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Structural Basis for the Allosteric Regulation of Human Topoisomerase 2Α

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Structural Basis for the Allosteric Regulation of Human Topoisomerase 2Α bioRxiv preprint doi: https://doi.org/10.1101/2020.08.23.263558; this version posted August 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Structural basis for the allosteric regulation of Human Topoisomerase 2α 2 Authors: Arnaud Vanden Broeck 1, 2, Christophe Lotz 1, 2, Robert Drillien 1, 2, Claire Bedez 1, 2 & 3 Valérie Lamour 1, 2, 3 * 4 1 Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire 5 (IGBMC), UMR 7104, U1258, IllkircH, France 6 2 Department of Integrated Structural Biology, IGBMC, 1 Rue Laurent Fries, 67404, IllkircH Cedex, France 7 3 Hôpitaux Universitaires de Strasbourg, 1 Place de l’Hôpital, 67091, Strasbourg Cedex, France 8 * Correspondence to Valérie Lamour, [email protected] 9 10 Abstract 11 The human type IIA topoisomerases (Top2) are essential enzymes that regulate DNA topology and 12 chromosome organization. The Top2a isoform is a prime target for antineoplastic compounds used in 13 cancer therapy that form ternary cleavage complexes with the DNA. Despite extensive studies, 14 structural information on this large dimeric assembly is limited to the catalytic domains, hindering the 15 exploration of allosteric mechanism governing the enzyme activities and the contribution of its non- 16 conserved C-terminal domain (CTD). Herein we present cryo-EM structures of the entire human 17 Top2α nucleoprotein complex in different conformations solved at subnanometer resolutions. Our data 18 unveils the molecular determinants that fine tune the allosteric connections between the ATPase 19 domain and the DNA binding/cleavage domain. Strikingly, the reconstruction of the DNA- 20 binding/cleavage domain uncovers a linker leading to the CTD, which plays a critical role in 21 modulating the enzyme’s activities and opens perspective for the analysis of post-translational 22 modifications. 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.23.263558; this version posted August 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 23 Introduction 24 Type II DNA topoisomerases (Top2) are evolutionary conserved enzymes whose primordial activity is 25 to regulate the homeostasis of DNA topology in eukaryotes and bacteria 1. The Top2 are involved in 26 essential cellular processes such as DNA replication, DNA transcription, and chromosome segregation 27 2. The human Top2α isoform is highly expressed during mitosis, essential for cell division 3 and a 28 biomarker for cell proliferation 4. As such, Top2α is a major target for antineoplastic drugs that hamper 29 its catalytic activities 5. 30 This large homodimeric enzyme introduces a double strand break in a first DNA duplex, called G- 31 segment, and directs the transport of a second DNA duplex, called T-segment, through the transient 32 break in order to change the topology of a DNA crossover. The passage of the T-segment requires 33 ATP hydrolysis and is thought to occur along with the opening and closing of several dimeric 34 interfaces constituting molecular gates 6,7. The crystal structures of the ATPase and DNA 35 binding/cleavage domains of eukaryotic Top2 have been determined and present cavities compatible 36 with the binding of a DNA double helix 8–13. Biochemical and structural studies have provided 37 evidence that the ATPase domain or N-gate, and the DNA binding/cleavage domain forming the 38 DNA- and C-gates, are allosterically connected, a key feature of its activity 14,15. However, hinge 39 regions connecting the catalytic sites of the human enzyme remain largely unexplored, hindering 40 efforts to apprehend the quaternary organization of this enzyme and the landscape of conformations it 41 adopts during the catalytic cycle. 42 In addition, the Top2 catalytic domains are flanked by C-terminal extensions that vary from one 43 species to another 16,17. These domains contain nuclear localization signals and are submitted to 44 extensive post-translational modifications that condition the cellular localization of Top2, its 45 interactions with cellular partners and progression of the cell cycle 18,19. Several studies have suggested 46 that different regions of the Top2α CTD contribute to the enzyme’s catalytic activities through DNA 47 binding 20–23. In contrast with prokaryotic enzymes that harbor a pinwheel-structured CTD 24–26, the 48 same region in eukaryotic enzymes presents no homology to any known fold, hence limiting structure- 49 function analysis. It has become clear that the analysis of the molecular determinants of the enzyme’s 2 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.23.263558; this version posted August 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 50 allostery and the modulation of its activity by the CTD now requires the availability of a complete 51 molecular structure of the Top2α. 52 In this work, we determined the cryo-EM structure of the full length human Top2α isoform bound to 53 DNA in different conformations trapped by the anti-cancer drug etoposide. The structures reveal the 54 connections between the ATPase and DNA binding/cleavage domains, allowing the identification of 55 conserved sequence patterns in humans that control the allosteric signaling between the catalytic sites. 