1
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Ghosh S, Sanchez AM, Schwer B, Prucker I, Jork N, Jessen HJ, Shuman S. Activities and genetic interactions of fission yeast Aps1, a Nudix-type inositol pyrophosphatase and inorganic polyphosphatase. mBio 2024; 15:e0108424. [PMID: 38940614 PMCID: PMC11323792 DOI: 10.1128/mbio.01084-24] [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: 04/11/2024] [Accepted: 05/28/2024] [Indexed: 06/29/2024] Open
Abstract
Inositol pyrophosphate 1,5-IP8 regulates expression of a fission yeast phosphate homeostasis regulon, comprising phosphate acquisition genes pho1, pho84, and tgp1, via its action as an agonist of precocious termination of transcription of the upstream lncRNAs that repress PHO mRNA synthesis. 1,5-IP8 levels are dictated by a balance between the Asp1 N-terminal kinase domain that converts 5-IP7 to 1,5-IP8 and three inositol pyrophosphatases-the Asp1 C-terminal domain (a histidine acid phosphatase), Siw14 (a cysteinyl-phosphatase), and Aps1 (a Nudix enzyme). In this study, we report the biochemical and genetic characterization of Aps1 and an analysis of the effects of Asp1, Siw14, and Aps1 mutations on cellular inositol pyrophosphate levels. We find that Aps1's substrate repertoire embraces inorganic polyphosphates, 5-IP7, 1-IP7, and 1,5-IP8. Aps1 displays a ~twofold preference for hydrolysis of 1-IP7 versus 5-IP7 and aps1∆ cells have twofold higher levels of 1-IP7 vis-à-vis wild-type cells. While neither Aps1 nor Siw14 is essential for growth, an aps1∆ siw14∆ double mutation is lethal on YES medium. This lethality is a manifestation of IP8 toxicosis, whereby excessive 1,5-IP8 drives derepression of tgp1, leading to Tgp1-mediated uptake of glycerophosphocholine. We were able to recover an aps1∆ siw14∆ mutant on ePMGT medium lacking glycerophosphocholine and to suppress the severe growth defect of aps1∆ siw14∆ on YES by deleting tgp1. However, the severe growth defect of an aps1∆ asp1-H397A strain could not be alleviated by deleting tgp1, suggesting that 1,5-IP8 levels in this double-pyrophosphatase mutant exceed a threshold beyond which overzealous termination affects other genes, which results in cytotoxicity. IMPORTANCE Repression of the fission yeast PHO genes tgp1, pho1, and pho84 by lncRNA-mediated interference is sensitive to changes in the metabolism of 1,5-IP8, a signaling molecule that acts as an agonist of precocious lncRNA termination. 1,5-IP8 is formed by phosphorylation of 5-IP7 and catabolized by inositol pyrophosphatases from three distinct enzyme families: Asp1 (a histidine acid phosphatase), Siw14 (a cysteinyl phosphatase), and Aps1 (a Nudix hydrolase). This study entails a biochemical characterization of Aps1 and an analysis of how Asp1, Siw14, and Aps1 mutations impact growth and inositol pyrophosphate pools in vivo. Aps1 catalyzes hydrolysis of inorganic polyphosphates, 5-IP7, 1-IP7, and 1,5-IP8 in vitro, with a ~twofold preference for 1-IP7 over 5-IP7. aps1∆ cells have twofold higher levels of 1-IP7 than wild-type cells. An aps1∆ siw14∆ double mutation is lethal because excessive 1,5-IP8 triggers derepression of tgp1, leading to toxic uptake of glycerophosphocholine.
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Affiliation(s)
- Shreya Ghosh
- Molecular Biology Program, Sloan Kettering Institute, New York, New York, USA
| | - Ana M. Sanchez
- Molecular Biology Program, Sloan Kettering Institute, New York, New York, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Isabel Prucker
- Institute of Organic Chemistry, University of Freiburg, Freiburg, Germany
| | - Nikolaus Jork
- Institute of Organic Chemistry, University of Freiburg, Freiburg, Germany
| | - Henning J. Jessen
- Institute of Organic Chemistry, University of Freiburg, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Stewart Shuman
- Molecular Biology Program, Sloan Kettering Institute, New York, New York, USA
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2
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Mihiret YE, Schaaf G, Kamleitner M. Protein pyrophosphorylation by inositol phosphates: a novel post-translational modification in plants? FRONTIERS IN PLANT SCIENCE 2024; 15:1347922. [PMID: 38455731 PMCID: PMC10917965 DOI: 10.3389/fpls.2024.1347922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/01/2024] [Indexed: 03/09/2024]
Abstract
Inositol pyrophosphates (PP-InsPs) are energy-rich molecules harboring one or more diphosphate moieties. PP-InsPs are found in all eukaryotes evaluated and their functional versatility is reflected in the various cellular events in which they take part. These include, among others, insulin signaling and intracellular trafficking in mammals, as well as innate immunity and hormone and phosphate signaling in plants. The molecular mechanisms by which PP-InsPs exert such functions are proposed to rely on the allosteric regulation via direct binding to proteins, by competing with other ligands, or by protein pyrophosphorylation. The latter is the focus of this review, where we outline a historical perspective surrounding the first findings, almost 20 years ago, that certain proteins can be phosphorylated by PP-InsPs in vitro. Strikingly, in vitro phosphorylation occurs by an apparent enzyme-independent but Mg2+-dependent transfer of the β-phosphoryl group of an inositol pyrophosphate to an already phosphorylated serine residue at Glu/Asp-rich protein regions. Ribosome biogenesis, vesicle trafficking and transcription are among the cellular events suggested to be modulated by protein pyrophosphorylation in yeast and mammals. Here we discuss the latest efforts in identifying targets of protein pyrophosphorylation, pointing out the methodological challenges that have hindered the full understanding of this unique post-translational modification, and focusing on the latest advances in mass spectrometry that finally provided convincing evidence that PP-InsP-mediated pyrophosphorylation also occurs in vivo. We also speculate about the relevance of this post-translational modification in plants in a discussion centered around the protein kinase CK2, whose activity is critical for pyrophosphorylation of animal and yeast proteins. This enzyme is widely present in plant species and several of its functions overlap with those of PP-InsPs. Until now, there is virtually no data on pyrophosphorylation of plant proteins, which is an exciting field that remains to be explored.
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Affiliation(s)
| | | | - Marília Kamleitner
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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3
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Hostachy S, Wang H, Zong G, Franke K, Riley AM, Schmieder P, Potter BVL, Shears SB, Fiedler D. Fluorination Influences the Bioisostery of Myo-Inositol Pyrophosphate Analogs. Chemistry 2023; 29:e202302426. [PMID: 37773020 PMCID: PMC7615343 DOI: 10.1002/chem.202302426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/14/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023]
Abstract
Inositol pyrophosphates (PP-IPs) are densely phosphorylated messenger molecules involved in numerous biological processes. PP-IPs contain one or two pyrophosphate group(s) attached to a phosphorylated myo-inositol ring. 5PP-IP5 is the most abundant PP-IP in human cells. To investigate the function and regulation by PP-IPs in biological contexts, metabolically stable analogs have been developed. Here, we report the synthesis of a new fluorinated phosphoramidite reagent and its application for the synthesis of a difluoromethylene bisphosphonate analog of 5PP-IP5 . Subsequently, the properties of all currently reported analogs were benchmarked using a number of biophysical and biochemical methods, including co-crystallization, ITC, kinase activity assays and chromatography. Together, the results showcase how small structural alterations of the analogs can have notable effects on their properties in a biochemical setting and will guide in the choice of the most suitable analog(s) for future investigations.
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Affiliation(s)
- Sarah Hostachy
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Straße 1013125BerlinGermany
| | - Huanchen Wang
- Inositol Signaling GroupNational Institutes of HealthResearch Triangle ParkNorth Carolina27709USA
| | - Guangning Zong
- Inositol Signaling GroupNational Institutes of HealthResearch Triangle ParkNorth Carolina27709USA
| | - Katy Franke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Straße 1013125BerlinGermany
| | - Andrew M. Riley
- Medicinal Chemistry & Drug Discovery Department of PharmacologyUniversity of OxfordOxfordOX1 3QTUK
| | - Peter Schmieder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Straße 1013125BerlinGermany
| | - Barry V. L. Potter
- Medicinal Chemistry & Drug Discovery Department of PharmacologyUniversity of OxfordOxfordOX1 3QTUK
| | - Stephen B. Shears
- Inositol Signaling GroupNational Institutes of HealthResearch Triangle ParkNorth Carolina27709USA
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Straße 1013125BerlinGermany
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
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4
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Ritter K, Jork N, Unmüßig AS, Köhn M, Jessen HJ. Assigning the Absolute Configuration of Inositol Poly- and Pyrophosphates by NMR Using a Single Chiral Solvating Agent. Biomolecules 2023; 13:1150. [PMID: 37509185 PMCID: PMC10377360 DOI: 10.3390/biom13071150] [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: 05/30/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Inositol phosphates constitute a family of highly charged messenger molecules that play diverse roles in cellular processes. The various phosphorylation patterns they exhibit give rise to a vast array of different compounds. To fully comprehend the biological interconnections, the precise molecular identification of each compound is crucial. Since the myo-inositol scaffold possesses an internal mirror plane, enantiomeric pairs can be formed. Most commonly employed methods for analyzing InsPs have been geared towards resolving regioisomers, but they have not been capable of resolving enantiomers. In this study, we present a general approach for enantiomer assignment using NMR measurements. To achieve this goal, we used 31P-NMR in the presence of L-arginine amide as a chiral solvating agent, which enables the differentiation of enantiomers. Using chemically synthesized standard compounds allows for an unambiguous assignment of the enantiomers. This method was applied to highly phosphorylated inositol pyrophosphates, as well as to lowly phosphorylated inositol phosphates and bisphosphonate analogs. Our method will facilitate the assignment of biologically relevant isomers when isolating naturally occurring compounds from biological specimens.
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Affiliation(s)
- Kevin Ritter
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Jork
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Anne-Sophie Unmüßig
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Maja Köhn
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
- Institute of Biology 3, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- BIOSS-Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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5
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Shipton ML, Jamion FA, Wheeler S, Riley AM, Plasser F, Potter BVL, Butler SJ. Expedient synthesis and luminescence sensing of the inositol pyrophosphate cellular messenger 5-PP-InsP 5. Chem Sci 2023; 14:4979-4985. [PMID: 37206391 PMCID: PMC10189900 DOI: 10.1039/d2sc06812e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/07/2023] [Indexed: 05/21/2023] Open
Abstract
Inositol pyrophosphates are important biomolecules associated with apoptosis, cell growth and kinase regulation, yet their exact biological roles are still emerging and probes do not exist for their selective detection. We report the first molecular probe for the selective and sensitive detection of the most abundant cellular inositol pyrophosphate 5-PP-InsP5, as well as an efficient new synthesis. The probe is based on a macrocyclic Eu(iii) complex bearing two quinoline arms providing a free coordination site at the Eu(iii) metal centre. Bidentate binding of the pyrophosphate group of 5-PP-InsP5 to the Eu(iii) ion is proposed, supported by DFT calculations, giving rise to a selective enhancement in Eu(iii) emission intensity and lifetime. We demonstrate the use of time-resolved luminescence as a bioassay tool for monitoring enzymatic processes in which 5-PP-InsP5 is consumed. Our probe offers a potential screening methodology to identify drug-like compounds that modulate the activity of enzymes of inositol pyrophosphate metabolism.
