1
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Bhola M, Abe K, Orozco P, Rahnamoun H, Avila-Lopez P, Taylor E, Muhammad N, Liu B, Patel P, Marko JF, Starner AC, He C, Van Nostrand EL, Mondragón A, Lauberth SM. RNA interacts with topoisomerase I to adjust DNA topology. Mol Cell 2024; 84:3192-3208.e11. [PMID: 39173639 PMCID: PMC11380577 DOI: 10.1016/j.molcel.2024.07.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 07/07/2023] [Accepted: 07/31/2024] [Indexed: 08/24/2024]
Abstract
Topoisomerase I (TOP1) is an essential enzyme that relaxes DNA to prevent and dissipate torsional stress during transcription. However, the mechanisms underlying the regulation of TOP1 activity remain elusive. Using enhanced cross-linking and immunoprecipitation (eCLIP) and ultraviolet-cross-linked RNA immunoprecipitation followed by total RNA sequencing (UV-RIP-seq) in human colon cancer cells along with RNA electrophoretic mobility shift assays (EMSAs), biolayer interferometry (BLI), and in vitro RNA-binding assays, we identify TOP1 as an RNA-binding protein (RBP). We show that TOP1 directly binds RNA in vitro and in cells and that most RNAs bound by TOP1 are mRNAs. Using a TOP1 RNA-binding mutant and topoisomerase cleavage complex sequencing (TOP1cc-seq) to map TOP1 catalytic activity, we reveal that RNA opposes TOP1 activity as RNA polymerase II (RNAPII) commences transcription of active genes. We further demonstrate the inhibitory role of RNA in regulating TOP1 activity by employing DNA supercoiling assays and magnetic tweezers. These findings provide insight into the coordinated actions of RNA and TOP1 in regulating DNA topological stress intrinsic to RNAPII-dependent transcription.
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Affiliation(s)
- Mannan Bhola
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kouki Abe
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Paola Orozco
- Section of Molecular Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Homa Rahnamoun
- Section of Molecular Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Pedro Avila-Lopez
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Elijah Taylor
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208-3108, USA
| | - Nefertiti Muhammad
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Bei Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Prachi Patel
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - John F Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208-3108, USA
| | - Anne C Starner
- Verna & Marrs McLean Department of Biochemistry & Molecular Pharmacology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Eric L Van Nostrand
- Verna & Marrs McLean Department of Biochemistry & Molecular Pharmacology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208-3108, USA
| | - Shannon M Lauberth
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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2
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Moreira F, Arenas M, Videira A, Pereira F. Evolution of TOP1 and TOP1MT Topoisomerases in Chordata. J Mol Evol 2023; 91:192-203. [PMID: 36651963 PMCID: PMC10081982 DOI: 10.1007/s00239-022-10091-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 12/30/2022] [Indexed: 01/19/2023]
Abstract
Type IB topoisomerases relax the torsional stress associated with DNA metabolism in the nucleus and mitochondria and constitute important molecular targets of anticancer drugs. Vertebrates stand out among eukaryotes by having two Type IB topoisomerases acting specifically in the nucleus (TOP1) and mitochondria (TOP1MT). Despite their major importance, the origin and evolution of these paralogues remain unknown. Here, we examine the molecular evolutionary processes acting on both TOP1 and TOP1MT in Chordata, taking advantage of the increasing number of available genome sequences. We found that both TOP1 and TOP1MT evolved under strong purifying selection, as expected considering their essential biological functions. Critical active sites, including those associated with resistance to anticancer agents, were found particularly conserved. However, TOP1MT presented a higher rate of molecular evolution than TOP1, possibly related with its specialized activity on the mitochondrial genome and a less critical role in cells. We could place the duplication event that originated the TOP1 and TOP1MT paralogues early in the radiation of vertebrates, most likely associated with the first round of vertebrate tetraploidization (1R). Moreover, our data suggest that cyclostomes present a specialized mitochondrial Type IB topoisomerase. Interestingly, we identified two missense mutations replacing amino acids in the Linker region of TOP1MT in Neanderthals, which appears as a rare event when comparing the genome of both species. In conclusion, TOP1 and TOP1MT differ in their rates of evolution, and their evolutionary histories allowed us to better understand the evolution of chordates.
