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Cinzia Tesauro
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Alessio Ottaviani
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Bini Chhetri Soren
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Jagadish Babu Dasari
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Beatrice Messina
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Anil Thareparambil
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Paola Fiorani
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133, Rome, Italy; Institute of Translational Pharmacology, National Research Council, CNR, Via Del Fosso del Cavaliere 100, Rome, 00133, Italy.
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10
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Salim V, Jones AD, DellaPenna D. Camptotheca acuminata 10-hydroxycamptothecin O-methyltransferase: an alkaloid biosynthetic enzyme co-opted from flavonoid metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:112-125. [PMID: 29681057 DOI: 10.1111/tpj.13936] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 04/02/2018] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
Abstract
The medicinal plant Camptotheca acuminata accumulates camptothecin, 10-hydroxycamptothecin, and 10-methoxycamptothecin as its major bioactive monoterpene indole alkaloids. Here, we describe identification and functional characterization of 10-hydroxycamptothecin O-methyltransferase (Ca10OMT), a member of the Diverse subclade of class II OMTs. Ca10OMT is highly active toward both its alkaloid substrate and a wide range of flavonoids in vitro and in this way contrasts with other alkaloid OMTs in the subclade that only utilize alkaloid substrates. Ca10OMT shows a strong preference for the A-ring 7-OH of flavonoids, which is structurally equivalent to the 10-OH of 10-hydroxycamptothecin. The substrates of other alkaloid OMTs in the subclade bear little similarity to flavonoids, but the 3-D positioning of the 7-OH, A- and C-rings of flavonoids is nearly identical to the 10-OH, A- and B-rings of 10-hydroxycamptothecin. This structural similarity likely explains the retention of flavonoid OMT activity by Ca10OMT and also why kaempferol and quercetin aglycones are potent inhibitors of its 10-hydroxycamptothecin activity. The catalytic promiscuity and strong inhibition of Ca10OMT by flavonoid aglycones in vitro prompted us to investigate the potential physiological roles of the enzyme in vivo. Based on its regioselectivity, kinetic parameters and absence of 7-OMT flavonoids in vivo, we conclude that the major and likely only substrate of Ca10OMTin vivo is 10-hydroxycamptothecin. This is likely accomplished by Ca10OMT being kept spatially separated at the tissue levels from potentially inhibitory flavonoid aglycones, and flavonoid aglycones being rapidly glycosylated to non-inhibitory flavonoid glycosides.
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Affiliation(s)
- Vonny Salim
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824-1319, USA
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824-1319, USA
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824-1319, USA
| | - Dean DellaPenna
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824-1319, USA
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11
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One-step targeted accumulation and detection of camptothecin analogues from fruits of Camptotheca acuminata Decne using bilayer solid-phase extraction coupled with ultra-high-performance liquid chromatography-tandem mass spectrometry. J Chromatogr A 2017; 1524:37-48. [DOI: 10.1016/j.chroma.2017.09.073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 08/27/2017] [Accepted: 09/30/2017] [Indexed: 12/21/2022]
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12
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Zhang P, Zhang L, Zhang Y, Mao L, Jiang H. Substitutions in Spodoptera exigua topoisomerase I modulate its relaxation activity and camptothecin sensitivity. PEST MANAGEMENT SCIENCE 2017; 73:1179-1186. [PMID: 27643798 DOI: 10.1002/ps.4440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/25/2016] [Accepted: 09/12/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Topoisomerase I (Top I) is referred as the cellular target of the camptothecins (CPTs) which are now being explored as potential pesticides for insect control. Three amino acid substitutions, including L530P, A653T and S729T, in Top Is of insects were found in our previous studies. In order to investigate