1
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Ono M, Matsumura T, Sung EJ, Koyama T, Ochiai M, Shears SB, Hayakawa Y. Drosophila cytokine GBP2 exerts immune responses and regulates GBP1 expression through GPCR receptor Mthl10. Insect Biochem Mol Biol 2024; 167:104086. [PMID: 38295885 DOI: 10.1016/j.ibmb.2024.104086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/10/2023] [Accepted: 01/25/2024] [Indexed: 03/03/2024]
Abstract
Growth-blocking peptide (GBP), an insect cytokine, was first found in armyworm Mythimna separata. A functional analogue of GBP, stress-responsive peptide (SRP), was also identified in the same species. SRP gene expression has been demonstrated to be enhanced by GBP, indicating that both cytokines are organized within a hierarchical regulatory network. Although GBP1 (CG15917) and GBP2 (CG11395) have been identified in Drosophila melanogaster, immunological functions have only been characterized for GBP1. It is expected that the biological responses of two structurally similar peptides should be coordinated, but there is little information on this topic. Here, we demonstrate that GBP2 replicates the GBP1-mediated cellular immune response from Drosophila S2 cells. Moreover, the GBP2-induced response was silenced by pre-treatment with dsRNA targeting the GBP receptor gene, Mthl10. Furthermore, treatment of S2 cells with GBP2 enhanced GBP1 expression levels, but GBP1 did not affect GBP2 expression. GBP2 derived enhancement of GBP1 expression was not observed in the presence of GBP1, indicating that GBP2 is an upstream expressional regulator of a GBP1/GBP2 cytokine network. GBP2-induced enhancement of GBP1 expression was not observed in Mthl10 knockdown cells. Enhancement of GBP2 expression was observed in both Drosophila larvae and S2 cells under heat stress conditions; expressional enhancement of both GBP1 and GBP2 was eliminated in Mthl10 knockdown cells and larvae. Finally, Ca2+ mobilization assay in GCaMP3-expressing S2 cells demonstrated that GBP2 mobilizes Ca2+ upstream of Mthl10. Our finding revealed that Drosophila GBP1 and GBP2 control immune responses as well as their own expression levels through a hierarchical cytokine network, indicating that Drosophila GBP1/GBP2 system can be a simple model that is useful to investigate the detailed regulatory mechanism of related cytokine complexes.
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Affiliation(s)
- Masaya Ono
- Department of Applied Biological Sciences, Saga University, Saga, 840-8502, Japan
| | - Takashi Matsumura
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Eui Jae Sung
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Takashi Koyama
- Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Masanori Ochiai
- Institute of Low Temperature Science, Hokkaido University, Sapporo, 060-0819, Japan
| | - Stephen B Shears
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Yoichi Hayakawa
- Department of Applied Biological Sciences, Saga University, Saga, 840-8502, Japan.
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2
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Zong G, Desfougères Y, Portela-Torres P, Kwon YU, Saiardi A, Shears SB, Wang H. Biochemical and structural characterization of an inositol pyrophosphate kinase from a giant virus. EMBO J 2024; 43:462-480. [PMID: 38216735 PMCID: PMC10897400 DOI: 10.1038/s44318-023-00005-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/11/2023] [Accepted: 11/15/2023] [Indexed: 01/14/2024] Open
Abstract
Kinases that synthesize inositol phosphates (IPs) and pyrophosphates (PP-IPs) control numerous biological processes in eukaryotic cells. Herein, we extend this cellular signaling repertoire to viruses. We have biochemically and structurally characterized a minimalist inositol phosphate kinase (i.e., TvIPK) encoded by Terrestrivirus, a nucleocytoplasmic large ("giant") DNA virus (NCLDV). We show that TvIPK can synthesize inositol pyrophosphates from a range of scyllo- and myo-IPs, both in vitro and when expressed in yeast cells. We present multiple crystal structures of enzyme/substrate/nucleotide complexes with individual resolutions from 1.95 to 2.6 Å. We find a heart-shaped ligand binding pocket comprising an array of positively charged and flexible side chains, underlying the observed substrate diversity. A crucial arginine residue in a conserved "G-loop" orients the γ-phosphate of ATP to allow substrate pyrophosphorylation. We highlight additional conserved catalytic and architectural features in TvIPK, and support their importance through site-directed mutagenesis. We propose that NCLDV inositol phosphate kinases may have assisted evolution of inositol pyrophosphate signaling, and we discuss the potential biogeochemical significance of TvIPK in soil niches.