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Affiliation(s)
- Filipa Moreira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos S/N 4450-208, Matosinhos, Portugal
- ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310, Vigo, Spain
| | - Arnaldo Videira
- ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Filipe Pereira
- IDENTIFICA Genetic Testing, Rua Simão Bolívar 259 3º Dir Tras, 4470-214, Maia, Portugal.
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal.
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3
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Madeddu F, Di Martino J, Pieroni M, Del Buono D, Bottoni P, Botta L, Castrignanò T, Saladino R. Molecular Docking and Dynamics Simulation Revealed the Potential Inhibitory Activity of New Drugs against Human Topoisomerase I Receptor. Int J Mol Sci 2022; 23:ijms232314652. [PMID: 36498979 PMCID: PMC9737192 DOI: 10.3390/ijms232314652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022] Open
Abstract
Human Topoisomerase I (hTop1p) is a ubiquitous enzyme that relaxes supercoiled DNA through a conserved mechanism involving transient breakage, rotation, and binding. Htop1p is the molecular target of the chemotherapeutic drug camptothecin (CPT). It causes the hTop1p-DNA complex to slow down the binding process and clash with the replicative machinery during the S phase of the cell cycle, forcing cells to activate the apoptotic response. This gives hTop1p a central role in cancer therapy. Recently, two artesunic acid derivatives (compounds c6 and c7) have been proposed as promising inhibitors of hTop1p with possible antitumor activity. We used several computational approaches to obtain in silico confirmations of the experimental data and to form a comprehensive dynamic description of the ligand-receptor system. We performed molecular docking analyses to verify the ability of the two new derivatives to access the enzyme-DNA interface, and a classical molecular dynamics simulation was performed to assess the capacity of the two compounds to maintain a stable binding pose over time. Finally, we calculated the noncovalent interactions between the two new derivatives and the hTop1p receptor in order to propose a possible inhibitory mechanism like that adopted by CPT.
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Affiliation(s)
- Francesco Madeddu
- Department of Computer Science, “Sapienza” University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Jessica Di Martino
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy
| | - Michele Pieroni
- Department of Computer Science, “Sapienza” University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Davide Del Buono
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy
| | - Paolo Bottoni
- Department of Computer Science, “Sapienza” University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Lorenzo Botta
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy
| | - Tiziana Castrignanò
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy
- Correspondence:
| | - Raffaele Saladino
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy
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Botta L, Filippi S, Zippilli C, Cesarini S, Bizzarri BM, Cirigliano A, Rinaldi T, Paiardini A, Fiorucci D, Saladino R, Negri R, Benedetti P. Artemisinin Derivatives with Antimelanoma Activity Show Inhibitory Effect against Human DNA Topoisomerase 1. ACS Med Chem Lett 2020; 11:1035-1040. [PMID: 32435422 DOI: 10.1021/acsmedchemlett.0c00131] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 04/10/2020] [Indexed: 02/07/2023] Open
Abstract
Artesunic acid and artemisinin are natural substances with promiscuous anticancer activity against different types of cancer cell lines. The mechanism of action of these compounds is associated with the formation of reactive radical species by cleavage of the sesquiterpene pharmacophore endoperoxide bridge. Here we suggested topoisomerase 1 as a possible molecular target for the improvement of the anticancer activity of these compounds. In this context, we report that novel hybrid and dimer derivatives of artesunic acid and artemisinin, bearing camptothecin and SN38 as side-chain biological effectors, can inhibit growth of yeast cells overexpressing human topoisomerase 1 and its enzymatic activity in vitro. These derivatives showed also anticancer activity in melanoma cell lines higher than camptothecin and paclitaxel. In silico molecular docking calculations highlighted a common binding mode for the novel derivatives, with the sesquiterpene lactone scaffold being located near the traditional recognition site for camptothecin, while the bioactive side-chain effector laid in the camptothecin cleft.