the effect of these three substitutions, a comparative analysis was conducted between the wild-type and mutant Top Is in Spodoptera exigua Hübner. RESULTS The optimal salt concentration of A653T and S729T was 150 mm, which is consistent with that of the wild-type Top I, while the mutant L530P showed maximum relaxation activity at a lower KCl concentration (100 mm). The mutated L530P and A653T Top Is showed a higher relaxation efficiency owing to an increased relaxation velocity toward the negatively supercoiled plasmid pBR322 DNA, which rendered L530P and A653T resistant to CPTs, whereas mutant S729T exhibited sensitivity to CPTs as a result of a decreased relaxation activity toward plasmid pBR322 DNA. CONCLUSIONS These results suggested that the polymorphism in Top I of insects was related to the biological activity of CPTs, which provided the basic information for reasonable usage of CPTs to control insect pests. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Pei Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanning Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liangang Mao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongyun Jiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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13
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Cubells-Baeza N, Gómez-Casado C, Tordesillas L, Ramírez-Castillejo C, Garrido-Arandia M, González-Melendi P, Herrero M, Pacios LF, Díaz-Perales A. Identification of the ligand of Pru p 3, a peach LTP. PLANT MOLECULAR BIOLOGY 2017; 94:33-44. [PMID: 28299506 DOI: 10.1007/s11103-017-0590-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 01/28/2017] [Indexed: 06/06/2023]
Abstract
Pru p 3, a peach LTP, is located in pollinated flower styles and secreting downy hairs, transporting a derivative of camptothecin bound to phytosphingosine. Pru p 3 may inhibit a second pollination and may keep away herbivores until seed maturation. The allergen Pru p 3, a peach lipid transfer protein, has been well studied. However, its physiological function remains to be elucidated. Our results showed that Pru p 3 usually carries a lipid ligand that play an essential role in its function in plants. Using ESI-qToF, we observed that the ligand was a derivative of camptothecin binding to phytosphingosine, wich that is inserted into the hydrophobic tunnel of the protein. In addition, the described ligand displayed topoisomerase I activity inhibition and self-fluorescence, both recognized as camptothecin properties. During flower development, the highest expression of Pru p 3 was detected in the styles of pollinated flowers, in contrast to its non-expression in unpollinated pistils, where expression decreased after anthesis. During ripening, the expression of Pru p 3 were observed mainly in peel but not in pulp. In this sense, Pru p 3 protein was also localized in trichomes covering the fruit epidermis.
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Affiliation(s)
- Nuria Cubells-Baeza
- Centre for Plant Biotechnology and Genomics (UPM-INIA), Campus de Montegancedo, 28223, Pozuelo de Alarcón, Madrid, Spain
- Department of Biotechnology-Plant Biology, ETSIAAB, Technical University of Madrid, Madrid, Spain
| | | | | | - Carmen Ramírez-Castillejo
- Centre for Plant Biotechnology and Genomics (UPM-INIA), Campus de Montegancedo, 28223, Pozuelo de Alarcón, Madrid, Spain
- Department of Biotechnology-Plant Biology, ETSIAAB, Technical University of Madrid, Madrid, Spain
| | - María Garrido-Arandia
- Centre for Plant Biotechnology and Genomics (UPM-INIA), Campus de Montegancedo, 28223, Pozuelo de Alarcón, Madrid, Spain
- Department of Biotechnology-Plant Biology, ETSIAAB, Technical University of Madrid, Madrid, Spain
| | - Pablo González-Melendi
- Centre for Plant Biotechnology and Genomics (UPM-INIA), Campus de Montegancedo, 28223, Pozuelo de Alarcón, Madrid, Spain
- Department of Biotechnology-Plant Biology, ETSIAAB, Technical University of Madrid, Madrid, Spain
| | - María Herrero
- Estación Experimental de Aula Dei (CSIC), Zaragoza, Spain
| | - Luis F Pacios
- Centre for Plant Biotechnology and Genomics (UPM-INIA), Campus de Montegancedo, 28223, Pozuelo de Alarcón, Madrid, Spain
- Department of Natural Systems and Resources, ETSI Montes, Technical University of Madrid, Madrid, Spain
| | - Araceli Díaz-Perales
- Centre for Plant Biotechnology and Genomics (UPM-INIA), Campus de Montegancedo, 28223, Pozuelo de Alarcón, Madrid, Spain.
- Department of Biotechnology-Plant Biology, ETSIAAB, Technical University of Madrid, Madrid, Spain.