56 In addition, we were able to localize the linker between the DNA binding/cleavage domain and the 57 CTD inserting below the G-segment. We show that this region directly stimulates the Top2α catalytic 58 activity suggesting that the bulk of the CTD domain may counterbalance this effect, potentially 59 through post-translational modifications. 60 Results 61 Cryo-EM reconstructions of the hTop2α nucleoprotein complex 62 The full-length hTop2α was overexpressed in mammalian cells and purified using tandem affinity 63 chromatography followed by a heparin step (see Methods and Supplementary Fig. 1). Samples were 64 tested for enzymatic activity and mixed with asymmetric DNA oligonucleotides mimicking a doubly- 65 nicked 30bp DNA 11 (Supplementary Fig. 1b and Table 2). The antineoplastic drug etoposide and 66 AMP-PNP, the non-hydrolysable homolog of ATP, were added to the nucleoprotein complex in order 67 to minimize the conformational heterogeneity of the sample. 68 The DNA-bound hTop2α complex was analyzed by single-particle cryo-EM. Six different datasets 69 were recorded on a Titan Krios microscope yielding a total of 13,484 micrographs. Using automated 70 picking procedure in RELION2 27, a total of 1,908,092 particles were extracted from the micrographs. 71 The dataset was curated using a combination of 2D and 3D ab-initio classifications in RELION2 and 72 cryoSPARC 28, respectively, yielding a final stack of 162,332 particles (Supplementary Fig. 2). Using 73 a low-pass filtered 3D ab-initio model generated in cryoSPARC, a first 3D reconstruction of the DNA- 74 bound hTop2α was obtained at 6.6 Å resolution (Supplementary Fig. 3). The flexibility of the complex 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.23.263558; this version posted August 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 75 is visible from the 2D class averages showing the dimerized ATPase domain adopting different 76 positions relative to the DNA-binding/cleavage domain (Supplementary Fig. 2b,d). 77 To isolate the different conformations and improve the overall resolution, we used a combination of 78 global and local approaches to deconvolute the structures of the hTop2α complex. Using 3D focused 79 refinements, reconstructions of the DNA-binding/cleavage domain were generated for two different 80 states. State 1 was solved at 4.2 Å using 57,976 particles and State 2 was solved at 5.0 Å using 34,922 81 particles (Supplementary Fig. 3). Each particle stack was submitted to 3D-refinement without mask to 82 yield two reconstructions of the entire complex in State 1 at 5.6 Å resolution, and in State 2 at 7.2 Å 83 resolution (Supplementary Fig. 3). Due to the flexibility of the ATPase domain, the densities of the 84 linkers with the DNA binding/cleavage domain were not well resolved in the cryo-EM maps. To get 85 information on this region, a 3D-focused classification was performed on the ATPase domain yielding 86 one class comprising 36,610 particles with a well-resolved connection between the two functional 87 domains which was refined at 7.6 Å resolution (Supplementary Fig. 3). 88 Model building of the hTop2α complex in different states 89 Near-atomic resolution features of the 4.2 Å map in State 1 allowed us to fit, build and refine the 90 atomic model of the hTop2α DNA-binding/cleavage domain in complex with DNA and etoposide 29 91 (Figure 1a-c, Supplementary Fig. 5). Strikingly, we were also able to identify EM density for the 92 etoposide molecule, intercalating in the DNA duplex between positions -1 and +1 (Figure 1d), with 93 similar protein and DNA contacts as previously reported in crystallographic structures (Supplementary 94 Fig. 7) 10,29. 95 The resulting DNA-binding/cleavage domain model together with the crystal structure of the ATPase 96 domain bound to AMP-PNP 8 were then combined to refine the complete atomic structure of the full- 97 length hTop2α in State 1 (Figure 2). The 27-aa linkers between the two domains, missing from the 98 crystal structure of the isolated ATPase domain, were built as alpha helices based on secondary 99 structure predictions and using well-defined linker densities of the cryo-EM map obtained by focused 100 classification on the ATPase domain (Supplementary Fig.
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