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Affiliation(s)
- Megan L Shipton
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford Mansfield Road Oxford OX1 3QT UK
| | - Fathima A Jamion
- Department of Chemistry, Loughborough University Epinal Way, Loughborough LE11 3TU UK
| | - Simon Wheeler
- Department of Chemistry, Loughborough University Epinal Way, Loughborough LE11 3TU UK
| | - Andrew M Riley
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford Mansfield Road Oxford OX1 3QT UK
| | - Felix Plasser
- Department of Chemistry, Loughborough University Epinal Way, Loughborough LE11 3TU UK
| | - Barry V L Potter
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford Mansfield Road Oxford OX1 3QT UK
| | - Stephen J Butler
- Department of Chemistry, Loughborough University Epinal Way, Loughborough LE11 3TU UK
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6
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Pipercevic J, Kohl B, Gerasimaite R, Comte-Miserez V, Hostachy S, Müntener T, Agustoni E, Jessen HJ, Fiedler D, Mayer A, Hiller S. Inositol pyrophosphates activate the vacuolar transport chaperone complex in yeast by disrupting a homotypic SPX domain interaction. Nat Commun 2023; 14:2645. [PMID: 37156835 PMCID: PMC10167327 DOI: 10.1038/s41467-023-38315-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 04/25/2023] [Indexed: 05/10/2023] Open
Abstract
Many proteins involved in eukaryotic phosphate homeostasis are regulated by SPX domains. In yeast, the vacuolar transporter chaperone (VTC) complex contains two such domains, but mechanistic details of its regulation are not well understood. Here, we show at the atomic level how inositol pyrophosphates interact with SPX domains of subunits Vtc2 and Vtc3 to control the activity of the VTC complex. Vtc2 inhibits the catalytically active VTC subunit Vtc4 by homotypic SPX-SPX interactions via the conserved helix α1 and the previously undescribed helix α7. Binding of inositol pyrophosphates to Vtc2 abrogates this interaction, thus activating the VTC complex. Accordingly, VTC activation is also achieved by site-specific point mutations that disrupt the SPX-SPX interface. Structural data suggest that ligand binding induces reorientation of helix α1 and exposes the modifiable helix α7, which might facilitate its post-translational modification in vivo. The variable composition of these regions within the SPX domain family might contribute to the diversified SPX functions in eukaryotic phosphate homeostasis.
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Affiliation(s)
- Joka Pipercevic
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Bastian Kohl
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Ruta Gerasimaite
- Department of Immunobiology, University of Lausanne, Chemin des Boveresses 155, CP51 1066, Epalinges, Switzerland
- Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Véronique Comte-Miserez
- Department of Immunobiology, University of Lausanne, Chemin des Boveresses 155, CP51 1066, Epalinges, Switzerland
| | - Sarah Hostachy
- Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Thomas Müntener
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Elia Agustoni
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Henning Jacob Jessen
- Institute of Organic Chemistry, University of Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Dorothea Fiedler
- Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Andreas Mayer
- Department of Immunobiology, University of Lausanne, Chemin des Boveresses 155, CP51 1066, Epalinges, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
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7
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Qiu D, Gu C, Liu G, Ritter K, Eisenbeis VB, Bittner T, Gruzdev A, Seidel L, Bengsch B, Shears SB, Jessen HJ. Capillary electrophoresis mass spectrometry identifies new isomers of inositol pyrophosphates in mammalian tissues. Chem Sci 2023; 14:658-667. [PMID: 36741535 PMCID: PMC9847636 DOI: 10.1039/d2sc05147h] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Technical challenges have to date prevented a complete profiling of the levels of myo-inositol phosphates (InsPs) and pyrophosphates (PP-InsPs) in mammalian tissues. Here, we have deployed capillary electrophoresis mass spectrometry to identify and record the levels of InsPs and PP-InsPs in several tissues obtained from wild type mice and a newly created PPIP5K2 knockout strain. We observe that the mouse colon harbours unusually high levels of InsPs and PP-InsPs. Additionally, the PP-InsP profile is considerably more complex than previously reported for animal cells: using chemically synthesized internal stable isotope references and high-resolution mass spectra, we characterize two new PP-InsP isomers as 4/6-PP-InsP5 and 2-PP-InsP5. The latter has not previously been described in nature. The analysis of feces and the commercial mouse diet suggests that the latter is one potential source of noncanonical isomers in the colon. However, we also identify both molecules in the heart, indicating unknown synthesis pathways in mammals. We also demonstrate that the CE-MS method is sensitive enough to measure PP-InsPs from patient samples such as colon biopsies and peripheral blood mononuclear cells (PBMCs). Strikingly, PBMCs also contain 4/6-PP-InsP5 and 2-PP-InsP5. In summary, our study substantially expands PP-InsP biology in mammals.
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Affiliation(s)
- Danye Qiu
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg79104FreiburgGermany,CIBSS – Centre for Integrative Biological Signaling Studies, University of FreiburgGermany
| | - Chunfang Gu
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle ParkNC27709USA
| | - Guizhen Liu
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg79104FreiburgGermany
| | - Kevin Ritter
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg79104FreiburgGermany
| | - Verena B. Eisenbeis
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg79104FreiburgGermany
| | - Tamara Bittner
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg79104FreiburgGermany
| | - Artiom Gruzdev
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle ParkNC27709USA
| | - Lea Seidel
- CIBSS – Centre for Integrative Biological Signaling Studies, University of FreiburgGermany,Clinic for Internal Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of FreiburgFreiburgGermany,SGBM – Spemann Graduate School of Biology and Medicine, University of FreiburgGermany
| | - Bertram Bengsch
- CIBSS – Centre for Integrative Biological Signaling Studies, University of FreiburgGermany,Clinic for Internal Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Stephen B. Shears
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle ParkNC27709USA
| | - Henning J. Jessen
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg79104FreiburgGermany,CIBSS – Centre for Integrative Biological Signaling Studies, University of FreiburgGermany
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8
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Nguyen Trung M, Furkert D, Fiedler D. Versatile signaling mechanisms of inositol pyrophosphates. Curr Opin Chem Biol 2022; 70:102177. [PMID: 35780751 DOI: 10.1016/j.cbpa.2022.102177] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 01/03/2023]
Abstract
Inositol pyrophosphates (PP-InsPs) constitute a group of highly charged messengers, which regulate central biological processes in health and disease, such as cellular phosphate and general energy homeostasis. Deciphering the molecular mechanisms underlying PP-InsP-mediated signaling remains a challenge due to the unique properties of these molecules, the different modes of action they can access, and a somewhat limited chemical and analytical toolset. Herein, we summarize the most recent mechanistic insights into PP-InsP signaling, which illustrate our progress in connecting mechanism and function of PP-InsPs.
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Affiliation(s)
- Minh Nguyen Trung
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - David Furkert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany.
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9
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Gaugler P, Schneider R, Liu G, Qiu D, Weber J, Schmid J, Jork N, Häner M, Ritter K, Fernández-Rebollo N, Giehl RFH, Trung MN, Yadav R, Fiedler D, Gaugler V, Jessen HJ, Schaaf G, Laha D. Arabidopsis PFA-DSP-Type Phosphohydrolases Target Specific Inositol Pyrophosphate Messengers. Biochemistry 2022; 61:1213-1227. [PMID: 35640071 DOI: 10.1021/acs.biochem.2c00145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inositol pyrophosphates are signaling molecules containing at least one phosphoanhydride bond that regulate a wide range of cellular processes in eukaryotes. With a cyclic array of phosphate esters and diphosphate groups around myo-inositol, these molecular messengers possess the highest charge density found in nature. Recent work deciphering inositol pyrophosphate biosynthesis in Arabidopsis revealed important functions of these messengers in nutrient sensing, hormone signaling, and plant immunity. However, despite the rapid hydrolysis of these molecules in plant extracts, very little is known about the molecular identity of the phosphohydrolases that convert these messengers back to their inositol polyphosphate precursors. Here, we investigate whether Arabidopsis Plant and Fungi Atypical Dual Specificity Phosphatases (PFA-DSP1-5) catalyze inositol pyrophosphate phosphohydrolase activity. We find that recombinant proteins of all five Arabidopsis PFA-DSP homologues display phosphohydrolase activity with a high specificity for the 5-β-phosphate of inositol pyrophosphates and only minor activity against the β-phosphates of 4-InsP7 and 6-InsP7. We further show that heterologous expression of Arabidopsis PFA-DSP1-5 rescues wortmannin sensitivity and deranged inositol pyrophosphate homeostasis caused by the deficiency of the PFA-DSP-type inositol pyrophosphate phosphohydrolase Siw14 in yeast. Heterologous expression in Nicotiana benthamiana leaves provided evidence that Arabidopsis PFA-DSP1 also displays 5-β-phosphate-specific inositol pyrophosphate phosphohydrolase activity in planta. Our findings lay the biochemical basis and provide the genetic tools to uncover the roles of inositol pyrophosphates in plant physiology and plant development.
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Affiliation(s)
- Philipp Gaugler
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Robin Schneider
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Guizhen Liu
- Department of Chemistry and Pharmacy and CIBSS-Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Danye Qiu
- Department of Chemistry and Pharmacy and CIBSS-Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Jonathan Weber
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Jochen Schmid
- Center for Plant Molecular Biology, Department of Plant Physiology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Nikolaus Jork
- Department of Chemistry and Pharmacy and CIBSS-Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
| | - Markus Häner
- Department of Chemistry and Pharmacy and CIBSS-Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Kevin Ritter
- Department of Chemistry and Pharmacy and CIBSS-Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Nicolás Fernández-Rebollo
- Center for Plant Molecular Biology, Department of Plant Physiology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Ricardo F H Giehl
- Department of Physiology & Cell Biology, Leibniz-Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Minh Nguyen Trung
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany.,Department of Chemistry, Humboldt Universität zu Berlin, 12489 Berlin, Germany
| | - Ranjana Yadav
- Department of Biochemistry, Indian Institute of Science (IISc), Bengaluru 560012, India
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany.,Department of Chemistry, Humboldt Universität zu Berlin, 12489 Berlin, Germany
| | - Verena Gaugler
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Henning J Jessen
- Department of Chemistry and Pharmacy and CIBSS-Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Gabriel Schaaf
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Debabrata Laha
- Department of Biochemistry, Indian Institute of Science (IISc), Bengaluru 560012, India
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10
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Activities and Structure-Function Analysis of Fission Yeast Inositol Pyrophosphate (IPP) Kinase-Pyrophosphatase Asp1 and Its Impact on Regulation of pho1 Gene Expression. mBio 2022; 13:e0103422. [PMID: 35536002 PMCID: PMC9239264 DOI: 10.1128/mbio.01034-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Inositol pyrophosphates (IPPs) are signaling molecules that regulate cellular phosphate homeostasis in diverse eukaryal taxa. In fission yeast, mutations that increase 1,5-IP8 derepress the PHO regulon while mutations that ablate IP8 synthesis are PHO hyper-repressive. Fission yeast Asp1, the principal agent of 1,5-IP8 dynamics, is a bifunctional enzyme composed of an N-terminal IPP kinase domain and a C-terminal IPP pyrophosphatase domain. Here we conducted a biochemical characterization and mutational analysis of the autonomous Asp1 kinase domain (aa 1-385). Reaction of Asp1 kinase with IP6 and ATP resulted in both IP6 phosphorylation to 1-IP7 and hydrolysis of the ATP γ-phosphate, with near-equal partitioning between productive 1-IP7 synthesis and unproductive ATP hydrolysis under optimal kinase conditions. By contrast, reaction of Asp1 kinase with 5-IP7 is 22-fold faster than with IP6 and is strongly biased in favor of IP8 synthesis versus ATP hydrolysis. Alanine scanning identified essential constituents of the active site. We deployed the Ala mutants to show that derepression of pho1 expression correlated with Asp1's kinase activity. In the case of full-length Asp1, the activity of the C-terminal pyrophosphatase domain stifled net phosphorylation of the 1-position during reaction of Asp1 with ATP and either IP6 or 5-IP7. We report that inorganic phosphate is a concentration-dependent enabler of net IP8 synthesis by full-length Asp1 in vitro, by virtue of its antagonism of IP8 turnover. IMPORTANCE Expression of the fission yeast phosphate regulon is sensitive to the intracellular level of the inositol pyrophosphate (IPP) signaling molecule 1,5-IP8. IP8 dynamics are determined by Asp1, a bifunctional enzyme comprising N-terminal IPP 1-kinase and C-terminal IPP 1-pyrophosphatase domains that catalyze IP8 synthesis and catabolism, respectively. Here, we interrogated the activities and specificities of the Asp1 kinase domain and full length Asp1. We find that reaction of Asp1 kinase with 5-IP7 is 22-fold faster than with IP6 and is strongly biased in favor of IP8 synthesis versus the significant unproductive ATP hydrolysis seen during its reaction with IP6. We report that full-length Asp1 catalyzes futile cycles of 1-phosphate phosphorylation by its kinase component and 1-pyrophosphate hydrolysis by its pyrophosphatase component that result in unproductive net consumption of the ATP substrate. Net synthesis of 1,5-IP8 is enabled by physiological concentrations of inorganic phosphate that selectively antagonize IP8 turnover.