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Affiliation(s)
- Guangning Zong
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Yann Desfougères
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Paloma Portela-Torres
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Yong-Uk Kwon
- Department of Chemistry and Nanoscience, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, South Korea
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK.
| | - 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.
| | - Huanchen Wang
- 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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3
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Gu C, Li X, Zong G, Wang H, Shears SB. IP8: A quantitatively minor inositol pyrophosphate signaling molecule that punches above its weight. Adv Biol Regul 2024; 91:101002. [PMID: 38064879 DOI: 10.1016/j.jbior.2023.101002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 02/25/2024]
Abstract
The inositol pyrophosphates (PP-IPs) are specialized members of the wider inositol phosphate signaling family that possess functionally significant diphosphate groups. The PP-IPs exhibit remarkable functionally versatility throughout the eukaryotic kingdoms. However, a quantitatively minor PP-IP - 1,5 bisdiphosphoinositol tetrakisphosphate (1,5-IP8) - has received considerably less attention from the cell signalling community. The main purpose of this review is to summarize recently-published data which have now brought 1,5-IP8 into the spotlight, by expanding insight into the molecular mechanisms by which this polyphosphate regulates many fundamental biological processes.
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Affiliation(s)
- Chunfang Gu
- Inositol signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709 USA
| | - Xingyao Li
- Inositol signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709 USA
| | - Guangning Zong
- Inositol signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709 USA
| | - Huanchen Wang
- Inositol signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709 USA.
| | - Stephen B Shears
- Inositol signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709 USA.
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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Yu J, Leibiger B, Yang SN, Shears SB, Leibiger IB, Berggren PO, Barker CJ. Multiple Inositol Polyphosphate Phosphatase Compartmentalization Separates Inositol Phosphate Metabolism from Inositol Lipid Signaling. Biomolecules 2023; 13:885. [PMID: 37371464 DOI: 10.3390/biom13060885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 06/29/2023] Open
Abstract
Multiple inositol polyphosphate phosphatase (MINPP1) is an enigmatic enzyme that is responsible for the metabolism of inositol hexakisphosphate (InsP6) and inositol 1,3,4,5,6 pentakisphosphate (Ins(1,3,4,5,6)P5 in mammalian cells, despite being restricted to the confines of the ER. The reason for this compartmentalization is unclear. In our previous studies in the insulin-secreting HIT cell line, we expressed MINPP1 in the cytosol to artificially reduce the concentration of these higher inositol phosphates. Undocumented at the time, we noted cytosolic MINPP1 expression reduced cell growth. We were struck by the similarities in substrate preference between a number of different enzymes that are able to metabolize both inositol phosphates and lipids, notably IPMK and PTEN. MINPP1 was first characterized as a phosphatase that could remove the 3-phosphate from inositol 1,3,4,5-tetrakisphosphate (Ins(1,3,4,5)P4). This molecule shares strong structural homology with the major product of the growth-promoting Phosphatidyl 3-kinase (PI3K), phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) and PTEN can degrade both this lipid and Ins(1,3,4,5)P4. Because of this similar substrate preference, we postulated that the cytosolic version of MINPP1 (cyt-MINPP1) may not only attack inositol polyphosphates but also PtdIns(3,4,5)P3, a key signal in mitogenesis. Our experiments show that expression of cyt-MINPP1 in HIT cells lowers the concentration of PtdIns(3,4,5)P3. We conclude this reflects a direct effect of MINPP1 upon the lipid because cyt-MINPP1 actively dephosphorylates synthetic, di(C4:0)PtdIns(3,4,5)P3 in vitro. These data illustrate the importance of MINPP1's confinement to the ER whereby important aspects of inositol phosphate metabolism and inositol lipid signaling can be separately regulated and give one important clarification for MINPP1's ER seclusion.
