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D'Agostino M, Simonetti A, Motta S, Wolff P, Romagnoli A, Piccinini A, Spinozzi F, Di Marino D, La Teana A, Ennifar E. Crystal structure of archaeal IF5A-DHS complex reveals insights into the hypusination mechanism. Structure 2024; 32:878-888.e4. [PMID: 38582076 DOI: 10.1016/j.str.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/12/2024] [Accepted: 03/12/2024] [Indexed: 04/08/2024]
Abstract
The translation factor IF5A is highly conserved in Eukarya and Archaea and undergoes a unique post-translational hypusine modification by the deoxyhypusine synthase (DHS) enzyme. DHS transfers the butylamine moiety from spermidine to IF5A using NAD as a cofactor, forming a deoxyhypusine intermediate. IF5A is a key player in protein synthesis, preventing ribosome stalling in proline-rich sequences during translation elongation and facilitating translation elongation and termination. Additionally, human eIF5A participates in various essential cellular processes and contributes to cancer metastasis, with inhibiting hypusination showing anti-proliferative effects. The hypusination pathway of IF5A is therefore an attractive new therapeutic target. We elucidated the 2.0 Å X-ray crystal structure of the archaeal DHS-IF5A complex, revealing hetero-octameric architecture and providing a detailed view of the complex active site including the hypusination loop. This structure, along with biophysical data and molecular dynamics simulations, provides new insights into the catalytic mechanism of the hypusination reaction.
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Affiliation(s)
- Mattia D'Agostino
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy; Architecture et Réactivité de l'ARN, CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Angelita Simonetti
- Architecture et Réactivité de l'ARN, CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Philippe Wolff
- Architecture et Réactivité de l'ARN, CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Alice Romagnoli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy; New York-Marche Structural Biology Center (Ny-Masbic), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Astra Piccinini
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Francesco Spinozzi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy; New York-Marche Structural Biology Center (Ny-Masbic), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy; Neuronal Death and Neuroprotection Unit, Department of Neuroscience, Mario Negri Institute for Pharmacological Research-IRCCS, Via Mario Negri 2, 20156 Milano, Italy.
| | - Anna La Teana
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy; New York-Marche Structural Biology Center (Ny-Masbic), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy.
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN, CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France.
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2
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Wątor E, Wilk P, Kochanowski P, Grudnik P. Structural characterization of the (deoxy)hypusination in Trichomonas vaginalis questions the bifunctionality of deoxyhypusine synthase. FEBS J 2024. [PMID: 38923395 DOI: 10.1111/febs.17207] [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: 02/20/2024] [Revised: 04/14/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
Trichomonas vaginalis, the causative agent of trichomoniasis, is a prevalent anaerobic protozoan parasite responsible for the most common nonviral sexually transmitted infection globally. While metronidazole and its derivatives are approved drugs for this infection, rising resistance necessitates the exploration of new antiparasitic therapies. Protein posttranslational modifications (PTMs) play crucial roles in cellular processes, and among them, hypusination, involving eukaryotic translation factor 5A (eIF5A), has profound implications. Despite extensive studies in various organisms, the role of hypusination in T. vaginalis and its potential impact on parasite biology and pathogenicity remain poorly understood. This study aims to unravel the structural basis of the hypusination pathway in T. vaginalis using X-ray crystallography and cryo-electron microscopy. The results reveal high structural homology between T. vaginalis and human orthologs, providing insights into the molecular architecture of eIF5A and deoxyhypusine synthase (DHS) and their interaction. Contrary to previous suggestions of bifunctionality, our analyses indicate that the putative hydroxylation site in tvDHS is nonfunctional, and biochemical assays demonstrate exclusive deoxyhypusination capability. These findings challenge the notion of tvDHS functioning as both deoxyhypusine synthase and hydroxylase. The study enhances understanding of the hypusination pathway in T. vaginalis, shedding light on its functional relevance and potential as a drug target, and contributing to the development of novel therapeutic strategies against trichomoniasis.
