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Endsley CE, Moore KA, Townsley TD, Durston KK, Deweese JE. Bioinformatic Analysis of Topoisomerase IIα Reveals Interdomain Interdependencies and Critical C-Terminal Domain Residues. Int J Mol Sci 2024; 25:5674. [PMID: 38891861 PMCID: PMC11172036 DOI: 10.3390/ijms25115674] [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: 03/23/2024] [Revised: 05/01/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
DNA Topoisomerase IIα (Top2A) is a nuclear enzyme that is a cancer drug target, and there is interest in identifying novel sites on the enzyme to inhibit cancer cells more selectively and to reduce off-target toxicity. The C-terminal domain (CTD) is one potential target, but it is an intrinsically disordered domain, which prevents structural analysis. Therefore, we set out to analyze the sequence of Top2A from 105 species using bioinformatic analysis, including the PSICalc algorithm, Shannon entropy analysis, and other approaches. Our results demonstrate that large (10th-order) interdependent clusters are found including non-proximal positions across the major domains of Top2A. Further, CTD-specific clusters of the third, fourth, and fifth order, including positions that had been previously analyzed via mutation and biochemical assays, were identified. Some of these clusters coincided with positions that, when mutated, either increased or decreased relaxation activity. Finally, sites of low Shannon entropy (i.e., low variation in amino acids at a given site) were identified and mapped as key positions in the CTD. Included in the low-entropy sites are phosphorylation sites and charged positions. Together, these results help to build a clearer picture of the critical positions in the CTD and provide potential sites/regions for further analysis.
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Affiliation(s)
- Clark E. Endsley
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
| | - Kori A. Moore
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
| | | | - Kirk K. Durston
- Department of Research and Publications, Digital Strategies, Langley, BC V2Y 1N5, Canada
| | - Joseph E. Deweese
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
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Goldtzvik Y, Sen N, Lam SD, Orengo C. Protein diversification through post-translational modifications, alternative splicing, and gene duplication. Curr Opin Struct Biol 2023; 81:102640. [PMID: 37354790 DOI: 10.1016/j.sbi.2023.102640] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/05/2023] [Accepted: 05/24/2023] [Indexed: 06/26/2023]
Abstract
Proteins provide the basis for cellular function. Having multiple versions of the same protein within a single organism provides a way of regulating its activity or developing novel functions. Post-translational modifications of proteins, by means of adding/removing chemical groups to amino acids, allow for a well-regulated and controlled way of generating functionally distinct protein species. Alternative splicing is another method with which organisms possibly generate new isoforms. Additionally, gene duplication events throughout evolution generate multiple paralogs of the same genes, resulting in multiple versions of the same protein within an organism. In this review, we discuss recent advancements in the study of these three methods of protein diversification and provide illustrative examples of how they affect protein structure and function.
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Affiliation(s)
- Yonathan Goldtzvik
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Neeladri Sen
- Department of Structural and Molecular Biology, University College London, London, United Kingdom. https://twitter.com/@NeeladriSen
| | - Su Datt Lam
- Department of Structural and Molecular Biology, University College London, London, United Kingdom; Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Christine Orengo
- Department of Structural and Molecular Biology, University College London, London, United Kingdom.
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Bartas M, Slychko K, Červeň J, Pečinka P, Arndt-Jovin DJ, Jovin TM. Extensive Bioinformatics Analyses Reveal a Phylogenetically Conserved Winged Helix (WH) Domain (Zτ) of Topoisomerase IIα, Elucidating Its Very High Affinity for Left-Handed Z-DNA and Suggesting Novel Putative Functions. Int J Mol Sci 2023; 24:10740. [PMID: 37445918 DOI: 10.3390/ijms241310740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/13/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
The dynamic processes operating on genomic DNA, such as gene expression and cellular division, lead inexorably to topological challenges in the form of entanglements, catenanes, knots, "bubbles", R-loops, and other outcomes of supercoiling and helical disruption. The resolution of toxic topological stress is the function attributed to DNA topoisomerases. A prominent example is the negative supercoiling (nsc) trailing processive enzymes such as DNA and RNA polymerases. The multiple equilibrium states that nscDNA can adopt by redistribution of helical twist and writhe include the left-handed double-helical conformation known as Z-DNA. Thirty years ago, one of our labs isolated a protein from Drosophila cells and embryos with a 100-fold greater affinity for Z-DNA than for B-DNA, and identified it as topoisomerase II (gene Top2, orthologous to the human UniProt proteins TOP2A and TOP2B). GTP increased the affinity and selectivity for Z-DNA even further and also led to inhibition of the isomerase enzymatic activity. An allosteric mechanism was proposed, in which topoII acts as a Z-DNA-binding protein (ZBP) to stabilize given states of topological (sub)domains and associated multiprotein complexes. We have now explored this possibility by comprehensive bioinformatic analyses of the available protein sequences of topoII representing organisms covering the whole tree of life. Multiple alignment of these sequences revealed an extremely high level of evolutionary conservation, including a winged-helix protein segment, here denoted as Zτ, constituting the putative structural homolog of Zα, the canonical Z-DNA/Z-RNA binding domain previously identified in the interferon-inducible RNA Adenosine-to-Inosine-editing deaminase, ADAR1p150. In contrast to Zα, which is separate from the protein segment responsible for catalysis, Zτ encompasses the active site tyrosine of topoII; a GTP-binding site and a GxxG sequence motif are in close proximity. Quantitative Zτ-Zα similarity comparisons and molecular docking with interaction scoring further supported the "B-Z-topoII hypothesis" and has led to an expanded mechanism for topoII function incorporating the recognition of Z-DNA segments ("Z-flipons") as an inherent and essential element. We further propose that the two Zτ domains of the topoII homodimer exhibit a single-turnover "conformase" activity on given G(ate) B-DNA segments ("Z-flipins"), inducing their transition to the left-handed Z-conformation. Inasmuch as the topoII-Z-DNA complexes are isomerase inactive, we infer that they fulfill important structural roles in key processes such as mitosis. Topoisomerases are preeminent targets of anti-cancer drug discovery, and we anticipate that detailed elucidation of their structural-functional interactions with Z-DNA and GTP will facilitate the design of novel, more potent and selective anti-cancer chemotherapeutic agents.