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Affiliation(s)
- Jia Yu
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Barbara Leibiger
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Shao-Nian Yang
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Stephen B Shears
- Inositol Signaling Section, NIEHS, 111, Alexander Drive, Research Triangle Park, Durham, NC 27709, USA
| | - Ingo B Leibiger
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Per-Olof Berggren
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Christopher J Barker
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Sahu S, Gordon J, Gu C, Sobhany M, Fiedler D, Stanley RE, Shears SB. Nucleolar Architecture Is Modulated by a Small Molecule, the Inositol Pyrophosphate 5-InsP 7. Biomolecules 2023; 13:biom13010153. [PMID: 36671538 PMCID: PMC9855682 DOI: 10.3390/biom13010153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/28/2022] [Accepted: 01/09/2023] [Indexed: 01/14/2023] Open
Abstract
Inositol pyrophosphates (PP-InsPs); are a functionally diverse family of eukaryotic molecules that deploy a highly-specialized array of phosphate groups as a combinatorial cell-signaling code. One reductive strategy to derive a molecular-level understanding of the many actions of PP-InsPs is to individually characterize the proteins that bind them. Here, we describe an alternate approach that seeks a single, collective rationalization for PP-InsP binding to an entire group of proteins, i.e., the multiple nucleolar proteins previously reported to bind 5-InsP7 (5-diphospho-inositol-1,2,3,4,6-pentakisphosphate). Quantitative confocal imaging of the outer nucleolar granular region revealed its expansion when cellular 5-InsP7 levels were elevated by either (a) reducing the 5-InsP7 metabolism by a CRISPR-based knockout (KO) of either NUDT3 or PPIP5Ks; or (b), the heterologous expression of wild-type inositol hexakisphosphate kinase, i.e., IP6K2; separate expression of a kinase-dead IP6K2 mutant did not affect granular volume. Conversely, the nucleolar granular region in PPIP5K KO cells shrank back to the wild-type volume upon attenuating 5-InsP7 synthesis using either a pan-IP6K inhibitor or the siRNA-induced knockdown of IP6K1+IP6K2. Significantly, the inner fibrillar volume of the nucleolus was unaffected by 5-InsP7. We posit that 5-InsP7 acts as an 'electrostatic glue' that binds together positively charged surfaces on separate proteins, overcoming mutual protein-protein electrostatic repulsion the latter phenomenon is a known requirement for the assembly of a non-membranous biomolecular condensate.
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Affiliation(s)
- Soumyadip Sahu
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Jacob Gordon
- Nucleolar Integrity Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Keith Peters Building, Hills Rd, Cambridge CB2 0XY, UK
- Department of Haematology, University of Cambridge School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Chunfang Gu
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Mack Sobhany
- Nucleolar Integrity Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Robin E. Stanley
- Nucleolar Integrity 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
- Correspondence: ; Tel.: +1-984-287-3483
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8
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Zong G, Shears SB, Wang H. Structural and catalytic analyses of the InsP 6 kinase activities of higher plant ITPKs. FASEB J 2022; 36:e22380. [PMID: 35635723 PMCID: PMC9202514 DOI: 10.1096/fj.202200393r] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/04/2022] [Accepted: 05/16/2022] [Indexed: 09/21/2023]
Abstract