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Affiliation(s)
- Elżbieta Wątor
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Piotr Wilk
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Paweł Kochanowski
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Przemysław Grudnik
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
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3
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Wu B, Liu S. Structural Insights into the Mechanisms Underlying Polyaminopathies. Int J Mol Sci 2024; 25:6340. [PMID: 38928047 PMCID: PMC11203672 DOI: 10.3390/ijms25126340] [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: 05/12/2024] [Revised: 06/01/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Polyamines are ubiquitous in almost all biological entities and involved in various crucial physiological processes. They are also closely associated with the onset and progression of many diseases. Polyaminopathies are a group of rare genetic disorders caused by alterations in the function of proteins within the polyamine metabolism network. Although the identified polyaminopathies are all rare diseases at present, they are genetically heritable, rendering high risks not only to the carriers but also to their descendants. Meanwhile, more polyaminopathic patients might be discovered with the increasing accessibility of gene sequencing. This review aims to provide a comprehensive overview of the structural variations of mutated proteins in current polyaminopathies, in addition to their causative genes, types of mutations, clinical symptoms, and therapeutic approaches. We focus on analyzing how alterations in protein structure lead to protein dysfunction, thereby facilitating the onset of diseases. We hope this review will offer valuable insights and references for the future clinical diagnosis and precision treatment of polyaminopathies.
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Affiliation(s)
- Bing Wu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Wuhan 430068, China
- Hubei Key Laboratory of Industrial Microbiology, National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
| | - Sen Liu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Wuhan 430068, China
- Hubei Key Laboratory of Industrial Microbiology, National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
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4
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Kobayashi T, Sakamoto A, Hisano T, Kashiwagi K, Igarashi K, Takao K, Uemura T, Furuchi T, Sugita Y, Moriya T, Oshima T, Terui Y. Caldomycin, a new guanidopolyamine produced by a novel agmatine homocoupling enzyme involved in homospermidine biosynthesis. Sci Rep 2024; 14:7566. [PMID: 38555406 PMCID: PMC10981699 DOI: 10.1038/s41598-024-58296-0] [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: 12/06/2023] [Accepted: 03/27/2024] [Indexed: 04/02/2024] Open
Abstract
An extreme thermophilic bacterium, Thermus thermophilus produces more than 20 unusual polyamines, but their biosynthetic pathways, including homospermidine, are not yet fully understood. Two types of homospermidine synthases have been identified in plants and bacteria, which use spermidine and putrescine or two molecules of putrescine as substrates. However, homospermidine synthases with such substrate specificity have not been identified in T. thermophilus. Here we identified a novel agmatine homocoupling enzyme that is involved in homospermidine biosynthesis in T. thermophilus. The reaction mechanism is different from that of a previously described homospermidine synthase, and involves conjugation of two molecules of agmatine, which produces a diamidino derivative of homospermidine (caldomycin) as an immediate precursor of homospermidine. We conclude that there is a homospermidine biosynthetic pathway from agmatine via caldomycin synthase followed by ureohydrolase in T. thermophilus. Furthermore, it is shown that caldomycin is a novel compound existing in nature.
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Affiliation(s)
- Teruyuki Kobayashi
- Faculty of Pharmacy, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba, 288-0025, Japan
| | - Akihiko Sakamoto
- Faculty of Pharmacy, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba, 288-0025, Japan
- Department of Pathophysiology and Therapeutics, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Shinagawa, Tokyo, Japan
| | - Tamao Hisano
- RIKEN Center for Biosystems Dynamics Research (BDR), Tsurumi, Kanagawa, Japan
| | - Keiko Kashiwagi
- Faculty of Pharmacy, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba, 288-0025, Japan
| | - Kazuei Igarashi
- Amine Pharma Research Institute, Innovation Plaza at Chiba University, Chiba, Japan
| | - Koichi Takao
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, Sakado, Saitama, Japan
| | - Takeshi Uemura
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, Sakado, Saitama, Japan
| | - Takemitsu Furuchi
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, Sakado, Saitama, Japan
| | - Yoshiaki Sugita
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, Sakado, Saitama, Japan
| | - Toshiyuki Moriya
- Institute of Environmental Biology, Kyowa-Kako, Machida, Tokyo, Japan
| | - Tairo Oshima
- Institute of Environmental Biology, Kyowa-Kako, Machida, Tokyo, Japan
| | - Yusuke Terui
- Faculty of Pharmacy, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba, 288-0025, Japan.
- School of Pharmacy, International University of Health and Welfare, Otawara, Tochigi, Japan.