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Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Kristyna Slychko
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Donna J Arndt-Jovin
- Emeritus Laboratory of Cellular Dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Thomas M Jovin
- Emeritus Laboratory of Cellular Dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
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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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Morotomi-Yano K, Hiromoto Y, Higaki T, Yano KI. Disease-associated H58Y mutation affects the nuclear dynamics of human DNA topoisomerase IIβ. Sci Rep 2022; 12:20627. [PMID: 36450898 PMCID: PMC9712534 DOI: 10.1038/s41598-022-24883-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
DNA topoisomerase II (TOP2) is an enzyme that resolves DNA topological problems and plays critical roles in various nuclear processes. Recently, a heterozygous H58Y substitution in the ATPase domain of human TOP2B was identified from patients with autism spectrum disorder, but its biological significance remains unclear. In this study, we analyzed the nuclear dynamics of TOP2B with H58Y (TOP2B H58Y). Although wild-type TOP2B was highly mobile in the nucleus of a living cell, the nuclear mobility of TOP2B H58Y was markedly reduced, suggesting that the impact of H58Y manifests as low protein mobility. We found that TOP2B H58Y is insensitive to ICRF-187, a TOP2 inhibitor that halts TOP2 as a closed clamp on DNA. When the ATPase activity of TOP2B was compromised, the nuclear mobility of TOP2B H58Y was restored to wild-type levels, indicating the contribution of the ATPase activity to the low nuclear mobility. Analysis of genome-edited cells harboring TOP2B H58Y showed that TOP2B H58Y retains sensitivity to the TOP2 poison etoposide, implying that TOP2B H58Y can undergo at least a part of its catalytic reactions. Collectively, TOP2 H58Y represents a unique example of the relationship between a disease-associated mutation and perturbed protein dynamics.
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Affiliation(s)
- Keiko Morotomi-Yano
- grid.274841.c0000 0001 0660 6749Institute of Industrial Nanomaterials, Kumamoto University, Kumamoto, Japan
| | - Yukiko Hiromoto
- grid.274841.c0000 0001 0660 6749Faculty of Science, Kumamoto University, Kumamoto, Japan
| | - Takumi Higaki
- grid.274841.c0000 0001 0660 6749Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan ,grid.274841.c0000 0001 0660 6749International Research Organization for Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Ken-ichi Yano
- grid.274841.c0000 0001 0660 6749Institute of Industrial Nanomaterials, Kumamoto University, Kumamoto, Japan ,grid.274841.c0000 0001 0660 6749Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
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Ling EM, Baslé A, Cowell IG, van den Berg B, Blower TR, Austin CA. A comprehensive structural analysis of the ATPase domain of human DNA topoisomerase II beta bound to AMPPNP, ADP, and the bisdioxopiperazine, ICRF193. Structure 2022; 30:1129-1145.e3. [PMID: 35660158 PMCID: PMC9592559 DOI: 10.1016/j.str.2022.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/25/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2022]
Abstract
Human topoisomerase II beta (TOP2B) modulates DNA topology using energy from ATP hydrolysis. To investigate the conformational changes that occur during ATP hydrolysis, we determined the X-ray crystallographic structures of the human TOP2B ATPase domain bound to AMPPNP or ADP at 1.9 Å and 2.6 Å resolution, respectively. The GHKL domains of both structures are similar, whereas the QTK loop within the transducer domain can move for product release. As TOP2B is the clinical target of bisdioxopiperazines, we also determined the structure of a TOP2B:ADP:ICRF193 complex to 2.3 Å resolution and identified key drug-binding residues. Biochemical characterization revealed the N-terminal strap reduces the rate of ATP hydrolysis. Mutagenesis demonstrated residue E103 as essential for ATP hydrolysis in TOP2B. Our data provide fundamental insights into the tertiary structure of the human TOP2B ATPase domain and a potential regulatory mechanism for ATP hydrolysis. Three structures of the TOP2B ATPase domain bound to AMPPNP, ADP, or ICRF193 The QTK loop in the ADP complex is further from the active site An SO4 ion is in place of the ATP hydrolysis product, Pi Biochemical data show the N-terminal strap reduces the ATPase hydrolysis activity
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Affiliation(s)
- Elise M Ling
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Arnaud Baslé
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ian G Cowell
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Bert van den Berg
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK.
| | - Caroline A Austin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
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