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11
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Wang H, Perera L, Jork N, Zong G, Riley AM, Potter BVL, Jessen HJ, Shears SB. A structural exposé of noncanonical molecular reactivity within the protein tyrosine phosphatase WPD loop. Nat Commun 2022; 13:2231. [PMID: 35468885 PMCID: PMC9038691 DOI: 10.1038/s41467-022-29673-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 03/25/2022] [Indexed: 01/06/2023] Open
Abstract
Structural snapshots of protein/ligand complexes are a prerequisite for gaining atomic level insight into enzymatic reaction mechanisms. An important group of enzymes has been deprived of this analytical privilege: members of the protein tyrosine phosphatase (PTP) superfamily with catalytic WPD-loops lacking the indispensable general-acid/base within a tryptophan-proline-aspartate/glutamate context. Here, we provide the ligand/enzyme crystal complexes for one such PTP outlier: Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1 (AtPFA-DSP1), herein unveiled as a regioselective and efficient phosphatase towards inositol pyrophosphate (PP-InsP) signaling molecules. Although the WPD loop is missing its canonical tripeptide motif, this structural element contributes to catalysis by assisting PP-InsP delivery into the catalytic pocket, for a choreographed exchange with phosphate reaction product. Subsequently, an intramolecular proton donation by PP-InsP substrate is posited to substitute functionally for the absent aspartate/glutamate general-acid. Overall, we expand mechanistic insight into adaptability of the conserved PTP structural elements.
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Affiliation(s)
- Huanchen Wang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Nikolaus Jork
- Institute of Organic Chemistry, and CIBSS - the Center for Integrative Biological Signaling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - Guangning Zong
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Andrew M Riley
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Barry V L Potter
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Henning J Jessen
- Institute of Organic Chemistry, and CIBSS - the Center for Integrative Biological Signaling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - Stephen B Shears
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
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12
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Jessen HJ, Dürr-Mayer T, Haas TM, Ripp A, Cummins CC. Lost in Condensation: Poly-, Cyclo-, and Ultraphosphates. Acc Chem Res 2021; 54:4036-4050. [PMID: 34648267 DOI: 10.1021/acs.accounts.1c00370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Much like linear, branched, and cyclic alkanes, condensed phosphates exist as linear, branched, and cyclic structures. Inasmuch as alkanes are the cornerstone of organic chemistry, generating an inexplorably large chemical space, a comparable richness in structures can be expected for condensed phosphates, as also for them the concepts of isomerism apply. Little of their chemical space has been charted, and only a few different synthesis methods are available to construct isomers of condensed phosphates. Here, we will discuss the application of phosphoramidites with one, two, or three P-N bonds that can be substituted selectively to access different condensed phosphates in a highly controllable manner. Work directed toward the further exploration of this chemical space will contribute to our understanding of the fundamental chemistry of phosphates.In biology, condensed phosphates play important roles in the form of inorganic representatives, such as pyrophosphate, polyphosphate, and cyclophosphate, and also in conjugation with organic molecules, such as esters and amidates. Phosphorus is one of the six biogenic elements; the omnipresence of phosphates in biology points toward their critical involvement in prebiotic chemistry and the emergence of life itself. Indeed, it is hard to imagine any life without phosphate. It is therefore desirable to achieve through synthesis a better understanding of the chemistry of the condensed phosphates to further explore their biology.There is a rich but underexplored chemistry of the family of condensed phosphates per se, which is further diversified by their conjugation to important biomolecules and metabolites. For example, proteins may be polyphosphorylated on lysins, a very recent addition to posttranslational modifications. Adenosine triphosphate, as a representative of the small molecules, on the other hand, is well known as the universal cellular energy currency. In this Account, we will describe our motivations and our approaches to construct, modify, and synthetically apply different representatives of the condensed phosphates. We also describe the generation of hybrids composed of cyclic and linear structures of different oxidation states and develop them into reagents of great utility. A pertinent example is provided in the step-economic synthesis of the magic spot nucleotides (p)ppGpp. Finally, we provide an overview of 31P NMR data collected over the years in our laboratories, helping as a waymarker for not getting lost in condensation.
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Affiliation(s)
- Henning J. Jessen
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT − Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Tobias Dürr-Mayer
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Thomas M. Haas
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Alexander Ripp
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT − Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Christopher C. Cummins
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
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13
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Couto D, Richter A, Walter H, Furkert D, Hothorn M, Fiedler D. Using Biotinylated myo-Inositol Hexakisphosphate to Investigate Inositol Pyrophosphate-Protein Interactions with Surface-Based Biosensors. Biochemistry 2021; 60:2739-2748. [PMID: 34499474 DOI: 10.1021/acs.biochem.1c00497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Inositol pyrophosphates (PP-InsPs) are highly phosphorylated molecules that have emerged as central nutrient messengers in eukaryotic organisms. They can bind to structurally diverse target proteins to regulate biological functions, such as protein-protein interactions. PP-InsPs are strongly negatively charged and interact with highly basic surface patches in proteins, making their quantitative biochemical analysis challenging. Here, we present the synthesis of biotinylated myo-inositol hexakisphosphates and their application in surface plasmon resonance and grating-coupled interferometry assays, to enable the rapid identification, validation, and kinetic characterization of InsP- and PP-InsP-protein interactions.
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Affiliation(s)
- Daniel Couto
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Annika Richter
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Henriette Walter
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - David Furkert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
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14
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Hostachy S, Utesch T, Franke K, Dornan GL, Furkert D, Türkaydin B, Haucke V, Sun H, Fiedler D. Dissecting the activation of insulin degrading enzyme by inositol pyrophosphates and their bisphosphonate analogs. Chem Sci 2021; 12:10696-10702. [PMID: 34476054 PMCID: PMC8372538 DOI: 10.1039/d1sc02975d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/06/2021] [Indexed: 11/21/2022] Open
Abstract
Inositol poly- and pyrophosphates (InsPs and PP-InsPs) are densely phosphorylated eukaryotic messengers, which are involved in numerous cellular processes. To elucidate their signaling functions at the molecular level, non-hydrolyzable bisphosphonate analogs of inositol pyrophosphates, PCP-InsPs, have been instrumental. Here, an efficient synthetic strategy to obtain these analogs in unprecedented quantities is described - relying on the use of combined phosphate ester-phosphoramidite reagents. The PCP-analogs, alongside their natural counterparts, were applied to investigate their regulatory effect on insulin-degrading enzyme (IDE), using a range of biochemical, biophysical and computational methods. A unique interplay between IDE, its substrates and the PP-InsPs was uncovered, in which the PP-InsPs differentially modulated the activity of the enzyme towards short peptide substrates. Aided by molecular docking and molecular dynamics simulations, a flexible binding mode for the InsPs/PP-InsPs was identified at the anion binding site of IDE. Targeting IDE for therapeutic purposes should thus take regulation by endogenous PP-InsP metabolites into account.
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Affiliation(s)
- Sarah Hostachy
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
| | - Tillmann Utesch
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
| | - Katy Franke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
| | - Gillian Leigh Dornan
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
| | - David Furkert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
- Institut für Chemie, Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Berke Türkaydin
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
| | - Han Sun
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle Str. 10 13125 Berlin Germany
- Institut für Chemie, Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
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15
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Mohanrao R, Manorama R, Ganguli S, Madhusudhanan MC, Bhandari R, Sureshan KM. Novel Substrates for Kinases Involved in the Biosynthesis of Inositol Pyrophosphates and Their Enhancement of ATPase Activity of a Kinase. Molecules 2021; 26:molecules26123601. [PMID: 34208421 PMCID: PMC8231259 DOI: 10.3390/molecules26123601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 11/16/2022] Open
Abstract
IP6K and PPIP5K are two kinases involved in the synthesis of inositol pyrophosphates. Synthetic analogs or mimics are necessary to understand the substrate specificity of these enzymes and to find molecules that can alter inositol pyrophosphate synthesis. In this context, we synthesized four scyllo-inositol polyphosphates-scyllo-IP5, scyllo-IP6, scyllo-IP7 and Bz-scyllo-IP5-from myo-inositol and studied their activity as substrates for mouse IP6K1 and the catalytic domain of VIP1, the budding yeast variant of PPIP5K. We incubated these scyllo-inositol polyphosphates with these kinases and ATP as the phosphate donor. We tracked enzyme activity by measuring the amount of radiolabeled scyllo-inositol pyrophosphate product formed and the amount of ATP consumed. All scyllo-inositol polyphosphates are substrates for both the kinases but they are weaker than the corresponding myo-inositol phosphate. Our study reveals the importance of axial-hydroxyl/phosphate for IP6K1 substrate recognition. We found that all these derivatives enhance the ATPase activity of VIP1. We found very weak ligand-induced ATPase activity for IP6K1. Benzoyl-scyllo-IP5 was the most potent ligand to induce IP6K1 ATPase activity despite being a weak substrate. This compound could have potential as a competitive inhibitor.
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Affiliation(s)
- Raja Mohanrao
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695551, India; (R.M.); (M.C.M.)
| | - Ruth Manorama
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India; (R.M.); (S.G.)
| | - Shubhra Ganguli
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India; (R.M.); (S.G.)
- Manipal Academy of Higher Education, Manipal 576104, India
| | - Mithun C. Madhusudhanan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695551, India; (R.M.); (M.C.M.)
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India; (R.M.); (S.G.)
- Correspondence: (R.B.); (K.M.S.)
| | - Kana M. Sureshan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695551, India; (R.M.); (M.C.M.)
- Correspondence: (R.B.); (K.M.S.)
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16
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Mantilla BS, Do Amaral LD, Jessen HJ, Docampo R. The Inositol Pyrophosphate Biosynthetic Pathway of Trypanosoma cruzi. ACS Chem Biol 2021; 16:283-292. [PMID: 33411501 PMCID: PMC10466500 DOI: 10.1021/acschembio.0c00759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inositol phosphates (IPs) are phosphorylated derivatives of myo-inositol involved in the regulation of several cellular processes through their interaction with specific proteins. Their synthesis relies on the activity of specific kinases that use ATP as phosphate donor. Here, we combined reverse genetics and liquid chromatography coupled to mass spectrometry (LC-MS) to dissect the inositol phosphate biosynthetic pathway and its metabolic intermediates in the main life cycle stages (epimastigotes, cell-derived trypomastigotes, and amastigotes) of Trypanosoma cruzi, the etiologic agent of Chagas disease. We found evidence of the presence of highly phosphorylated IPs, like inositol hexakisphosphate (IP6), inositol heptakisphosphate (IP7), and inositol octakisphosphate (IP8), that were not detected before by HPLC analyses of the products of radiolabeled exogenous inositol. The kinases involved in their synthesis (inositol polyphosphate multikinase (TcIPMK), inositol 5-phosphate kinase (TcIP5K), and inositol 6-phosphate kinase (TcIP6K)) were also identified. TcIPMK is dispensable in epimastigotes, important for the synthesis of polyphosphate, and critical for the virulence of the infective stages. TcIP5K is essential for normal epimastigote growth, while TcIP6K mutants displayed defects in epimastigote motility and growth. Our results demonstrate the relevance of highly phosphorylated IPs in the life cycle of T. cruzi.