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5
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Guo JS, Liu KL, Qin YX, Hou L, Jian LY, Yang YH, Li XY. Hypusination-induced DHPS/eIF5A pathway as a new therapeutic strategy for human diseases: A mechanistic review and structural classification of DHPS inhibitors. Biomed Pharmacother 2023; 167:115440. [PMID: 37683595 DOI: 10.1016/j.biopha.2023.115440] [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: 07/04/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023] Open
Abstract
The discovery of new therapeutic strategies for diseases is essential for drug research. Deoxyhypusine synthase (DHPS) is a critical enzyme that modifies the conversion of the eukaryotic translation initiation factor 5A (eIF5A) precursor into physiologically active eIF5A (eIF5A-Hyp). Recent studies have revealed that the hypusine modifying of DHPS on eIF5A has an essential regulatory role in human diseases. The hypusination-induced DHPS/eIF5A pathway has been shown to play an essential role in various cancers, and it could regulate immune-related diseases, glucose metabolism-related diseases, neurological-related diseases, and aging. In addition, DHPS has a more defined substrate and a well-defined structure within the active pocket than eIF5A. More and more researchers are focusing on the prospect of advanced development of DHPS inhibitors. This review summarizes the regulatory mechanisms of the hypusination-induced DHPS/eIF5A pathway in a variety of diseases in addition to the inhibitors related to this pathway; it highlights and analyzes the structural features and mechanisms of action of DHPS inhibitors and expands the prospects of future drug development using DHPS as an anticancer target.
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Affiliation(s)
- Jing-Si Guo
- Department of Pharmacy, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Shenyang 110004, PR China
| | - Kai-Li Liu
- School of Pharmacy, China Medical University, No. 77 Puhe, Shenyang 110122, PR China
| | - Yu-Xi Qin
- Department of Pharmacy, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Shenyang 110004, PR China
| | - Lin Hou
- Department of Pharmacy, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Shenyang 110004, PR China
| | - Ling-Yan Jian
- Department of Pharmacy, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Shenyang 110004, PR China
| | - Yue-Hui Yang
- Department of Pharmacy, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Shenyang 110004, PR China
| | - Xin-Yang Li
- Department of Pharmacy, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Shenyang 110004, PR China.
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6
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Wątor E, Wilk P, Biela A, Rawski M, Zak KM, Steinchen W, Bange G, Glatt S, Grudnik P. Cryo-EM structure of human eIF5A-DHS complex reveals the molecular basis of hypusination-associated neurodegenerative disorders. Nat Commun 2023; 14:1698. [PMID: 36973244 PMCID: PMC10042821 DOI: 10.1038/s41467-023-37305-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
Hypusination is a unique post-translational modification of the eukaryotic translation factor 5A (eIF5A) that is essential for overcoming ribosome stalling at polyproline sequence stretches. The initial step of hypusination, the formation of deoxyhypusine, is catalyzed by deoxyhypusine synthase (DHS), however, the molecular details of the DHS-mediated reaction remained elusive. Recently, patient-derived variants of DHS and eIF5A have been linked to rare neurodevelopmental disorders. Here, we present the cryo-EM structure of the human eIF5A-DHS complex at 2.8 Å resolution and a crystal structure of DHS trapped in the key reaction transition state. Furthermore, we show that disease-associated DHS variants influence the complex formation and hypusination efficiency. Hence, our work dissects the molecular details of the deoxyhypusine synthesis reaction and reveals how clinically-relevant mutations affect this crucial cellular process.
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Affiliation(s)
- Elżbieta Wątor
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Piotr Wilk
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Artur Biela
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Michał Rawski
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Krzysztof M Zak
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Wieland Steinchen
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany
| | - Gert Bange
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Molecular Physiology of Microbes, Marburg, Germany
| | - Sebastian Glatt
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Przemysław Grudnik
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.