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Affiliation(s)
- Lorenzo Botta
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Silvia Filippi
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Claudio Zippilli
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Silvia Cesarini
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Bruno Mattia Bizzarri
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Angela Cirigliano
- Istituto di Biologia e Patologia Molecolari, CNR Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Teresa Rinaldi
- Sapienza University of Rome, Department of Biology and Biotechnology, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Diego Fiorucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Raffaele Saladino
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Rodolfo Negri
- Sapienza University of Rome, Department of Biology and Biotechnology, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Pietro Benedetti
- Dipartimento di Biologia, Università di Padova Distaccato presso il “Centro Linceo Beniamino Segre” Accademia Nazionale dei Lincei, Palazzo Corsini, Via della Lungara 10, 00165 Rome, Italy
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5
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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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6
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Gáspári Z, Nyitray L. Coiled coils as possible models of protein structure evolution. Biomol Concepts 2015; 2:199-210. [PMID: 25962029 DOI: 10.1515/bmc.2011.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 03/01/2011] [Indexed: 01/05/2023] Open
Abstract
Coiled coils are formed by two or more α-helices wrapped around one another. This structural motif often guides di-, tri- or multimerization of proteins involved in diverse biological processes such as membrane fusion, signal transduction and the organization of the cytoskeleton. Although coiled coil motifs seem conceptually simple and their existence was proposed in the early 1950s, the high variability of the motif makes coiled coil prediction from sequence a difficult task. They might be confused with intrinsically disordered sequences and even more with a recently described structural motif, the charged single α-helix. By contrast, the versatility of coiled coil structures renders them an ideal candidate for protein (re)design and many novel variants have been successfully created to date. In this paper, we review coiled coils in the light of protein evolution by putting our present understanding of the motif and its variants in the context of structural interconversions. We argue that coiled coils are ideal subjects for studies of subtle and large-scale structural changes because of their well-characterized and versatile nature.
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7
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Wright CM, van der Merwe M, DeBrot AH, Bjornsti MA. DNA topoisomerase I domain interactions impact enzyme activity and sensitivity to camptothecin. J Biol Chem 2015; 290:12068-78. [PMID: 25795777 DOI: 10.1074/jbc.m114.635078] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Indexed: 11/06/2022] Open
Abstract
During processes such as DNA replication and transcription, DNA topoisomerase I (Top1) catalyzes the relaxation of DNA supercoils. The nuclear enzyme is also the cellular target of camptothecin (CPT) chemotherapeutics. Top1 contains four domains: the highly conserved core and C-terminal domains involved in catalysis, a coiled-coil linker domain of variable length, and a poorly conserved N-terminal domain. Yeast and human Top1 share a common reaction mechanism and domain structure. However, the human Top1 is ∼100-fold more sensitive to CPT. Moreover, substitutions of a conserved Gly(717) residue, which alter intrinsic enzyme sensitivity to CPT, induce distinct phenotypes in yeast. To address the structural basis for these differences, reciprocal swaps of yeast and human Top1 domains were engineered in chimeric enzymes. Here we report that intrinsic Top1 sensitivity to CPT is dictated by the composition of the conserved core and C-terminal domains. However, independent of CPT, biochemically similar chimeric enzymes produced strikingly distinct phenotypes in yeast. Expression of a human Top1 chimera containing the yeast linker domain proved toxic, even in the context of a catalytically inactive Y723F enzyme. Lethality was suppressed either by splicing the yeast N-terminal domain into the chimera, deleting the human N-terminal residues, or in enzymes reconstituted by polypeptide complementation. These data demonstrate a functional interaction between the N-terminal and linker domains, which, when mispaired between yeast and human enzymes, induces cell lethality. Because toxicity was independent of enzyme catalysis, the inappropriate coordination of N-terminal and linker domains may induce aberrant Top1-protein interactions to impair cell growth.