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Affiliation(s)
- Brian S. Mantilla
- Center for Tropical and Emerging Global Diseases, and Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Leticia D. Do Amaral
- Center for Tropical and Emerging Global Diseases, and Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Henning J. Jessen
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, 79104 Freiburg, Germany
| | - Roberto Docampo
- Center for Tropical and Emerging Global Diseases, and Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
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17
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Zong G, Jork N, Hostachy S, Fiedler D, Jessen HJ, Shears SB, Wang H. New structural insights reveal an expanded reaction cycle for inositol pyrophosphate hydrolysis by human DIPP1. FASEB J 2021; 35:e21275. [PMID: 33475202 DOI: 10.1096/fj.202001489r] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/30/2020] [Accepted: 11/30/2020] [Indexed: 11/11/2022]
Abstract
Nudix hydrolases attract considerable attention for their wide range of specialized activities in all domains of life. One particular group of Nudix phosphohydrolases (DIPPs), through their metabolism of diphosphoinositol polyphosphates (PP-InsPs), regulates the actions of these polyphosphates upon bioenergetic homeostasis. In the current study, we describe, at an atomic level, hitherto unknown properties of human DIPP1.We provide X-ray analysis of the catalytic core of DIPP1 in crystals complexed with either natural PP-InsPs, alternative PP-InsP stereoisomers, or non-hydrolysable methylene bisphosphonate analogs ("PCP-InsPs"). The conclusions that we draw from these data are interrogated by studying the impact upon catalytic activity upon mutagenesis of certain key residues. We present a picture of a V-shaped catalytic furrow with overhanging ridges constructed from flexible positively charged side chains; within this cavity, the labile phosphoanhydride bond is appropriately positioned at the catalytic site by an extensive series of interlocking polar contacts which we analogize as "suspension cables." We demonstrate functionality for a triglycine peptide within a β-strand which represents a non-canonical addition to the standard Nudix catalytic core structure. We describe pre-reaction enzyme/substrate states which we posit to reflect a role for electrostatic steering in substrate capture. Finally, through time-resolved analysis, we uncover a chronological sequence of DIPP1/product post-reaction states, one of which may rationalize a role for InsP6 as an inhibitor of catalytic activity.
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Affiliation(s)
- Guangning Zong
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Nikolaus Jork
- Institute of Organic Chemistry, CIBSS - Center for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Sarah Hostachy
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, CIBSS - Center for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Stephen B Shears
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Huanchen Wang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
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18
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Qiu D, Wilson MS, Eisenbeis VB, Harmel RK, Riemer E, Haas TM, Wittwer C, Jork N, Gu C, Shears SB, Schaaf G, Kammerer B, Fiedler D, Saiardi A, Jessen HJ. Analysis of inositol phosphate metabolism by capillary electrophoresis electrospray ionization mass spectrometry. Nat Commun 2020; 11:6035. [PMID: 33247133 PMCID: PMC7695695 DOI: 10.1038/s41467-020-19928-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/06/2020] [Indexed: 12/22/2022] Open
Abstract
The analysis of myo-inositol phosphates (InsPs) and myo-inositol pyrophosphates (PP-InsPs) is a daunting challenge due to the large number of possible isomers, the absence of a chromophore, the high charge density, the low abundance, and the instability of the esters and anhydrides. Given their importance in biology, an analytical approach to follow and understand this complex signaling hub is desirable. Here, capillary electrophoresis (CE) coupled to electrospray ionization mass spectrometry (ESI-MS) is implemented to analyze complex mixtures of InsPs and PP-InsPs with high sensitivity. Stable isotope labeled (SIL) internal standards allow for matrix-independent quantitative assignment. The method is validated in wild-type and knockout mammalian cell lines and in model organisms. SIL-CE-ESI-MS enables the accurate monitoring of InsPs and PP-InsPs arising from compartmentalized cellular synthesis pathways, by feeding cells with either [13C6]-myo-inositol or [13C6]-D-glucose. In doing so, we provide evidence for the existence of unknown inositol synthesis pathways in mammals, highlighting the potential of this method to dissect inositol phosphate metabolism and signalling. Myo-Inositol phosphates (InsPs) and pyrophosphates (PP-InsPs) are important second messengers but their analysis remains challenging. Here, the authors develop a capillary electrophoresis-mass spectrometry method for the identification and quantitation of InsP and PP-InsP isomers in cells and tissues.
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Affiliation(s)
- Danye Qiu
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104, Freiburg, Germany.
| | - Miranda S Wilson
- Medical Research Council, Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK
| | - Verena B Eisenbeis
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Robert K Harmel
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Esther Riemer
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, Rheinische Friedrich-Wilhelms-University Bonn, 53115, Bonn, Germany
| | - Thomas M Haas
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Christopher Wittwer
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Nikolaus Jork
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Chunfang Gu
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Stephen B Shears
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Gabriel Schaaf
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, Rheinische Friedrich-Wilhelms-University Bonn, 53115, Bonn, Germany
| | - Bernd Kammerer
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Adolfo Saiardi
- Medical Research Council, Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK.
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104, Freiburg, Germany. .,CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.
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19
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Wang Z, Jork N, Bittner T, Wang H, Jessen HJ, Shears SB. Rapid stimulation of cellular Pi uptake by the inositol pyrophosphate InsP 8 induced by its photothermal release from lipid nanocarriers using a near infra-red light-emitting diode. Chem Sci 2020; 11:10265-10278. [PMID: 33659052 PMCID: PMC7891704 DOI: 10.1039/d0sc02144j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 09/07/2020] [Indexed: 11/21/2022] Open
Abstract
Inositol pyrophosphates (PP-InsPs), including diphospho-myo-inositol pentakisphosphate (5-InsP7) and bis-diphospho-myo-inositol tetrakisphosphate (1,5-InsP8), are highly polar, membrane-impermeant signaling molecules that control many homeostatic responses to metabolic and bioenergetic imbalance. To delineate their molecular activities, there is an increasing need for a toolbox of methodologies for real-time modulation of PP-InsP levels inside large populations of cultured cells. Here, we describe procedures to package PP-InsPs into thermosensitive phospholipid nanocapsules that are impregnated with a near infra-red photothermal dye; these liposomes are readily accumulated into cultured cells. The PP-InsPs remain trapped inside the liposomes until the cultures are illuminated with a near infra-red light-emitting diode (LED) which permeabilizes the liposomes to promote PP-InsP release. Additionally, so as to optimize these procedures, a novel stably fluorescent 5-InsP7 analogue (i.e., 5-FAM-InsP7) was synthesized with the assistance of click-chemistry; the delivery and deposition of the analogue inside cells was monitored by flow cytometry and by confocal microscopy. We describe quantitatively-controlled PP-InsP release inside cells within 5 min of LED irradiation, without measurable effect upon cell integrity, using a collimated 22 mm beam that can irradiate up to 106 cultured cells. Finally, to interrogate the biological value of these procedures, we delivered 1,5-InsP8 into HCT116 cells and showed it to dose-dependently stimulate the rate of [33P]-Pi uptake; these observations reveal a rheostatic range of concentrations over which 1,5-InsP8 is biologically functional in Pi homeostasis.
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Affiliation(s)
- Zhenzhen Wang
- Signal Transduction Laboratory , National Institute of Environmental Health Sciences , National Institutes of Health , Research Triangle Park , NC 27709 , USA . ; Tel: +1-984-287-3483
| | - Nikolaus Jork
- Institute of Organic Chemistry , CIBSS , Center for Integrative Biological Signalling Studies , University of Freiburg , 79104 Freiburg , Germany
| | - Tamara Bittner
- Institute of Organic Chemistry , CIBSS , Center for Integrative Biological Signalling Studies , University of Freiburg , 79104 Freiburg , Germany
| | - Huanchen Wang
- Signal Transduction Laboratory , National Institute of Environmental Health Sciences , National Institutes of Health , Research Triangle Park , NC 27709 , USA . ; Tel: +1-984-287-3483
| | - Henning J Jessen
- Institute of Organic Chemistry , CIBSS , Center for Integrative Biological Signalling Studies , University of Freiburg , 79104 Freiburg , Germany
| | - Stephen B Shears
- Signal Transduction Laboratory , National Institute of Environmental Health Sciences , National Institutes of Health , Research Triangle Park , NC 27709 , USA . ; Tel: +1-984-287-3483
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20
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Shears SB, Wang H. Metabolism and Functions of Inositol Pyrophosphates: Insights Gained from the Application of Synthetic Analogues. Molecules 2020; 25:E4515. [PMID: 33023101 PMCID: PMC7583957 DOI: 10.3390/molecules25194515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 12/17/2022] Open
Abstract
Inositol pyrophosphates (PP-InsPs) comprise an important group of intracellular, diffusible cellular signals that a wide range of biological processes throughout the yeast, plant, and animal kingdoms. It has been difficult to gain a molecular-level mechanistic understanding of the actions of these molecules, due to their highly phosphorylated nature, their low levels, and their rapid metabolic turnover. More recently, these obstacles to success are being surmounted by the chemical synthesis of a number of insightful PP-InsP analogs. This review will describe these analogs and will indicate the important chemical and biological information gained by using them.
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Affiliation(s)
- Stephen B. Shears
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA;
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21
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InsP 7 is a small-molecule regulator of NUDT3-mediated mRNA decapping and processing-body dynamics. Proc Natl Acad Sci U S A 2020; 117:19245-19253. [PMID: 32727897 DOI: 10.1073/pnas.1922284117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Regulation of enzymatic 5' decapping of messenger RNA (mRNA), which normally commits transcripts to their destruction, has the capacity to dynamically reshape the transcriptome. For example, protection from 5' decapping promotes accumulation of mRNAs into processing (P) bodies-membraneless, biomolecular condensates. Such compartmentalization of mRNAs temporarily removes them from the translatable pool; these repressed transcripts are stabilized and stored until P-body dissolution permits transcript reentry into the cytosol. Here, we describe regulation of mRNA stability and P-body dynamics by the inositol pyrophosphate signaling molecule 5-InsP7 (5-diphosphoinositol pentakisphosphate). First, we demonstrate 5-InsP7 inhibits decapping by recombinant NUDT3 (Nudix [nucleoside diphosphate linked moiety X]-type hydrolase 3) in vitro. Next, in intact HEK293 and HCT116 cells, we monitored the stability of a cadre of NUDT3 mRNA substrates following CRISPR-Cas9 knockout of PPIP5Ks (diphosphoinositol pentakisphosphate 5-kinases type 1 and 2, i.e., PPIP5K KO), which elevates cellular 5-InsP7 levels by two- to threefold (i.e., within the physiological rheostatic range). The PPIP5K KO cells exhibited elevated levels of NUDT3 mRNA substrates and increased P-body abundance. Pharmacological and genetic attenuation of 5-InsP7 synthesis in the KO background reverted both NUDT3 mRNA substrate levels and P-body counts to those of wild-type cells. Furthermore, liposomal delivery of a metabolically resistant 5-InsP7 analog into wild-type cells elevated levels of NUDT3 mRNA substrates and raised P-body abundance. In the context that cellular 5-InsP7 levels normally fluctuate in response to changes in the bioenergetic environment, regulation of mRNA structure by this inositol pyrophosphate represents an epitranscriptomic control process. The associated impact on P-body dynamics has relevance to regulation of stem cell differentiation, stress responses, and, potentially, amelioration of neurodegenerative diseases and aging.
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22
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Bittner T, Wittwer C, Hauke S, Wohlwend D, Mundinger S, Dutta AK, Bezold D, Dürr T, Friedrich T, Schultz C, Jessen HJ. Photolysis of Caged Inositol Pyrophosphate InsP 8 Directly Modulates Intracellular Ca 2+ Oscillations and Controls C2AB Domain Localization. J Am Chem Soc 2020; 142:10606-10611. [PMID: 32459478 DOI: 10.1021/jacs.0c01697] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Inositol pyrophosphates constitute a family of hyperphosphorylated signaling molecules involved in the regulation of glucose uptake and insulin sensitivity. While our understanding of the biological roles of inositol heptaphosphates (PP-InsP5) has greatly improved, the functions of the inositol octaphosphates ((PP)2-InsP4) have remained unclear. Here we present the synthesis of two enantiomeric cell-permeant and photocaged (PP)2-InsP4 derivatives and apply them to study the functions in living β-cells. Photorelease of the naturally occurring isomer 1,5-(PP)2-InsP4 led to an immediate and concentration-dependent reduction of intracellular calcium oscillations, while other caged inositol pyrophosphates (3,5-(PP)2-InsP4, 5-PP-InsP5, 1-PP-InsP5, 3-PP-InsP5) showed no immediate effect. Furthermore, uncaging of 1,5-(PP)2-InsP4 but not 3,5-(PP)2-InsP4 induced translocation of the C2AB domain of granuphilin from the plasma membrane to the cytosol. Granuphilin is involved in membrane docking of secretory vesicles. This suggests that 1,5-(PP)2-InsP4 impacts β-cell activity by regulating granule localization and/or priming and calcium signaling in concert.