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7
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Mudryi V, Peske F, Rodnina M. Translation Factor Accelerating Peptide Bond Formation on the Ribosome: EF-P and eIF5A as Entropic Catalysts and a Potential Drug Targets. BBA ADVANCES 2023; 3:100074. [PMID: 37082265 PMCID: PMC10074943 DOI: 10.1016/j.bbadva.2023.100074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2023] Open
Abstract
Elongation factor P (EF-P) and its eukaryotic homolog eIF5A are auxiliary translation factors that facilitate peptide bond formation when several sequential proline (Pro) residues are incorporated into the nascent chain. EF-P and eIF5A bind to the exit (E) site of the ribosome and contribute to favorable entropy of the reaction by stabilizing tRNA binding in the peptidyl transferase center of the ribosome. In most organisms, EF-P and eIF5A carry a posttranslational modification that is crucial for catalysis. The chemical nature of the modification varies between different groups of bacteria and between pro- and eukaryotes, making the EF-P-modification enzymes promising targets for antibiotic development. In this review, we summarize our knowledge of the structure and function of EF-P and eIF5A, describe their modification enzymes, and present an approach for potential drug screening aimed at EarP, an enzyme that is essential for EF-P modification in several pathogenic bacteria.
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8
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Prakashrao AS, Beuerle T, Simões ARG, Hopf C, Çiçek SS, Stegemann T, Ober D, Kaltenegger E. The long road of functional recruitment-The evolution of a gene duplicate to pyrrolizidine alkaloid biosynthesis in the morning glories (Convolvulaceae). PLANT DIRECT 2022; 6:e420. [PMID: 35865076 PMCID: PMC9295680 DOI: 10.1002/pld3.420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
In plants, homospermidine synthase (HSS) is a pathway-specific enzyme initiating the biosynthesis of pyrrolizidine alkaloids (PAs), which function as a chemical defense against herbivores. In PA-producing Convolvulaceae ("morning glories"), HSS originated from deoxyhypusine synthase at least >50 to 75 million years ago via a gene duplication event and subsequent functional diversification. To study the recruitment of this ancient gene duplicate to PA biosynthesis, the presence of putative hss gene copies in 11 Convolvulaceae species was analyzed. Additionally, various plant parts from seven of these species were screened for the presence of PAs. Although all of these species possess a putative hss copy, PAs could only be detected in roots of Ipomoea neei (Spreng.) O'Donell and Distimake quinquefolius (L.) A.R.Simões & Staples in this study. A precursor of PAs was detected in roots of Ipomoea alba L. Thus, despite sharing high sequence identities, the presence of an hss gene copy does not correlate with PA accumulation in particular species of Convolvulaceae. In vitro activity assays of the encoded enzymes revealed a broad spectrum of enzyme activity, further emphasizing a functional diversity of the hss gene copies. A recently identified HSS specific amino acid motif seems to be important for the loss of the ancestral protein function-the activation of the eukaryotic initiation factor 5A (eIF5A). Thus, the motif might be indicative for a change of function but allows not to predict the new function. This emphasizes the challenges in annotating functions for duplicates, even for duplicates from closely related species.
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Affiliation(s)
- Arunraj Saranya Prakashrao
- Department Biochemical Ecology and Molecular Evolution, Botanical InstituteChristian‐Albrechts‐UniversityKielGermany
- Present address:
Heart Research Center GöttingenUniversity Medical Center GöttingenGöttingenGermany.
| | - Till Beuerle
- Institute of Pharmaceutical BiologyTechnische Universität BraunschweigBraunschweigGermany
| | - Ana Rita G. Simões
- Royal Botanic Gardens, KewRichmondUK
- Systematic and Evolutionary Botany LabGhent UniversityGhentBelgium
| | - Christina Hopf
- Department of Structural Biology, Zoological InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Serhat Sezai Çiçek
- Department of Pharmaceutical Biology, Pharmaceutical InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Thomas Stegemann
- Department Biochemical Ecology and Molecular Evolution, Botanical InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Dietrich Ober
- Department Biochemical Ecology and Molecular Evolution, Botanical InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Elisabeth Kaltenegger
- Department Biochemical Ecology and Molecular Evolution, Botanical InstituteChristian‐Albrechts‐UniversityKielGermany
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9
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Biogenic Polyamines and Related Metabolites. Biomolecules 2021; 12:biom12010014. [PMID: 35053162 PMCID: PMC8773558 DOI: 10.3390/biom12010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022] Open
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10
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Pálfi P, Bakacsy L, Kovács H, Szepesi Á. Hypusination, a Metabolic Posttranslational Modification of eIF5A in Plants during Development and Environmental Stress Responses. PLANTS 2021; 10:plants10071261. [PMID: 34206171 PMCID: PMC8309165 DOI: 10.3390/plants10071261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/15/2021] [Accepted: 06/21/2021] [Indexed: 12/25/2022]
Abstract
Hypusination is a unique posttranslational modification of eIF5A, a eukaryotic translation factor. Hypusine is a rare amino acid synthesized in this process and is mediated by two enzymes, deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH). Despite the essential participation of this conserved eIF5A protein in plant development and stress responses, our knowledge of its proper function is limited. In this review, we demonstrate the main findings regarding how eIF5A and hypusination could contribute to plant-specific responses in growth and stress-related processes. Our aim is to briefly discuss the plant-specific details of hypusination and decipher those signal pathways which can be effectively modified by this process. The diverse functions of eIF5A isoforms are also discussed in this review.