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Affiliation(s)
- Christine M Wright
- From the Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama 35294 and
| | - Marié van der Merwe
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Amanda H DeBrot
- From the Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama 35294 and
| | - Mary-Ann Bjornsti
- From the Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama 35294 and
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8
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Ucuncuoglu N, Andricioaei I, Sari L. Insights from simulations into the mechanism of human topoisomerase I: Explanation for a seeming controversy in experiments. J Mol Graph Model 2013; 44:286-96. [DOI: 10.1016/j.jmgm.2013.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 07/01/2013] [Accepted: 07/05/2013] [Indexed: 11/27/2022]
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9
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Nyirenda J, Matsumoto S, Saitoh T, Maita N, Noda NN, Inagaki F, Kohda D. Crystallographic and NMR evidence for flexibility in oligosaccharyltransferases and its catalytic significance. Structure 2012. [PMID: 23177926 DOI: 10.1016/j.str.2012.10.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Oligosaccharyltransferase (OST) is a membrane-bound enzyme that catalyzes the transfer of an oligosaccharide to an asparagine residue in glycoproteins. It possesses a binding pocket that recognizes Ser and Thr residues at the +2 position in the N-glycosylation consensus, Asn-X-Ser/Thr. We determined the crystal structures of the C-terminal globular domains of the catalytic subunits of two archaeal OSTs. A comparison with previously determined structures identified a segment with remarkable conformational plasticity, induced by crystal contact effects. We characterized its dynamic properties in solution by (15)N NMR relaxation analyses. Intriguingly, the mobile region contains the +2 Ser/Thr-binding pocket. In agreement, the flexibility restriction forced by an engineered disulfide crosslink abolished the enzymatic activity, and its cleavage fully restored activity. These results suggest the necessity of multiple conformational states in the reaction. The dynamic nature of the Ser/Thr pocket could facilitate the efficient scanning of N-glycosylation sequons along nascent polypeptide chains.
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Affiliation(s)
- James Nyirenda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Shunsuke Matsumoto
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Takashi Saitoh
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Nobuo Maita
- Institute of Enzyme Research, Tokushima University, Tokushima 770-8503, Japan
| | - Nobuo N Noda
- Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Fuyuhiko Inagaki
- Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan; Research Center for Advanced Immunology, Kyushu University, Fukuoka 812-8582, Japan.
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10
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Gajewski S, Comeaux EQ, Jafari N, Bharatham N, Bashford D, White SW, van Waardenburg RCAM. Analysis of the active-site mechanism of tyrosyl-DNA phosphodiesterase I: a member of the phospholipase D superfamily. J Mol Biol 2011; 415:741-58. [PMID: 22155078 DOI: 10.1016/j.jmb.2011.11.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 11/21/2011] [Accepted: 11/25/2011] [Indexed: 11/28/2022]
Abstract
Tyrosyl-DNA phosphodiesterase I (Tdp1) is a member of the phospholipase D superfamily that hydrolyzes 3'-phospho-DNA adducts via two conserved catalytic histidines-one acting as the lead nucleophile and the second acting as a general acid/base. Substitution of the second histidine specifically to arginine contributes to the neurodegenerative disease spinocerebellar ataxia with axonal neuropathy (SCAN1). We investigated the catalytic role of this histidine in the yeast protein (His432) using a combination of X-ray crystallography, biochemistry, yeast genetics, and theoretical chemistry. The structures of wild-type Tdp1 and His432Arg both show a phosphorylated form of the nucleophilic histidine that is not observed in the structure of His432Asn. The phosphohistidine is stabilized in the His432Arg structure by the guanidinium group that also restricts the access of nucleophilic water molecule to the Tdp1-DNA intermediate. Biochemical analyses confirm that His432Arg forms an observable and unique Tdp1-DNA adduct during catalysis. Substitution of His432 by Lys does not affect catalytic activity or yeast phenotype, but substitutions with Asn, Gln, Leu, Ala, Ser, and Thr all result in severely compromised enzymes and DNA topoisomerase I-camptothecin dependent lethality. Surprisingly, His432Asn did not show a stable covalent Tdp1-DNA intermediate that suggests another catalytic defect. Theoretical calculations revealed that the defect resides in the nucleophilic histidine and that the pK(a) of this histidine is crucially dependent on the second histidine and on the incoming phosphate of the substrate. This represents a unique example of substrate-activated catalysis that applies to the entire phospholipase D superfamily.