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Affiliation(s)
- Tamara Bittner
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany
| | - Christopher Wittwer
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany
| | - Sebastian Hauke
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Daniel Wohlwend
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany
| | - Stephan Mundinger
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany
| | - Amit K Dutta
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany
| | - Dominik Bezold
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany
| | - Tobias Dürr
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany
| | - Thorsten Friedrich
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany
| | - Carsten Schultz
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Department of Chemical Physiology and Biochemistry, Oregon Health & Science University (OHSU), Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
| | - Henning J Jessen
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany.,CIBSS-Centre for Integrative Biological Signalling Studies, 79104 Freiburg i.B., Germany.,Freiburg Research Institute for Advanced Studies (FRIAS), Albert-Ludwigs University Freiburg, Albertstrasse 19, 79104 Freiburg i.B., Germany
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23
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Bezold D, Dürr T, Singh J, Jessen HJ. Cyclotriphosphate: A Brief History, Recent Developments, and Perspectives in Synthesis. Chemistry 2020; 26:2298-2308. [PMID: 31637774 PMCID: PMC7065162 DOI: 10.1002/chem.201904433] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/21/2019] [Indexed: 01/08/2023]
Abstract
There has been a recent upsurge in the study and application of approaches utilizing cyclotriphosphate 1 (cyclo-TP, also known as trimetaphosphate, TMP) and/or proceeding through its analogues in synthetic chemistry to access modified oligo- and polyphosphates. This is especially useful in the area of chemical nucleotide synthesis, but by no means restricted to it. Enabled by new high yielding and easy-to-implement methodologies, these approaches promise to open up an area of research that has previously been underappreciated. Additionally, refinements of concepts of prebiotic phosphorylation chemistry have been disclosed that ultimately rely on cyclo-TP 1 as a precursor, placing it as a potentially central compound in the emergence of life. Given the importance of such concepts for our understanding of prebiotic chemistry in combination with the need to readily access modified polyphosphates for structural and biological studies, this paper will discuss selected recent developments in the field of cyclo-TP chemistry, briefly touch on ultraphosphate chemistry, and highlight areas in which further developments can be expected.
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Affiliation(s)
- Dominik Bezold
- Institute of Organic ChemistryUniversity of Freiburg79104FreiburgGermany
| | - Tobias Dürr
- Institute of Organic ChemistryUniversity of Freiburg79104FreiburgGermany
| | - Jyoti Singh
- Institute of Organic ChemistryUniversity of Freiburg79104FreiburgGermany
| | - Henning J. Jessen
- Institute of Organic ChemistryUniversity of Freiburg79104FreiburgGermany
- Freiburg Research Institute for Advanced Studies (FRIAS)University of Freiburg79104FreiburgGermany
- Cluster of Excellence livMatS @ FIT—Freiburg Center for, Interactive Materials and Bioinspired TechnologiesUniversity of FreiburgGeorges-Köhler-Allee 10579110FreiburgGermany
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24
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Control of XPR1-dependent cellular phosphate efflux by InsP 8 is an exemplar for functionally-exclusive inositol pyrophosphate signaling. Proc Natl Acad Sci U S A 2020; 117:3568-3574. [PMID: 32019887 DOI: 10.1073/pnas.1908830117] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Homeostasis of cellular fluxes of inorganic phosphate (Pi) supervises its structural roles in bones and teeth, its pervasive regulation of cellular metabolism, and its functionalization of numerous organic compounds. Cellular Pi efflux is heavily reliant on Xenotropic and Polytropic Retrovirus Receptor 1 (XPR1), regulation of which is largely unknown. We demonstrate specificity of XPR1 regulation by a comparatively uncharacterized member of the inositol pyrophosphate (PP-InsP) signaling family: 1,5-bis-diphosphoinositol 2,3,4,6-tetrakisphosphate (InsP8). XPR1-mediated Pi efflux was inhibited by reducing cellular InsP8 synthesis, either genetically (knockout [KO] of diphosphoinositol pentakisphosphate kinases [PPIP5Ks] that synthesize InsP8) or pharmacologically [cell treatment with 2.5 µM dietary flavonoid or 10 µM N2-(m-trifluorobenzyl), N6-(p-nitrobenzyl) purine], to inhibit inositol hexakisphosphate kinases upstream of PPIP5Ks. Attenuated Pi efflux from PPIP5K KO cells was quantitatively phenocopied by KO of XPR1 itself. Moreover, Pi efflux from PPIP5K KO cells was rescued by restoration of InsP8 levels through transfection of wild-type PPIP5K1; transfection of kinase-dead PPIP5K1 was ineffective. Pi efflux was also rescued in a dose-dependent manner by liposomal delivery of a metabolically resistant methylene bisphosphonate (PCP) analog of InsP8; PCP analogs of other PP-InsP signaling molecules were ineffective. High-affinity binding of InsP8 to the XPR1 N-terminus (K d = 180 nM) was demonstrated by isothermal titration calorimetry. To derive a cellular biology perspective, we studied biomineralization in the Soas-2 osteosarcoma cell line. KO of PPIP5Ks or XPR1 strongly reduced Pi efflux and accelerated differentiation to the mineralization end point. We propose that catalytically compromising PPIP5K mutations might extend an epistatic repertoire for XPR1 dysregulation, with pathological consequences for bone maintenance and ectopic calcification.
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25
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Abstract
The multitudinous inositol phosphate family elicits a wide range of molecular effects that regulate countless biological responses. In this review, I provide a methodological viewpoint of the manner in which key advances in the field of inositol phosphate research were made. I also note some of the considerable challenges that still lie ahead.
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Affiliation(s)
- Stephen B Shears
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
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26
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Studying the Effects of Inositol Pyrophosphates in an In Vitro Vesicle-Vesicle Fusion Assay. Methods Mol Biol 2019. [PMID: 31773578 DOI: 10.1007/978-1-0716-0167-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
In a recent in vitro vesicle fusion study in which we monitored the fusion of reconstituted SNARE and synaptotagmin-containing proteoliposomes, we discovered that inositol pyrophosphate (5-IP7) is a potent inhibitor of neuronal exocytosis. We found that the inhibitory effect of 5-IP7, which is 10 times more potent than those of IP6 and 1-IP7, requires direct interaction with synaptotagmin. Here, we provide a detailed protocol for proteoliposome preparation and bulk observation of proteoliposome fusion based on FRET signals.
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27
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Dong J, Ma G, Sui L, Wei M, Satheesh V, Zhang R, Ge S, Li J, Zhang TE, Wittwer C, Jessen HJ, Zhang H, An GY, Chao DY, Liu D, Lei M. Inositol Pyrophosphate InsP 8 Acts as an Intracellular Phosphate Signal in Arabidopsis. MOLECULAR PLANT 2019; 12:1463-1473. [PMID: 31419530 DOI: 10.1016/j.molp.2019.08.002] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 08/04/2019] [Accepted: 08/06/2019] [Indexed: 05/21/2023]
Abstract
The maintenance of cellular phosphate (Pi) homeostasis is of great importance in living organisms. The SPX domain-containing protein 1 (SPX1) proteins from both Arabidopsis and rice have been proposed to act as sensors of Pi status. The molecular signal indicating the cellular Pi status and regulating Pi homeostasis in plants, however, remains to be identified, as Pi itself does not bind to the SPX domain. Here, we report the identification of the inositol pyrophosphate InsP8 as a signaling molecule that regulates Pi homeostasis in Arabidopsis. Polyacrylamide gel electrophoresis profiling of InsPs revealed that InsP8 level positively correlates with cellular Pi concentration. We demonstrated that the homologs of diphosphoinositol pentakisphosphate kinase (PPIP5K), VIH1 and VIH2, function redundantly to synthesize InsP8, and that the vih1 vih2 double mutant overaccumulates Pi. SPX1 directly interacts with PHR1, the central regulator of Pi starvation responses, to inhibit its function under Pi-replete conditions. However, this interaction is compromised in the vih1 vih2 double mutant, resulting in the constitutive induction of Pi starvation-induced genes, indicating that plant cells cannot sense cellular Pi status without InsP8. Furthermore, we showed that InsP8 could directly bind to the SPX domain of SPX1 and is essential for the interaction between SPX1 and PHR1. Collectively, our study suggests that InsP8 is the intracellular Pi signaling molecule serving as the ligand of SPX1 for controlling Pi homeostasis in plants.
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Affiliation(s)
- Jinsong Dong
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guojie Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academic of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liqian Sui
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mengwei Wei
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Viswanathan Satheesh
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ruyue Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shenghong Ge
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinkai Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong-En Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Christopher Wittwer
- Institute of Organic Chemistry, Albert-Ludwigs University, Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, Albert-Ludwigs University, Freiburg, Albertstrasse 21, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guo-Yong An
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academic of Sciences, Shanghai 200032, China
| | - Dong Liu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Mingguang Lei
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China.
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28
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Puschmann R, Harmel RK, Fiedler D. Scalable Chemoenzymatic Synthesis of Inositol Pyrophosphates. Biochemistry 2019; 58:3927-3932. [DOI: 10.1021/acs.biochem.9b00587] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robert Puschmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Robert K. Harmel
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
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29
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An Y, Jessen HJ, Wang H, Shears SB, Kireev D. Dynamics of Substrate Processing by PPIP5K2, a Versatile Catalytic Machine. Structure 2019; 27:1022-1028.e2. [PMID: 30956131 DOI: 10.1016/j.str.2019.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/18/2018] [Accepted: 03/12/2019] [Indexed: 10/27/2022]
Abstract
Processing of substrates by enzymes can only be fully understood through their conformational dynamics; this is particularly true for the diphosphoinositol pentakisphosphate kinase PPIP5K2, an enzyme with critical roles in cell signaling and bioenergetic homeostasis. PPIP5K2 is remarkable for the reversible nature of its kinase activity, its unique ligand-stimulated ATPase activity, and the substrate traveling between two ligand-binding sites. Here we use molecular dynamics and data analysis techniques to rationalize these PPIP5K2 activities, thereby increasing our understanding of complex enzymatic mechanisms. In particular, we demonstrate how the enzyme's distinctive, ratchet-like mechanism harnesses the energy of random fluctuations to significantly reduce the entropy toll for intramolecular substrate transfer. We show that pre-reaction pulling forces along the reaction coordinate are predictive of the various PPIP5K2 catalytic activities. An unexpected possibility, raised by these computational studies, that 3,5-IP8 might be a substrate for dephosphorylation was experimentally interrogated and confirmed in a luciferase assay.
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Affiliation(s)
- Yi An
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27513, USA
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Huanchen Wang
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Stephen B Shears
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27513, USA.
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30
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Singh J, Steck N, De D, Hofer A, Ripp A, Captain I, Keller M, Wender PA, Bhandari R, Jessen HJ. A Phosphoramidite Analogue of Cyclotriphosphate Enables Iterative Polyphosphorylations. Angew Chem Int Ed Engl 2019; 58:3928-3933. [DOI: 10.1002/anie.201814366] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Jyoti Singh
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Nicole Steck
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Debaditya De
- Laboratory of Cell Signaling, CDFD Hyderabad India
| | - Alexandre Hofer
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Alexander Ripp
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Ilya Captain
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Manfred Keller
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Paul A. Wender
- Stanford UniversityChemistry Department 333 Campus Drive Stanford CA 94305-5080 USA
| | | | - Henning J. Jessen
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
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31
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Singh J, Steck N, De D, Hofer A, Ripp A, Captain I, Keller M, Wender PA, Bhandari R, Jessen HJ. A Phosphoramidite Analogue of Cyclotriphosphate Enables Iterative Polyphosphorylations. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jyoti Singh
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Nicole Steck
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Debaditya De
- Laboratory of Cell Signaling, CDFD Hyderabad India
| | - Alexandre Hofer
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Alexander Ripp
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Ilya Captain
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Manfred Keller
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Paul A. Wender
- Stanford UniversityChemistry Department 333 Campus Drive Stanford CA 94305-5080 USA
| | | | - Henning J. Jessen
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
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32
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Hauke S, Dutta AK, Eisenbeis VB, Bezold D, Bittner T, Wittwer C, Thakor D, Pavlovic I, Schultz C, Jessen HJ. Photolysis of cell-permeant caged inositol pyrophosphates controls oscillations of cytosolic calcium in a β-cell line. Chem Sci 2019; 10:2687-2692. [PMID: 30996985 PMCID: PMC6419925 DOI: 10.1039/c8sc03479f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 01/09/2019] [Indexed: 12/16/2022] Open
Abstract
β-Cells respond directly to the intracellular photochemical release of caged inositol pyrophosphate isomers with modulations of oscillations in cytosolic Ca2+.