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11
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D'Agostino M, Motta S, Romagnoli A, Orlando P, Tiano L, La Teana A, Di Marino D. Insights Into the Binding Mechanism of GC7 to Deoxyhypusine Synthase in Sulfolobus solfataricus: A Thermophilic Model for the Design of New Hypusination Inhibitors. Front Chem 2021; 8:609942. [PMID: 33392152 PMCID: PMC7773846 DOI: 10.3389/fchem.2020.609942] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/16/2020] [Indexed: 12/18/2022] Open
Abstract
Translation factor 5A (eIF5A) is one of the most conserved proteins involved in protein synthesis. It plays a key role during the elongation of polypeptide chains, and its activity is critically dependent on hypusination, a post-translational modification of a specific lysine residue through two consecutive enzymatic steps carried out by deoxyhypusine synthase (DHS), with spermidine as substrate, and deoxyhypusine hydroxylase (DOHH). It is well-established that eIF5A is overexpressed in several cancer types, and it is involved in various diseases such as HIV-1 infection, malaria, and diabetes; therefore, the development of inhibitors targeting both steps of the hypusination process is considered a promising and challenging therapeutic strategy. One of the most efficient inhibitors of the hypusination process is the spermidine analog N1-guanyl-1,7-diaminoheptane (GC7). GC7 interacts in a specific binding pocket of the DHS completely blocking its activity; however, its therapeutic use is limited by poor selectivity and restricted bioavailability. Here we have performed a comparative study between human DHS (hDHS) and archaeal DHS from crenarchaeon Sulfolobus solfataricus (aDHS) to understand the structural and dynamical features of the GC7 inhibition. The advanced metadynamics (MetaD) classical molecular dynamics simulations show that the GC7 interaction is less stable in the thermophilic enzyme compared to hDHS that could underlie a lower inhibitory capacity of the hypusination process in Sulfolobus solfataricus. To confirm this hypothesis, we have tested GC7 activity on S. solfataricus by measuring cellular growth, and results have shown the lack of inhibition of aIF5A hypusination in contrast to the established effect on eukaryotic cellular growth. These results provide, for the first time, detailed molecular insights into the binding mechanism of GC7 to aDHS generating the basis for the design of new and more specific DHS inhibitors.
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Affiliation(s)
- Mattia D'Agostino
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Alice Romagnoli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.,New York-Marche Structural Biology Center (Ny-Masbic), Polytechnic University of Marche, Ancona, Italy
| | - Patrick Orlando
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Luca Tiano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Anna La Teana
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.,New York-Marche Structural Biology Center (Ny-Masbic), Polytechnic University of Marche, Ancona, Italy
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.,New York-Marche Structural Biology Center (Ny-Masbic), Polytechnic University of Marche, Ancona, Italy
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12
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Kaltenegger E, Prakashrao AS, Çiçek SS, Ober D. Development of an activity assay for characterizing deoxyhypusine synthase and its diverse reaction products. FEBS Open Bio 2021; 11:10-25. [PMID: 33247548 PMCID: PMC7780104 DOI: 10.1002/2211-5463.13046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/04/2020] [Accepted: 11/24/2020] [Indexed: 02/02/2023] Open
Abstract
Deoxyhypusine synthase transfers an aminobutyl moiety from spermidine to the eukaryotic translation initiation factor 5A (eIF5A) in the first step of eIF5A activation. This exclusive post-translational modification is conserved in all eukaryotes. Activated eIF5A has been shown to be essential for cell proliferation and viability. Recent reports have linked the activation of eIF5A to several human diseases. Deoxyhypusine synthase, which is encoded by a single gene copy in most eukaryotes, was duplicated in several plant lineages during evolution, the copies being repeatedly recruited to pyrrolizidine alkaloid biosynthesis. However, the function of many of these duplicates is unknown. Notably, deoxyhypusine synthase is highly promiscuous and can catalyze various reactions, often of unknown biological relevance. To facilitate in-depth biochemical studies of this enzyme, we report here the development of a simple and robust in vitro enzyme assay. It involves precolumn derivatization of the polyamines taking part in the reaction and avoids the need for the previously used radioactively labeled tracers. The derivatized polyamines are quantified after high-performance liquid chromatography coupled to diode array and fluorescence detectors. By performing kinetic analyses of deoxyhypusine synthase and its paralog from the pyrrolizidine alkaloid-producing plant Senecio vernalis, we demonstrate that the assay unequivocally differentiates the paralogous enzymes. Furthermore, it detects and quantifies, in a single assay, the side reactions that occur in parallel to the main reaction. The presented assay thus provides a detailed biochemical characterization of deoxyhypusine synthase and its paralogs.