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Affiliation(s)
- Stefan Gajewski
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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11
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Chou SM, Huang TH, Chen HC, Li TK. Calcium-induced cleavage of DNA topoisomerase I involves the cytoplasmic-nuclear shuttling of calpain 2. Cell Mol Life Sci 2011; 68:2769-84. [PMID: 21086148 PMCID: PMC11114693 DOI: 10.1007/s00018-010-0591-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 10/29/2010] [Accepted: 11/02/2010] [Indexed: 12/18/2022]
Abstract
Important to the function of calpains is temporal and spatial regulation of their proteolytic activity. Here, we demonstrate that cytoplasm-resident calpain 2 cleaves human nuclear topoisomerase I (hTOP1) via Ca(2+)-activated proteolysis and nucleoplasmic shuttling of proteases. This proteolysis of hTOP1 was induced by either ionomycin-caused Ca(2+) influx or addition of Ca(2+) in cellular extracts. Ca(2+) failed to induce hTOP1 proteolysis in calpain 2-knockdown cells. Moreover, calpain 2 cleaved hTOP1 in vitro. Furthermore, calpain 2 entered the nucleus upon Ca(2+) influx, and calpastatin interfered with this process. Calpain 2 cleavage sites were mapped at K(158) and K(183) of hTOP1. Calpain 2-truncated hTOP1 exhibited greater relaxation activity but remained able to interact with nucleolin and to form cleavable complexes. Interestingly, calpain 2 appears to be involved in ionomycin-induced protection from camptothecin-induced cytotoxicity. Thus, our data suggest that nucleocytoplasmic shuttling may serve as a novel type of regulation for calpain 2-mediated nuclear proteolysis.
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Affiliation(s)
- Shang-Min Chou
- Department and Graduate Institute of Microbiology, College of Medicine, Taipei, Taiwan
| | - Ting-Hsiang Huang
- Department and Graduate Institute of Microbiology, College of Medicine, Taipei, Taiwan
| | - Hsiang-Chin Chen
- Department and Graduate Institute of Microbiology, College of Medicine, Taipei, Taiwan
| | - Tsai-Kun Li
- Department and Graduate Institute of Microbiology, College of Medicine, Taipei, Taiwan
- Center for Biotechnology, National Taiwan University, Taipei, Taiwan
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12
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Wereszczynski J, Andricioaei I. Free energy calculations reveal rotating-ratchet mechanism for DNA supercoil relaxation by topoisomerase IB and its inhibition. Biophys J 2010; 99:869-78. [PMID: 20682265 DOI: 10.1016/j.bpj.2010.04.077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 04/06/2010] [Accepted: 04/21/2010] [Indexed: 11/16/2022] Open
Abstract
Topoisomerases maintain the proper topological state of DNA. Human topoisomerase I removes DNA supercoils by clamping a duplex DNA segment, nicking one strand at a phosphodiester bond, covalently attaching to the 3' end of the nick, and allowing the DNA downstream of the cut to rotate around the intact strand. Using molecular dynamics simulations and umbrella sampling free energy calculations, we show that the rotation of downstream DNA in the grip of the enzyme that brings about release of positive or negative supercoils occurs by thermally assisted diffusion on ratchet energy profiles. The ratchetlike free-energy-versus-rotation profile that we compute provides a model for the function of topoisomerase in which the periodic maxima along the profile modulate the rate of supercoil relaxation, while the minima provide metastable conformational states for DNA religation. The results confirm previous experimental and computational work, and suggest that relaxation of the two types of supercoils involves distinct protein pathways. Additionally, simulations performed with the ternary complex of topoisomerase, DNA, and the chemotherapeutic drug topotecan show important differences in the mechanisms for supercoil relaxation when the drug is present, accounting for the relative values of relaxation rates measured in single-molecule experiments. Good agreement is found between rate constants from tweezer experiments and those calculated from simulations. Evidence is presented for the existence of semiopen states of the protein, which facilitate rotations after the initial one, as a result of biasing the protein into a conformation more favorable to strand rotation than the closed state required for nicking of the DNA.
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Affiliation(s)
- Jeff Wereszczynski
- Department of Chemistry, University of California, Irvine, California, USA
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