Among many cellular functions, inositol pyrophosphates (PP-InsPs) are metabolic messengers involved in the regulation of glucose uptake, insulin sensitivity, and weight gain. However, their mechanisms of action are still poorly understood. So far, the influence of PP-InsPs on cellular metabolism has been studied by overexpression or knockout/inhibition of relevant metabolizing kinases (IP6Ks, PPIP5Ks). These approaches are, inter alia, limited by time-resolution and potential compensation mechanisms. Here, we describe the synthesis of cell-permeant caged PP-InsPs as tools to rapidly modulate intracellular levels of defined isomers of PP-InsPs in a genetically non-perturbed cellular environment. We show that caged prometabolites readily enter live cells where they are enzymatically converted into still inactive, metabolically stable, photocaged PP-InsPs. Upon light-triggered release of 5-PP-InsP5, the major cellular inositol pyrophosphate, oscillations of intracellular Ca2+ levels in MIN6 cells were transiently reduced to spontaneously recover again. In contrast, uncaging of 1-PP-InsP5, a minor cellular isomer, was without effect. These results provide evidence that PP-InsPs play an active role in regulating [Ca2+]i oscillations, a key element in triggering exocytosis and secretion in β-cells.
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Affiliation(s)
- S Hauke
- EMBL, Heidelberg , 69117 Heidelberg , Germany .
| | - A K Dutta
- University of Freiburg , Institute of Organic Chemistry , 79104 Freiburg , Germany .
| | - V B Eisenbeis
- University of Freiburg , Institute of Organic Chemistry , 79104 Freiburg , Germany .
| | - D Bezold
- University of Freiburg , Institute of Organic Chemistry , 79104 Freiburg , Germany .
| | - T Bittner
- University of Freiburg , Institute of Organic Chemistry , 79104 Freiburg , Germany .
| | - C Wittwer
- University of Freiburg , Institute of Organic Chemistry , 79104 Freiburg , Germany .
| | - D Thakor
- University of Freiburg , Institute of Organic Chemistry , 79104 Freiburg , Germany .
| | - I Pavlovic
- University of Freiburg , Institute of Organic Chemistry , 79104 Freiburg , Germany .
| | - C Schultz
- EMBL, Heidelberg , 69117 Heidelberg , Germany . .,OHSU , Dept. Physiology & Pharmacology , Portland , OR , USA .
| | - H J Jessen
- University of Freiburg , Institute of Organic Chemistry , 79104 Freiburg , Germany .
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Riley AM, Unterlass JE, Konieczny V, Taylor CW, Helleday T, Potter BVL. A synthetic diphosphoinositol phosphate analogue of inositol trisphosphate. MEDCHEMCOMM 2018; 9:1105-1113. [PMID: 30079174 PMCID: PMC6071853 DOI: 10.1039/c8md00149a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/01/2018] [Indexed: 01/17/2023]
Abstract
Diphosphoinositol phosphates (PP-InsPs) are inositol phosphates (InsPs) that contain PP (diphosphate) groups. Converting a phosphate group in an InsP into a diphosphate has been reported to enhance affinity for some binding proteins. We synthesised 1-PP-Ins(4,5)P2, the first diphosphate analogue of the intracellular signalling molecule InsP3, and examined its effects on InsP3 receptors, which are intracellular Ca2+ channels. 1-PP-Ins(4,5)P2 was indistinguishable from InsP3 in its ability to bind to and activate type 1 InsP3 receptors, indicating that the diphosphate modification of InsP3 affected neither affinity nor efficacy. Nevertheless, 1-PP-Ins(4,5)P2 is the most potent 1-phosphate modified analogue of InsP3 yet identified. PP-InsPs are generally hydrolysed by diphosphoinositol phosphate phosphohydrolases (DIPPs), but 1-PP-Ins(4,5)P2 was not readily metabolised by human DIPPs. Differential scanning fluorimetry showed that 1-PP-Ins(4,5)P2 stabilises DIPP proteins, but to a lesser extent than naturally occurring substrates 1-PP-InsP5 and 5-PP-InsP5. The non-hydrolysable InsP7 analogues 1-PCP-InsP5 and 5-PCP-InsP5 showed comparable stabilising abilities to their natural counterparts and may therefore be promising substrate analogues for co-crystallisation with DIPPs.
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Affiliation(s)
- Andrew M. Riley
- Medicinal Chemistry and Drug Discovery
, Department of Pharmacology
, University of Oxford
,
Mansfield Road
, Oxford OX1 3QT
, UK
.
; Fax: +44 (0)1865 271853
; Tel: +44 (0)1865 271945
| | - Judith E. Unterlass
- Science for Life Laboratory
, Department of Oncology-Pathology
, Karolinska Institutet
,
SE-171 21 Solna
, Sweden
| | - Vera Konieczny
- Department of Pharmacology
, University of Cambridge
,
Tennis Court Road
, Cambridge CB2 1PD
, UK
| | - Colin W. Taylor
- Department of Pharmacology
, University of Cambridge
,
Tennis Court Road
, Cambridge CB2 1PD
, UK
| | - Thomas Helleday
- Science for Life Laboratory
, Department of Oncology-Pathology
, Karolinska Institutet
,
SE-171 21 Solna
, Sweden
| | - Barry V. L. Potter
- Medicinal Chemistry and Drug Discovery
, Department of Pharmacology
, University of Oxford
,
Mansfield Road
, Oxford OX1 3QT
, UK
.
; Fax: +44 (0)1865 271853
; Tel: +44 (0)1865 271945
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34
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Wang H, Gu C, Rolfes RJ, Jessen HJ, Shears SB. Structural and biochemical characterization of Siw14: A protein-tyrosine phosphatase fold that metabolizes inositol pyrophosphates. J Biol Chem 2018; 293:6905-6914. [PMID: 29540476 PMCID: PMC5936820 DOI: 10.1074/jbc.ra117.001670] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 02/26/2018] [Indexed: 01/09/2023] Open
Abstract
Inositol pyrophosphates (PP-InsPs) are "energetic" intracellular signals that are ubiquitous in animals, plants, and fungi; structural and biochemical characterization of PP-InsP metabolic enzymes provides insight into their evolution, reaction mechanisms, and regulation. Here, we describe the 2.35-Å-resolution structure of the catalytic core of Siw14, a 5-PP-InsP phosphatase from Saccharomyces cerevisiae and a member of the protein tyrosine-phosphatase (PTP) superfamily. Conclusions that we derive from structural data are supported by extensive site-directed mutagenesis and kinetic analyses, thereby attributing new functional significance to several key residues. We demonstrate the high activity and exquisite specificity of Siw14 for the 5-diphosphate group of PP-InsPs. The three structural elements that demarcate a 9.2-Å-deep substrate-binding pocket each have spatial equivalents in PTPs, but we identify how these are specialized for Siw14 to bind and hydrolyze the intensely negatively charged PP-InsPs. (a) The catalytic P-loop with the CX5R(S/T) PTP motif contains additional, positively charged residues. (b) A loop between the α5 and α6 helices, corresponding to the Q-loop in PTPs, contains a lysine and an arginine that extend into the catalytic pocket due to displacement of the α5 helix orientation through intramolecular crowding caused by three bulky, hydrophobic residues. (c) The general-acid loop in PTPs is replaced in Siw14 with a flexible loop that does not use an aspartate or glutamate as a general acid. We propose that an acidic residue is not required for phosphoanhydride hydrolysis.
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Affiliation(s)
- Huanchen Wang
- From the Inositol Signaling Group, Signal Transduction Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, , To whom correspondence should be addressed:
Signal Transduction Laboratory, NIEHS, National Institutes of Health, 111 T. W. Alexander Dr., Research Triangle Park, NC 27709. E-mail:
| | - Chunfang Gu
- From the Inositol Signaling Group, Signal Transduction Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Ronda J. Rolfes
- Department of Biology, Georgetown University, Washington, D. C. 20057, and
| | - Henning J. Jessen
- Institute of Organic Chemistry, Albert Ludwigs University, Freiburg, 79104 Freiburg, Germany
| | - Stephen B. Shears
- From the Inositol Signaling Group, Signal Transduction Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
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Nair VS, Gu C, Janoshazi AK, Jessen HJ, Wang H, Shears SB. Inositol Pyrophosphate Synthesis by Diphosphoinositol Pentakisphosphate Kinase-1 is Regulated by Phosphatidylinositol(4,5)bisphosphate. Biosci Rep 2018; 38:BSR20171549. [PMID: 29459425 PMCID: PMC5857911 DOI: 10.1042/bsr20171549] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/14/2018] [Accepted: 02/17/2018] [Indexed: 11/17/2022] Open
Abstract
5-diphosphoinositol tetrakisphosphate (5-InsP7) and bisdiphosphoinositol tetrakisphosphate (InsP8) are 'energetic' inositol pyrophosphate signaling molecules that regulate bioenergetic homeostasis. Inositol pyrophosphate levels are regulated by diphosphoinositol pentakisphosphate kinases (PPIP5Ks); these are large modular proteins that host a kinase domain (which phosphorylates 5-InsP7 to InsP8), a phosphatase domain that catalyzes the reverse reaction, and a polyphosphoinositide-binding domain (PBD). Here, we describe new interactions between these three domains in the context of full-length human PPIP5K1. We determine that InsP7 kinase activity is dominant when PPIP5K1 is expressed in intact cells; in contrast, we found that InsP8 phosphatase activity prevails when the enzyme is isolated from its cellular environment. We approach a reconciliation of this disparity by showing that cellular InsP8 phosphatase activity is inhibited by C8-PtdIns(4,5)P2 (IC50 approx. 40 ìM). We recapitulate this phosphatase inhibition with natural PtdIns(4,5)P2 that was incorporated into large unilamellar vesicles. Additionally, PtdIns(4,5)P2 increases net InsP7 kinase activity 5-fold. We oftlinedemonstrate that PtdIns(4,5)P2 is not itself a phosphatase substrate; its inhibition of InsP8 phosphatase activity results from an unusual, functional overlap between the phosphatase domain and the PBD. Finally, we discuss the significance of PtdIns(4,5)P2 as a novel regulator of PPIP5K1, in relation to compartmentalization of InsP7/InsP8 signaling in vivo.
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Affiliation(s)
- Vasudha S Nair
- NIEHS, Research Triangle Park, North Carolina, United States
| | - Chunfang Gu
- NIEHS, Research Triangle Park, North Carolina, United States
| | | | | | - Huanchen Wang
- NIEHS, Research Triangle Park, North Carolina, United States
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Brown NW, Marmelstein AM, Fiedler D. Chemical tools for interrogating inositol pyrophosphate structure and function. Chem Soc Rev 2018; 45:6311-6326. [PMID: 27462803 DOI: 10.1039/c6cs00193a] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The inositol pyrophosphates (PP-InsPs) are a unique group of intracellular messengers that represent some of the most highly phosphorylated molecules in nature. Genetic perturbation of the PP-InsP biosynthetic network indicates a central role for these metabolites in maintaining cellular energy homeostasis and in controlling signal transduction networks. However, despite their discovery over two decades ago, elucidating their physiologically relevant isomers, the biochemical pathways connecting these molecules to their associated phenotypes, and their modes of signal transduction has often been stymied by technical challenges. Many of the advances in understanding these molecules to date have been facilitated by the total synthesis of the various PP-InsP isomers and by the development of new methods that are capable of identifying their downstream signalling partners. Chemical tools have also been developed to distinguish between the proposed PP-InsP signal transduction mechanisms: protein binding, and a covalent modification of proteins termed protein pyrophosphorylation. In this article, we review these recent developments, discuss how they have helped to illuminate PP-InsP structure and function, and highlight opportunities for future discovery.