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Affiliation(s)
- Elisabeth Kaltenegger
- Biochemical Ecology and Molecular Evolution GroupBotanical Institute and Kiel Botanic GardensChristian‐Albrechts‐UniversityKielGermany
| | - Arunraj S. Prakashrao
- Biochemical Ecology and Molecular Evolution GroupBotanical Institute and Kiel Botanic GardensChristian‐Albrechts‐UniversityKielGermany
| | - Serhat S. Çiçek
- Pharmacognosy GroupPharmaceutical InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Dietrich Ober
- Biochemical Ecology and Molecular Evolution GroupBotanical Institute and Kiel Botanic GardensChristian‐Albrechts‐UniversityKielGermany
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Structural Characterization of Glycerol Kinase from the Thermophilic Fungus Chaetomium thermophilum. Int J Mol Sci 2020; 21:ijms21249570. [PMID: 33339113 PMCID: PMC7765489 DOI: 10.3390/ijms21249570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/05/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
Glycerol is an organic compound that can be utilized as an alternative source of carbon by various organisms. One of the ways to assimilate glycerol by the cell is the phosphorylative catabolic pathway in which its activation is catalyzed by glycerol kinase (GK) and glycerol-3-phosphate (G3P) is formed. To date, several GK crystal structures from bacteria, archaea, and unicellular eukaryotic parasites have been solved. Herein, we present a series of crystal structures of GK from Chaetomium thermophilum (CtGK) in apo and glycerol-bound forms. In addition, we show the feasibility of an ADP-dependent glucokinase (ADPGK)-coupled enzymatic assay to measure the CtGK activity. New structures described in our work provide structural insights into the GK catalyzed reaction in the filamentous fungus and set the foundation for understanding the glycerol metabolism in eukaryotes.
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14
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Silva SF, Klippel AH, Ramos PZ, Santiago ADS, Valentini SR, Bengtson MH, Massirer KB, Bilsland E, Couñago RM, Zanelli CF. Structural features and development of an assay platform of the parasite target deoxyhypusine synthase of Brugia malayi and Leishmania major. PLoS Negl Trop Dis 2020; 14:e0008762. [PMID: 33044977 PMCID: PMC7581365 DOI: 10.1371/journal.pntd.0008762] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 10/22/2020] [Accepted: 08/31/2020] [Indexed: 01/03/2023] Open
Abstract
Deoxyhypusine synthase (DHS) catalyzes the first step of the post-translational modification of eukaryotic translation factor 5A (eIF5A), which is the only known protein containing the amino acid hypusine. Both proteins are essential for eukaryotic cell viability, and DHS has been suggested as a good candidate target for small molecule-based therapies against eukaryotic pathogens. In this work, we focused on the DHS enzymes from Brugia malayi and Leishmania major, the causative agents of lymphatic filariasis and cutaneous leishmaniasis, respectively. To enable B. malayi (Bm)DHS for future target-based drug discovery programs, we determined its crystal structure bound to cofactor NAD+. We also reported an in vitro biochemical assay for this enzyme that is amenable to a high-throughput screening format. The L. major genome encodes two DHS paralogs, and attempts to produce them recombinantly in bacterial cells were not successful. Nevertheless, we showed that ectopic expression of both LmDHS paralogs can rescue yeast cells lacking the endogenous DHS-encoding gene (dys1). Thus, functionally complemented dys1Δ yeast mutants can be used to screen for new inhibitors of the L. major enzyme. We used the known human DHS inhibitor GC7 to validate both in vitro and yeast-based DHS assays. Our results show that BmDHS is a homotetrameric enzyme that shares many features with its human homologue, whereas LmDHS paralogs are likely to form a heterotetrameric complex and have a distinct regulatory mechanism. We expect our work to facilitate the identification and development of new DHS inhibitors that can be used to validate these enzymes as vulnerable targets