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14
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Andersen MB, Tesauro C, Gonzalez M, Kristoffersen EL, Alonso C, Rubiales G, Coletta A, Frøhlich R, Stougaard M, Ho YP, Palacios F, Knudsen BR. Advantages of an optical nanosensor system for the mechanistic analysis of a novel topoisomerase I targeting drug: a case study. NANOSCALE 2017; 9:1886-1895. [PMID: 28094391 DOI: 10.1039/c6nr06848k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The continuous need for the development of new small molecule anti-cancer drugs calls for easily accessible sensor systems for measuring the effect of vast numbers of new drugs on their potential cellular targets. Here we demonstrate the use of an optical DNA biosensor to unravel the inhibitory mechanism of a member of a new family of small molecule human topoisomerase I inhibitors, the so-called indeno-1,5-naphthyridines. By analysing human topoisomerase I catalysis on the biosensor in the absence or presence of added drug complemented with a few traditional assays, we demonstrate that the investigated member of the indeno-1,5-naphthyridine family inhibited human topoisomerase I activity by blocking enzyme-DNA dissociation. To our knowledge, this represents the first characterized example of a small molecule drug that inhibits a post-ligation step of catalysis. The elucidation of a completely new and rather surprising drug mechanism-of-action using an optical real time sensor highlights the value of this assay system in the search for new topoisomerase I targeting small molecule drugs.
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Affiliation(s)
- Marie B Andersen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Cinzia Tesauro
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - María Gonzalez
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Emil L Kristoffersen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Concepción Alonso
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Gloria Rubiales
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Andrea Coletta
- Department of Chemistry, Langelandsgade 140, Aarhus University, 8000 Aarhus C, Denmark
| | - Rikke Frøhlich
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Magnus Stougaard
- Department of Pathology, Nørrebrogade 44 building 18B, Aarhus University, Denmark
| | - Yi-Ping Ho
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark. and Interdisciplinary Nanoscience Center, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark and Division of Biomedical Engineering, Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, China
| | - Francisco Palacios
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
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15
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Molecular Mechanism of DNA Topoisomerase I-Dependent rDNA Silencing: Sir2p Recruitment at Ribosomal Genes. J Mol Biol 2016; 428:4905-4916. [PMID: 27825925 DOI: 10.1016/j.jmb.2016.10.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/25/2016] [Accepted: 10/30/2016] [Indexed: 11/24/2022]
Abstract
Saccharomyces cerevisiae sir2Δ or top1Δ mutants exhibit similar phenotypes involving ribosomal DNA, including (i) loss of transcriptional silencing, resulting in non-coding RNA hyperproduction from cryptic RNA polymerase II promoters; (ii) alterations in recombination; and (iii) a general increase in histone acetylation. Given the distinct enzymatic activities of Sir2 and Top1 proteins, a histone deacetylase and a DNA topoisomerase, respectively, we investigated whether genetic and/or physical interactions between the two proteins could explain the shared ribosomal RNA genes (rDNA) phenotypes. We employed an approach of complementing top1Δ cells with yeast, human, truncated, and chimeric yeast/human TOP1 constructs and of assessing the extent of non-coding RNA silencing and histone H4K16 deacetylation. Our findings demonstrate that residues 115-125 within the yeast Top1p N-terminal domain are required for the complementation of the top1∆ rDNA phenotypes. In chromatin immunoprecipitation and co-immunoprecipitation experiments, we further demonstrate the physical interaction between Top1p and Sir2p. Our genetic and biochemical studies support a model whereby Top1p recruits Sir2p to the rDNA and clarifies a structural role of DNA topoisomerase I in the epigenetic regulation of rDNA, independent of its known catalytic activity.