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Affiliation(s)
- Nathaniel W Brown
- Princeton University, Frick Chemistry Laboratory, Washington Road, Princeton, NJ 08544, USA and Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str 10, 13125 Berlin, Berlin, Germany.
| | - Alan M Marmelstein
- Princeton University, Frick Chemistry Laboratory, Washington Road, Princeton, NJ 08544, USA and Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str 10, 13125 Berlin, Berlin, Germany.
| | - Dorothea Fiedler
- Princeton University, Frick Chemistry Laboratory, Washington Road, Princeton, NJ 08544, USA and Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str 10, 13125 Berlin, Berlin, Germany.
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Padiyar LT, Zulueta MML, Sabbavarapu NM, Hung SC. Yb(OTf) 3-Catalyzed Desymmetrization of myo-Inositol 1,3,5-Orthoformate and Its Application in the Synthesis of Chiral Inositol Phosphates. J Org Chem 2017; 82:11418-11430. [PMID: 29019688 DOI: 10.1021/acs.joc.7b01919] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A variety of inositol phosphates including myo-inositol 1,4,5-trisphosphate, which is a secondary messenger in transmembrane signaling, were selectively synthesized via Yb(OTf)3-catalyzed desymmetrization of myo-inositol 1,3,5-orthoformate using a proline-based chiral anhydride as an acylation precursor. The investigated catalytic system could regioselectively differentiate the enantiotopic hydroxy groups of myo-inositol 1,3,5-orthoformate in the presence of a chiral auxiliary. This key step to generate a suitably protected chiral myo-inositol derivatives is described here as a unified approach to access inositol phosphates.
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Affiliation(s)
- Laxmansingh T Padiyar
- Genomics Research Center, Academia Sinica , 128 Section 2 Academia Road, Taipei 115, Taiwan
| | - Medel Manuel L Zulueta
- Genomics Research Center, Academia Sinica , 128 Section 2 Academia Road, Taipei 115, Taiwan
| | | | - Shang-Cheng Hung
- Genomics Research Center, Academia Sinica , 128 Section 2 Academia Road, Taipei 115, Taiwan
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38
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Shears SB. Intimate connections: Inositol pyrophosphates at the interface of metabolic regulation and cell signaling. J Cell Physiol 2017; 233:1897-1912. [PMID: 28542902 DOI: 10.1002/jcp.26017] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 05/18/2017] [Indexed: 12/11/2022]
Abstract
Inositol pyrophosphates are small, diffusible signaling molecules that possess the most concentrated three-dimensional array of phosphate groups in Nature; up to eight phosphates are crammed around a six-carbon inositol ring. This review discusses the physico-chemical properties of these unique molecules, and their mechanisms of action. Also provided is information on the enzymes that regulate the levels and hence the signaling properties of these molecules. This review pursues the idea that many of the biological effects of inositol pyrophosphates can be rationalized by their actions at the interface of cell signaling and metabolism that is essential to cellular and organismal homeostasis.
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Affiliation(s)
- Stephen B Shears
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
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39
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Gerasimaite R, Pavlovic I, Capolicchio S, Hofer A, Schmidt A, Jessen HJ, Mayer A. Inositol Pyrophosphate Specificity of the SPX-Dependent Polyphosphate Polymerase VTC. ACS Chem Biol 2017; 12:648-653. [PMID: 28186404 DOI: 10.1021/acschembio.7b00026] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The free energy of nucleotide hydrolysis depends on phosphate concentration. Cells regulate cytosolic phosphate levels by orchestrating phosphate acquisition and storage through inositol pyrophosphates (PP-InsP) and SPX domains. Here, we report the synthesis of the novel 5-PPP-InsP5 containing a triphosphate subunit. Using this and a series of synthetic PP-InsP, we examined the ligand specificity of the SPX domain in the PP-InsP-controlled yeast polyphosphate polymerase VTC. SPX decodes the relative positioning of the phosphoric anhydrides, their structure (diphosphate vs triphosphate), and the presence of other phosphates on the inositol ring. Despite the higher potency of 1,5-(PP)2-InsP4, 5-PP-InsP5 is the primary activator of VTC in cells, indicating that its higher concentration compensates for its lower potency. 1,5-(PP)2-InsP4 levels rise and could become relevant under stress conditions. Thus, SPX domains may integrate PP-InsP dependent signaling to adapt cytosolic phosphate concentrations to different metabolic situations.
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Affiliation(s)
- Ruta Gerasimaite
- Department
of Biochemistry, University of Lausanne, Chemin de Boveresses 155, 1066 Epalinges, Switzerland
| | - Igor Pavlovic
- Department
of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Samanta Capolicchio
- Department
of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Alexandre Hofer
- Department
of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Andrea Schmidt
- Department
of Biochemistry, University of Lausanne, Chemin de Boveresses 155, 1066 Epalinges, Switzerland
| | - Henning J. Jessen
- Institute
of Organic Chemistry, Albert-Ludwigs University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Andreas Mayer
- Department
of Biochemistry, University of Lausanne, Chemin de Boveresses 155, 1066 Epalinges, Switzerland
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40
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Shah A, Ganguli S, Sen J, Bhandari R. Inositol Pyrophosphates: Energetic, Omnipresent and Versatile Signalling Molecules. J Indian Inst Sci 2017; 97:23-40. [PMID: 32214696 PMCID: PMC7081659 DOI: 10.1007/s41745-016-0011-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 11/16/2016] [Indexed: 12/21/2022]
Abstract
Inositol pyrophosphates (PP-IPs) are a class of energy-rich signalling molecules found in all eukaryotic cells. These are derivatives of inositol that contain one or more diphosphate (or pyrophosphate) groups in addition to monophosphates. The more abundant and best studied PP-IPs are diphosphoinositol pentakisphosphate (IP7) and bis-diphosphoinositol tetrakisphosphate (IP8). These molecules can influence protein function by two mechanisms: binding and pyrophosphorylation. The former involves the specific interaction of a particular inositol pyrophosphate with a binding site on a protein, while the latter is a unique attribute of inositol pyrophosphates, wherein the β-phosphate moiety is transferred from a PP-IP to a pre-phosphorylated serine residue in a protein to generate pyrophosphoserine. Both these events can result in changes in the target protein’s activity, localisation or its interaction with other partners. As a consequence of their ubiquitous presence in all eukaryotic organisms and all cell types examined till date, and their ability to modify protein function, PP-IPs have been found to participate in a wide range of metabolic, developmental, and signalling pathways. This review highlights
many of the known functions of PP-IPs in the context of their temporal and spatial distribution in eukaryotic cells.
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Affiliation(s)
- Akruti Shah
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana India
- Graduate Studies, Manipal University, Manipal, Karnataka India
| | - Shubhra Ganguli
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana India
- Graduate Studies, Manipal University, Manipal, Karnataka India
| | - Jayraj Sen
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana India
- Graduate Studies, Manipal University, Manipal, Karnataka India
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana India
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Abstract
To help define the molecular basis of cellular signalling cascades, and their biological functions, there is considerable value in utilizing a high-quality chemical 'probe' that has a well-defined interaction with a specific cellular protein. Such reagents include inhibitors of protein kinases and small molecule kinases, as well as mimics or antagonists of intracellular signals. The purpose of this review is to consider recent progress and promising future directions for the development of novel molecules that can interrogate and manipulate the cellular actions of inositol pyrophosphates (PP-IPs)--a specialized, 'energetic' group of cell-signalling molecules in which multiple phosphate and diphosphate groups are crammed around a cyclohexane polyol scaffold.
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Gu C, Wilson MSC, Jessen HJ, Saiardi A, Shears SB. Inositol Pyrophosphate Profiling of Two HCT116 Cell Lines Uncovers Variation in InsP8 Levels. PLoS One 2016; 11:e0165286. [PMID: 27788189 PMCID: PMC5082907 DOI: 10.1371/journal.pone.0165286] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 09/09/2016] [Indexed: 11/18/2022] Open
Abstract
The HCT116 cell line, which has a pseudo-diploid karotype, is a popular model in the fields of cancer cell biology, intestinal immunity, and inflammation. In the current study, we describe two batches of diverged HCT116 cells, which we designate as HCT116NIH and HCT116UCL. Using both gel electrophoresis and HPLC, we show that HCT116UCL cells contain 6-fold higher levels of InsP8 than HCT116NIH cells. This observation is significant because InsP8 is one of a group of molecules collectively known as ‘inositol pyrophosphates’ (PP-InsPs)—highly ‘energetic’ and conserved regulators of cellular and organismal metabolism. Variability in the cellular levels of InsP8 within divergent HCT116 cell lines could have impacted the phenotypic data obtained in previous studies. This difference in InsP8 levels is more remarkable for being specific; levels of other inositol phosphates, and notably InsP6 and 5-InsP7, are very similar in both HCT116NIH and HCT116UCL lines. We also developed a new HPLC procedure to record 1-InsP7 levels directly (for the first time in any mammalian cell line); 1-InsP7 comprised <2% of total InsP7 in HCT116NIH and HCT116UCL lines. The elevated levels of InsP8 in the HCT116UCL lines were not due to an increase in expression of the PP-InsP kinases (IP6Ks and PPIP5Ks), nor to a decrease in the capacity to dephosphorylate InsP8. We discuss how the divergent PP-InsP profiles of the newly-designated HCT116NIH and HCT116UCL lines should be considered an important research opportunity: future studies using these two lines may uncover new features that regulate InsP8 turnover, and may also yield new directions for studying InsP8 function.
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Affiliation(s)
- Chunfang Gu
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, North Carolina, 27709, United States of America
| | - Miranda S. C. Wilson
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Henning J. Jessen
- Institute of Organic Chemistry, Albert-Ludwigs-University, Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- * E-mail: (AS); (SS)
| | - Stephen B. Shears
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, North Carolina, 27709, United States of America
- * E-mail: (AS); (SS)
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43
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Hager A, Wu M, Wang H, Brown NW, Shears SB, Veiga N, Fiedler D. Cellular Cations Control Conformational Switching of Inositol Pyrophosphate Analogues. Chemistry 2016; 22:12406-14. [PMID: 27460418 PMCID: PMC5076471 DOI: 10.1002/chem.201601754] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Indexed: 12/21/2022]
Abstract
The inositol pyrophosphate messengers (PP-InsPs) are emerging as an important class of cellular regulators. These molecules have been linked to numerous biological processes, including insulin secretion and cancer cell migration, but how they trigger such a wide range of cellular responses has remained unanswered in many cases. Here, we show that the PP-InsPs exhibit complex speciation behaviour and propose that a unique conformational switching mechanism could contribute to their multifunctional effects. We synthesised non-hydrolysable bisphosphonate analogues and crystallised the analogues in complex with mammalian PPIP5K2 kinase. Subsequently, the bisphosphonate analogues were used to investigate the protonation sequence, metal-coordination properties, and conformation in solution. Remarkably, the presence of potassium and magnesium ions enabled the analogues to adopt two different conformations near physiological pH. Understanding how the intrinsic chemical properties of the PP-InsPs can contribute to their complex signalling outputs will be essential to elucidate their regulatory functions.
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Affiliation(s)
- Anastasia Hager
- Department of Chemistry, Princeton University, Washington Rd., Princeton, New Jersey, 08544, USA
| | - Mingxuan Wu
- Department of Chemistry, Princeton University, Washington Rd., Princeton, New Jersey, 08544, USA
| | - Huanchen Wang
- Inositol Signaling Group, National Institutes of Health, Research Triangle Park, North Carolina, 27709, USA
| | - Nathaniel W Brown
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle Strasse 10, 13125, Berlin, Germany
- Department of Chemistry, Princeton University, Washington Rd., Princeton, New Jersey, 08544, USA
| | - Stephen B Shears
- Inositol Signaling Group, National Institutes of Health, Research Triangle Park, North Carolina, 27709, USA
| | - Nicolás Veiga
- Cátedra de Química Inorgánica, Departamento Estrella Campos, Facultad de Química, Universidad de la República, CC 1157, Montevideo, Uruguay.
| | - Dorothea Fiedler
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle Strasse 10, 13125, Berlin, Germany.