for therapeutic interventions against B. malayi and L. major infections. Target-based drug discovery strategies hold the promise to discover safer and more effective treatments for Neglected Tropical Diseases (NTDs). Genetic manipulation techniques have been used to successfully identify essential genes in eukaryotic parasites. Unfortunately, the fact that a gene is essential under controlled laboratory conditions does not automatically make the corresponding gene-product vulnerable to pharmacological intervention in a clinical setting within the human host. To allow the discovery and development of small molecule tool compounds that can be used to validate pharmacologically vulnerable targets, one must first establish compound screening assays and obtain structural information for the candidate target. Eukaryotic cells lacking deoxyhypusine synthase (DHS) function are not viable. DHS catalyzes the first step in a post-translational modification that is critical for the function of eIF5A. Presence of mature eIF5A is also essential for eukaryotic cell viability. Here we reported compound screening assays (yeast-based for Brugia malayi and Leishmania major; in vitro for B. malayi only) and provided further regulatory and structural insights we hope will aid in the identification and development of inhibitors for the DHS enzymes from two NTD-causing organisms—B. malayi, the causative agent of lymphatic filariasis and L. major, the causative agent of cutaneous leishmaniasis.
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Affiliation(s)
| | | | - Priscila Zonzini Ramos
- Molecular Biology and Genetic Engineering Center (CBMEG), Medicinal Chemistry Center (CQMED), Structural Genomics Consortium (SGC-UNICAMP), University of Campinas-UNICAMP, Campinas, SP, Brazil
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas—UNICAMP, Campinas, SP, Brazil
| | - André da Silva Santiago
- Molecular Biology and Genetic Engineering Center (CBMEG), Medicinal Chemistry Center (CQMED), Structural Genomics Consortium (SGC-UNICAMP), University of Campinas-UNICAMP, Campinas, SP, Brazil
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas—UNICAMP, Campinas, SP, Brazil
| | | | - Mario Henrique Bengtson
- Molecular Biology and Genetic Engineering Center (CBMEG), Medicinal Chemistry Center (CQMED), Structural Genomics Consortium (SGC-UNICAMP), University of Campinas-UNICAMP, Campinas, SP, Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas—UNICAMP, Campinas, SP, Brazil
| | - Katlin Brauer Massirer
- Molecular Biology and Genetic Engineering Center (CBMEG), Medicinal Chemistry Center (CQMED), Structural Genomics Consortium (SGC-UNICAMP), University of Campinas-UNICAMP, Campinas, SP, Brazil
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas—UNICAMP, Campinas, SP, Brazil
| | - Elizabeth Bilsland
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas—UNICAMP, Campinas, SP, Brazil
| | - Rafael Miguez Couñago
- Molecular Biology and Genetic Engineering Center (CBMEG), Medicinal Chemistry Center (CQMED), Structural Genomics Consortium (SGC-UNICAMP), University of Campinas-UNICAMP, Campinas, SP, Brazil
- * E-mail: (RMC); (CFZ)
| | - Cleslei Fernando Zanelli
- School of Pharmaceutical Sciences, São Paulo State University—UNESP, Araraquara, SP, Brazil
- * E-mail: (RMC); (CFZ)
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15
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Tanaka Y, Kurasawa O, Yokota A, Klein MG, Saito B, Matsumoto S, Okaniwa M, Ambrus-Aikelin G, Uchiyama N, Morishita D, Kimura H, Imamura S. New Series of Potent Allosteric Inhibitors of Deoxyhypusine Synthase. ACS Med Chem Lett 2020; 11:1645-1652. [PMID: 34345355 PMCID: PMC8323115 DOI: 10.1021/acsmedchemlett.0c00331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/30/2020] [Indexed: 02/06/2023] Open
Abstract
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Deoxyhypusine synthase (DHPS) is
the primary enzyme responsible
for the hypusine modification and, thereby, activation of the eukaryotic
translation initiation factor 5A (eIF5A), which is key in regulating
the protein translation processes associated with tumor proliferation.