Inositol phosphate signaling in plants is of substantial agricultural interest, with a considerable focus on the inositol tris/tetrakisphosphate kinase (ITPK) family of inositol phosphate kinases. Historically, the 4-6 isoforms of ITPKs that higher plants each express have been studied for their multiplexing a metabolic pathway to synthesize inositol hexakisphosphate (ie InsP6 or phytate), through the phosphorylation and dephosphorylation of multiple inositol phosphates, including Ins(1,3,4,5,6)P5 (inositol-1,3,4,5,6-pentakisphosphate). A more recent discovery is ITPK-catalyzed phosphorylation of InsP6 to inositol pyrophosphates, which regulate plant immunity and phosphate homeostasis. However, a molecular-based explanation for these alternate catalytic activities has been missing, because no plant ITPK structure has previously been solved. Herein, we provide biochemical and structural analyses of ITPKs from Zea mays and Glycine max. For this work we introduce a simple, enzyme-coupled microplate-based assay of InsP6 kinase activity that should promote more general access to this important field. Furthermore, a ZmITPK1/InsP6 crystal complex is described at a resolution of 2.6 Å, which identifies a number of catalytically important residues; their functionality is confirmed by mutagenesis. We further demonstrate that ZmITPK1 adds a β-phosphate to the 3-position of Ins(1,2,3,4,5)P5 , yielding a candidate signal for regulating phosphate homeostasis. An impactful discovery is our description of a 29-residue catalytic specificity element; by interchanging this element between GmITPK1 and GmITPK2, we demonstrate how its isoform-specific sequence specifically determines whether the host protein phosphorylates InsP6 , without substantially affecting Ins(1,3,4,5,6)P5 metabolism. Our structural rationalization of key catalytic differences between alternate ITPK isoforms will complement future research into their functional diversity.
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Affiliation(s)
- Guangning Zong
- Inositol Signaling Section, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709 USA
| | - Stephen B. Shears
- Inositol Signaling Section, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709 USA
| | - Huanchen Wang
- Inositol Signaling Section, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709 USA
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9
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Zhou Y, Mukherjee S, Huang D, Chakraborty M, Gu C, Zong G, Stashko MA, Pearce KH, Shears SB, Chakraborty A, Wang H, Wang X. Development of Novel IP6K Inhibitors for the Treatment of Obesity and Obesity-Induced Metabolic Dysfunctions. J Med Chem 2022; 65:6869-6887. [PMID: 35467861 PMCID: PMC9383042 DOI: 10.1021/acs.jmedchem.2c00220] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Obesity and obesity-induced metabolic dysfunctions are significant risk factors for nonalcoholic fatty liver disease and cardiovascular diseases. Thus, obesity is an economic and social burden in developed countries. Blocking the synthesis of inositol pyrophosphates by inositol hexakisphosphate kinase (IP6K) has been identified as a potential therapeutic strategy for obesity and related diseases. We have developed a novel and potent IP6K inhibitor 20 (UNC7467) (IC50 values: IP6K1 8.9 nM; IP6K2 4.9 nM; IP6K3 1320 nM). Inositol phosphate profiling of the HCT116 colon cancer cell line demonstrates that 20 reduced levels of inositol pyrophosphates by 66-81%, without significantly perturbing levels of other inositol phosphates. Furthermore, intraperitoneal injection of 20 in diet-induced obese mice improved glycemic profiles, ameliorated hepatic steatosis, and reduced weight gain without altering food intake. Thus, inhibitor 20 can be used as an in vivo probe for IP6K-related research. Moreover, it may have therapeutic relevance in treating obesity and related diseases.