- Department of Chemistry, Princeton University, Washington Rd., Princeton, New Jersey, 08544, USA.
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Abstract
Inositol pyrophosphates such as 5-diphosphoinositol pentakisphosphate (5-IP7) are highly energetic inositol metabolites containing phosphoanhydride bonds. Although inositol pyrophosphates are known to regulate various biological events, including growth, survival, and metabolism, the molecular sites of 5-IP7 action in vesicle trafficking have remained largely elusive. We report here that elevated 5-IP7 levels, caused by overexpression of inositol hexakisphosphate (IP6) kinase 1 (IP6K1), suppressed depolarization-induced neurotransmitter release from PC12 cells. Conversely, IP6K1 depletion decreased intracellular 5-IP7 concentrations, leading to increased neurotransmitter release. Consistently, knockdown of IP6K1 in cultured hippocampal neurons augmented action potential-driven synaptic vesicle exocytosis at synapses. Using a FRET-based in vitro vesicle fusion assay, we found that 5-IP7, but not 1-IP7, exhibited significantly higher inhibitory activity toward synaptic vesicle exocytosis than IP6 Synaptotagmin 1 (Syt1), a Ca(2+) sensor essential for synaptic membrane fusion, was identified as a molecular target of 5-IP7 Notably, 5-IP7 showed a 45-fold higher binding affinity for Syt1 compared with IP6 In addition, 5-IP7-dependent inhibition of synaptic vesicle fusion was abolished by increasing Ca(2+) levels. Thus, 5-IP7 appears to act through Syt1 binding to interfere with the fusogenic activity of Ca(2+) These findings reveal a role of 5-IP7 as a potent inhibitor of Syt1 in controlling the synaptic exocytotic pathway and expand our understanding of the signaling mechanisms of inositol pyrophosphates.
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45
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Durantie E, Huwiler S, Leroux JC, Castagner B. A Chiral Phosphoramidite Reagent for the Synthesis of Inositol Phosphates. Org Lett 2016; 18:3162-5. [DOI: 10.1021/acs.orglett.6b01374] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Estelle Durantie
- Department of Chemistry and
Applied Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
| | - Samuel Huwiler
- Department of Chemistry and
Applied Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
| | | | - Bastien Castagner
- Department of Chemistry and
Applied Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
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46
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Hofer A, Marques E, Kieliger N, Gatter SKN, Jordi S, Ferrari E, Hofmann M, Fitzpatrick TB, Hottiger MO, Jessen HJ. Chemoselective Dimerization of Phosphates. Org Lett 2016; 18:3222-5. [PMID: 27308921 DOI: 10.1021/acs.orglett.6b01466] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A methodology for the synthesis of oligophosphate conjugates using phosphordiamidites is described. This strategy facilitates the straightforward preparation of C2-symmetric dinucleoside tri-, penta-, and heptaphosphates. Moreover, unsymmetric compounds such as thiamine adenosine triphosphate and thiamine cytidine triphosphate can be prepared. The material is used to study the inhibitory activity of thiaminylated nucleotides against adenosine diphosphate ribosyltransferases.
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Affiliation(s)
| | | | | | | | | | | | - Manuel Hofmann
- Plant Biochemistry & Physiology Laboratory, Department of Botany and Plant Biology, University of Geneva , Quai E. Ansermet 30, 1211 Geneva, Switzerland
| | - Teresa B Fitzpatrick
- Plant Biochemistry & Physiology Laboratory, Department of Botany and Plant Biology, University of Geneva , Quai E. Ansermet 30, 1211 Geneva, Switzerland
| | | | - Henning J Jessen
- Institute of Organic Chemistry, Albert-Ludwigs-University Freiburg , Albertstr. 21, 79104 Freiburg i. B., Germany
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47
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Vibhute AM, Konieczny V, Taylor CW, Sureshan KM. Triazolophostins: a library of novel and potent agonists of IP3 receptors. Org Biomol Chem 2016; 13:6698-710. [PMID: 25869535 PMCID: PMC4533600 DOI: 10.1039/c5ob00440c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IP3R initiate most cellular Ca2+ signaling. AdA is the most potent agonist of IP3R. The structural complexity of AdA makes synthesis of its analogs cumbersome. We report an easy method for generating a library of potent triazole-based analogs of AdA, triazolophostins, which are the most potent AdA analogs devoid of a nucleobase.
IP3 receptors are channels that mediate the release of Ca2+ from the intracellular stores of cells stimulated by hormones or neurotransmitters. Adenophostin A (AdA) is the most potent agonist of IP3 receptors, with the β-anomeric adenine contributing to the increased potency. The potency of AdA and its stability towards the enzymes that degrade IP3 have aroused interest in AdA analogs for biological studies. The complex structure of AdA poses problems that have necessitated optimization of synthetic conditions for each analog. Such lengthy one-at-a-time syntheses limit access to AdA analogs. We have addressed this problem by synthesizing a library of triazole-based AdA analogs, triazolophostins, by employing click chemistry. An advanced intermediate having all the necessary phosphates and a β-azide at the anomeric position was reacted with various alkynes under Cu(i) catalysis to yield triazoles, which upon deprotection gave triazolophostins. All eleven triazolophostins synthesized are more potent than IP3 and some are equipotent with AdA in functional analyses of IP3 receptors. We show that a triazole ring can replace adenine without compromising the potency of AdA and provide facile routes to novel AdA analogs.
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Affiliation(s)
- Amol M Vibhute
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala-695016, India.
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48
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Pavlovic I, Thakor DT, Vargas JR, McKinlay CJ, Hauke S, Anstaett P, Camuña RC, Bigler L, Gasser G, Schultz C, Wender PA, Jessen HJ. Cellular delivery and photochemical release of a caged inositol-pyrophosphate induces PH-domain translocation in cellulo. Nat Commun 2016; 7:10622. [PMID: 26842801 PMCID: PMC4743007 DOI: 10.1038/ncomms10622] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/05/2016] [Indexed: 02/07/2023] Open
Abstract
Inositol pyrophosphates, such as diphospho-myo-inositol pentakisphosphates (InsP7), are an important family of signalling molecules, implicated in many cellular processes and therapeutic indications including insulin secretion, glucose homeostasis and weight gain. To understand their cellular functions, chemical tools such as photocaged analogues for their real-time modulation in cells are required. Here we describe a concise, modular synthesis of InsP7 and caged InsP7. The caged molecule is stable and releases InsP7 only on irradiation. While photocaged InsP7 does not enter cells, its cellular uptake is achieved using nanoparticles formed by association with a guanidinium-rich molecular transporter. This novel synthesis and unprecedented polyphosphate delivery strategy enable the first studies required to understand InsP7 signalling in cells with controlled spatiotemporal resolution. It is shown herein that cytoplasmic photouncaging of InsP7 leads to translocation of the PH-domain of Akt, an important signalling-node kinase involved in glucose homeostasis, from the membrane into the cytoplasm. Photocaged inositol-pyrophosphates offer a tool to study cellular signalling, but their challenging synthesis has precluded any biological studies so far. Here, the authors report the synthesis and cellular delivery of a photocaged analogue, and show that it mediates protein translocation in cellulo.
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Affiliation(s)
- Igor Pavlovic
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Divyeshsinh T Thakor
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Jessica R Vargas
- Departments of Chemistry and Chemical and Systems Biology, Stanford University, Stanford, California 94305, USA
| | - Colin J McKinlay
- Departments of Chemistry and Chemical and Systems Biology, Stanford University, Stanford, California 94305, USA
| | - Sebastian Hauke
- European Molecular Biology Laboratory (EMBL), Cell Biology &Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Philipp Anstaett
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Rafael C Camuña
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Málaga, Malaga 29071, Spain
| | - Laurent Bigler
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Gilles Gasser
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL), Cell Biology &Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Paul A Wender
- Departments of Chemistry and Chemical and Systems Biology, Stanford University, Stanford, California 94305, USA
| | - Henning J Jessen
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
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49
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Steidle EA, Chong LS, Wu M, Crooke E, Fiedler D, Resnick AC, Rolfes RJ. A Novel Inositol Pyrophosphate Phosphatase in Saccharomyces cerevisiae: Siw14 PROTEIN SELECTIVELY CLEAVES THE β-PHOSPHATE FROM 5-DIPHOSPHOINOSITOL PENTAKISPHOSPHATE (5PP-IP5). J Biol Chem 2016; 291:6772-83. [PMID: 26828065 DOI: 10.1074/jbc.m116.714907] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Indexed: 11/06/2022] Open
Abstract
Inositol pyrophosphates are high energy signaling molecules involved in cellular processes, such as energetic metabolism, telomere maintenance, stress responses, and vesicle trafficking, and can mediate protein phosphorylation. Although the inositol kinases underlying inositol pyrophosphate biosynthesis are well characterized, the phosphatases that selectively regulate their cellular pools are not fully described. The diphosphoinositol phosphate phosphohydrolase enzymes of the Nudix protein family have been demonstrated to dephosphorylate inositol pyrophosphates; however, theSaccharomyces cerevisiaehomolog Ddp1 prefers inorganic polyphosphate over inositol pyrophosphates. We identified a novel phosphatase of the recently discovered atypical dual specificity phosphatase family as a physiological inositol pyrophosphate phosphatase. Purified recombinant Siw14 hydrolyzes the β-phosphate from 5-diphosphoinositol pentakisphosphate (5PP-IP5or IP7)in vitro. In vivo,siw14Δ yeast mutants possess increased IP7levels, whereas heterologousSIW14overexpression eliminates IP7from cells. IP7levels increased proportionately whensiw14Δ was combined withddp1Δ orvip1Δ, indicating independent activity by the enzymes encoded by these genes. We conclude that Siw14 is a physiological phosphatase that modulates inositol pyrophosphate metabolism by dephosphorylating the IP7isoform 5PP-IP5to IP6.
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Affiliation(s)
- Elizabeth A Steidle
- From the Department of Biology, Georgetown University, Washington, D. C. 20057
| | - Lucy S Chong
- the Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Mingxuan Wu
- the Department of Chemistry, Princeton University, Princeton, New Jersey 08544, and
| | - Elliott Crooke
- the Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, D. C. 20057
| | - Dorothea Fiedler
- the Department of Chemistry, Princeton University, Princeton, New Jersey 08544, and
| | - Adam C Resnick
- the Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104,
| | - Ronda J Rolfes
- From the Department of Biology, Georgetown University, Washington, D. C. 20057,
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50
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Thomas MP, Mills SJ, Potter BVL. The "Other" Inositols and Their Phosphates: Synthesis, Biology, and Medicine (with Recent Advances in myo-Inositol Chemistry). Angew Chem Int Ed Engl 2016; 55:1614-50. [PMID: 26694856 PMCID: PMC5156312 DOI: 10.1002/anie.201502227] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Indexed: 12/24/2022]
Abstract
Cell signaling via inositol phosphates, in particular via the second messenger myo-inositol 1,4,5-trisphosphate, and phosphoinositides comprises a huge field of biology. Of the nine 1,2,3,4,5,6-cyclohexanehexol isomers, myo-inositol is pre-eminent, with "other" inositols (cis-, epi-, allo-, muco-, neo-, L-chiro-, D-chiro-, and scyllo-) and derivatives rarer or thought not to exist in nature. However, neo- and d-chiro-inositol hexakisphosphates were recently revealed in both terrestrial and aquatic ecosystems, thus highlighting the paucity of knowledge of the origins and potential biological functions of such stereoisomers, a prevalent group of environmental organic phosphates, and their parent inositols. Some "other" inositols are medically relevant, for example, scyllo-inositol (neurodegenerative diseases) and d-chiro-inositol (diabetes). It is timely to consider exploration of the roles and applications of the "other" isomers and their derivatives, likely by exploiting techniques now well developed for the myo series.
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Affiliation(s)
- Mark P Thomas
- Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Stephen J Mills
- Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Barry V L Potter
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.
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