Although DHPS inhibitors could be a promising therapeutic option for
treating cancer, only a few studies reported druglike compounds with
this inhibition property. Thus, in this work, we designed and synthesized
a new chemical series possessing fused ring scaffolds designed from
high-throughput screening hit compounds, discovering a 5,6-dihydrothieno[2,3-c]pyridine derivative (26d) with potent inhibitory
activity; furthermore, the X-ray crystallographic analysis of the
DHPS complex with 26d demonstrated a distinct allosteric
binding mode compared to a previously reported inhibitor. These findings
could be significantly useful in the functional analysis of conformational
changes in DHPS as well as the structure-based design of allosteric
inhibitors.
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Affiliation(s)
- Yuta Tanaka
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Osamu Kurasawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Akihiro Yokota
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Michael G. Klein
- Department of Structural Biology, Takeda California, 10410 Science Center Drive, San Diego, California 92121, United States
| | - Bunnai Saito
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Shigemitsu Matsumoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masanori Okaniwa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Geza Ambrus-Aikelin
- Department of Structural Biology, Takeda California, 10410 Science Center Drive, San Diego, California 92121, United States
| | - Noriko Uchiyama
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Daisuke Morishita
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Hiromichi Kimura
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Shinichi Imamura
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
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16
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Chen M, Gai Z, Okada C, Ye Y, Yu J, Yao M. Flexible NAD + Binding in Deoxyhypusine Synthase Reflects the Dynamic Hypusine Modification of Translation Factor IF5A. Int J Mol Sci 2020; 21:ijms21155509. [PMID: 32752130 PMCID: PMC7432094 DOI: 10.3390/ijms21155509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 01/23/2023] Open
Abstract
The eukaryotic and archaeal translation factor IF5A requires a post-translational hypusine modification, which is catalyzed by deoxyhypusine synthase (DHS) at a single lysine residue of IF5A with NAD+ and spermidine as cofactors, followed by hydroxylation to form hypusine. While human DHS catalyzed reactions have been well characterized, the mechanism of the hypusination of archaeal IF5A by DHS is not clear. Here we report a DHS structure from Pyrococcus horikoshii OT3 (PhoDHS) at 2.2 Å resolution. The structure reveals two states in a single functional unit (tetramer): two NAD+-bound monomers with the NAD+ and spermidine binding sites observed in multi-conformations (closed and open), and two NAD+-free monomers. The dynamic loop region V288–P299, in the vicinity of the active site, adopts different positions in the closed and open conformations and is disordered when NAD+ is absent. Combined with NAD+ binding analysis, it is clear that PhoDHS can exist in three states: apo, PhoDHS-2 equiv NAD+, and PhoDHS-4 equiv NAD+, which are affected by the NAD+ concentration. Our results demonstrate the dynamic structure of PhoDHS at the NAD+ and spermidine binding site, with conformational changes that may be the response to the local NAD+ concentration, and thus fine-tune the regulation of the translation process via the hypusine modification of IF5A.
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Affiliation(s)
- Meirong Chen
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; (M.C.); (Z.G.); (C.O.); (Y.Y.); (J.Y.)
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zuoqi Gai
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; (M.C.); (Z.G.); (C.O.); (Y.Y.); (J.Y.)
| | - Chiaki Okada
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; (M.C.); (Z.G.); (C.O.); (Y.Y.); (J.Y.)
| | - Yuxin Ye
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; (M.C.); (Z.G.); (C.O.); (Y.Y.); (J.Y.)
| | - Jian Yu
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; (M.C.); (Z.G.); (C.O.); (Y.Y.); (J.Y.)
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; (M.C.); (Z.G.); (C.O.); (Y.Y.); (J.Y.)
- Correspondence: ; Tel./Fax: +81-11-706-4481
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