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16
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Girstun A, Ishikawa T, Kowalska-Loth B, Czubaty A, Staron K. Subnuclear Localization of Human Topoisomerase I. J Cell Biochem 2016; 118:407-419. [DOI: 10.1002/jcb.25654] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/14/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Agnieszka Girstun
- Department of Molecular Biology; Institute of Biochemistry; Faculty of Biology; University of Warsaw; Warsaw Poland
| | - Takao Ishikawa
- Department of Molecular Biology; Institute of Biochemistry; Faculty of Biology; University of Warsaw; Warsaw Poland
| | - Barbara Kowalska-Loth
- Department of Molecular Biology; Institute of Biochemistry; Faculty of Biology; University of Warsaw; Warsaw Poland
| | - Alicja Czubaty
- Department of Molecular Biology; Institute of Biochemistry; Faculty of Biology; University of Warsaw; Warsaw Poland
| | - Krzysztof Staron
- Department of Molecular Biology; Institute of Biochemistry; Faculty of Biology; University of Warsaw; Warsaw Poland
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17
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Sadre R, Magallanes-Lundback M, Pradhan S, Salim V, Mesberg A, Jones AD, DellaPenna D. Metabolite Diversity in Alkaloid Biosynthesis: A Multilane (Diastereomer) Highway for Camptothecin Synthesis in Camptotheca acuminata. THE PLANT CELL 2016; 28:1926-44. [PMID: 27432874 PMCID: PMC5006703 DOI: 10.1105/tpc.16.00193] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/20/2016] [Accepted: 07/09/2016] [Indexed: 05/27/2023]
Abstract
Camptothecin is a monoterpene indole alkaloid (MIA) used to produce semisynthetic antitumor drugs. We investigated camptothecin synthesis in Camptotheca acuminata by combining transcriptome and expression data with reverse genetics, biochemistry, and metabolite profiling. RNAi silencing of enzymes required for the indole and seco-iridoid (monoterpene) components identified transcriptional crosstalk coordinating their synthesis in roots. Metabolite profiling and labeling studies of wild-type and RNAi lines identified plausible intermediates for missing pathway steps and demonstrated nearly all camptothecin pathway intermediates are present as multiple isomers. Unlike previously characterized MIA-producing plants, C. acuminata does not synthesize 3-α(S)-strictosidine as its central MIA intermediate and instead uses an alternative seco-iridoid pathway that produces multiple isomers of strictosidinic acid. NMR analysis demonstrated that the two major strictosidinic acid isomers are (R) and (S) diastereomers at their glucosylated C21 positions. The presence of multiple diastereomers throughout the pathway is consistent with their use in synthesis before finally being resolved to a single camptothecin isomer after deglucosylation, much as a multilane highway allows parallel tracks to converge at a common destination. A model "diastereomer" pathway for camptothecin biosynthesis in C. acuminata is proposed that fundamentally differs from previously studied MIA pathways.
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Affiliation(s)
- Radin Sadre
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Maria Magallanes-Lundback
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Sujana Pradhan
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1319
| | - Vonny Salim
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Alex Mesberg
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319 Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1319
| | - Dean DellaPenna
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
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18
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Arumugam P, Song JM. Quantitative evaluation of ABC transporter-mediated drug resistance based on the determination of the anticancer activity of camptothecin against breast cancer stem cells using TIRF. Integr Biol (Camb) 2016; 8:704-11. [DOI: 10.1039/c6ib00021e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Total internal reflection fluorescence microscopy (TIRF) and Qdot probe based analytical method for the simultaneous evaluation of the cytotoxic ability of camptothecin and the drug resistance profile upon the inhibition of drug efflux pumps in breast cancer stem cells.
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Affiliation(s)
| | - Joon Myong Song
- College of Pharmacy
- Seoul National University
- Seoul 151-741
- South Korea
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19
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Yadav P, Owiti N, Kim N. The role of topoisomerase I in suppressing genome instability associated with a highly transcribed guanine-rich sequence is not restricted to preventing RNA:DNA hybrid accumulation. Nucleic Acids Res 2015; 44:718-29. [PMID: 26527723 PMCID: PMC4737143 DOI: 10.1093/nar/gkv1152] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/19/2015] [Indexed: 11/21/2022] Open
Abstract
Highly transcribed guanine-run containing sequences, in Saccharomyces cerevisiae, become unstable when topoisomerase I (Top1) is disrupted. Topological changes, such as the formation of extended RNA:DNA hybrids or R-loops or non-canonical DNA structures including G-quadruplexes has been proposed as the major underlying cause of the transcription-linked genome instability. Here, we report that R-loop accumulation at a guanine-rich sequence, which is capable of assembling into the four-stranded G4 DNA structure, is dependent on the level and the orientation of transcription. In the absence of Top1 or RNase Hs, R-loops accumulated to substantially higher extent when guanine-runs were located on the non-transcribed strand. This coincides with the orientation where higher genome instability was observed. However, we further report that there are significant differences between the disruption of RNase Hs and Top1 in regards to the orientation-specific elevation in genome instability at the guanine-rich sequence. Additionally, genome instability in Top1-deficient yeasts is not completely suppressed by removal of negative supercoils and further aggravated by expression of mutant Top1. Together, our data provide a strong support for a function of Top1 in suppressing genome instability at the guanine-run containing sequence that goes beyond preventing the transcription-associated RNA:DNA hybrid formation.
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Affiliation(s)
- Puja Yadav
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Norah Owiti
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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