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Affiliation(s)
- Yubai Zhou
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sandip Mukherjee
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, M370, Schwitalla Hall, 1402 South Grand Boulevard, Saint Louis, Missouri 63104, United States
| | - Daowei Huang
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Molee Chakraborty
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, M370, Schwitalla Hall, 1402 South Grand Boulevard, Saint Louis, Missouri 63104, United States
| | - Chunfang Gu
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, United States
| | - Guangning Zong
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, United States
| | - Michael A Stashko
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kenneth H Pearce
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephen B Shears
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, United States
| | - Anutosh Chakraborty
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, M370, Schwitalla Hall, 1402 South Grand Boulevard, Saint Louis, Missouri 63104, United States
| | - Huanchen Wang
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, United States
| | - Xiaodong Wang
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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10
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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: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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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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16
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Khaled ML, Bykhovskaya Y, Gu C, Liu A, Drewry MD, Chen Z, Mysona BA, Parker E, McNabb RP, Yu H, Lu X, Wang J, Li X, Al-Muammar A, Rotter JI, Porter LF, Estes A, Watsky MA, Smith SB, Xu H, Abu-Amero KK, Kuo A, Shears SB, Rabinowitz YS, Liu Y. PPIP5K2 and PCSK1 are Candidate Genetic Contributors to Familial Keratoconus. Sci Rep 2019; 9:19406. [PMID: 31852976 PMCID: PMC6920454 DOI: 10.1038/s41598-019-55866-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/02/2019] [Indexed: 12/30/2022] Open
Abstract
Keratoconus (KC) is the most common corneal ectatic disorder affecting >300,000 people in the US. KC normally has its onset in adolescence, progressively worsening through the third to fourth decades of life. KC patients report significant impaired vision-related quality of life. Genetic factors play an important role in KC pathogenesis. To identify novel genes in familial KC patients, we performed whole exome and genome sequencing in a four-generation family. We identified potential variants in the PPIP5K2 and PCSK1 genes. Using in vitro cellular model and in vivo gene-trap mouse model, we found critical evidence to support the role of PPIP5K2 in normal corneal function and KC pathogenesis. The gene-trap mouse showed irregular corneal surfaces and pathological corneal thinning resembling KC. For the first time, we have integrated corneal tomography and pachymetry mapping into characterization of mouse corneal phenotypes which could be widely implemented in basic and translational research for KC diagnosis and therapy in the future.
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Affiliation(s)
- Mariam Lofty Khaled
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, USA.,Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Yelena Bykhovskaya
- Department of Surgery and Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Chunfang Gu
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Alice Liu
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
| | - Michelle D Drewry
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, USA
| | - Zhong Chen
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, USA
| | - Barbara A Mysona
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, USA.,James and Jean Culver Vision Discovery Institute, Augusta University, Augusta, GA, USA
| | - Emily Parker
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, USA
| | - Ryan P McNabb
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
| | - Hongfang Yu
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, USA
| | - Xiaowen Lu
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, USA
| | - Jing Wang
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, USA
| | - Xiaohui Li
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics and Medicine at Harbor-UCLA, Torrance, CA, USA
| | - Abdulrahman Al-Muammar
- Department of Ophthalmology, Glaucoma Research Chair, King Saud University, Riyadh, Saudi Arabia
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics and Medicine at Harbor-UCLA, Torrance, CA, USA
| | - Louise F Porter
- Department of Eye and Vision Science, University of Liverpool, and St Paul's Eye Unit, Royal Liverpool Hospital, Liverpool, UK
| | - Amy Estes
- James and Jean Culver Vision Discovery Institute, Augusta University, Augusta, GA, USA.,Department of Ophthalmology, Augusta University, Augusta, GA, USA
| | - Mitchell A Watsky
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, USA.,James and Jean Culver Vision Discovery Institute, Augusta University, Augusta, GA, USA
| | - Sylvia B Smith
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, USA.,James and Jean Culver Vision Discovery Institute, Augusta University, Augusta, GA, USA.,Department of Ophthalmology, Augusta University, Augusta, GA, USA
| | - Hongyan Xu
- Department of Population Health Science, Augusta University, Augusta, GA, USA
| | - Khaled K Abu-Amero
- Department of Ophthalmology, Glaucoma Research Chair, King Saud University, Riyadh, Saudi Arabia
| | - Anthony Kuo
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
| | - Stephen B Shears
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Yaron S Rabinowitz
- Department of Surgery and Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, USA. .,James and Jean Culver Vision Discovery Institute, Augusta University, Augusta, GA, USA. .,Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA, USA.
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17
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Randall TA, Gu C, Li X, Wang H, Shears SB. A two-way switch for inositol pyrophosphate signaling: Evolutionary history and biological significance of a unique, bifunctional kinase/phosphatase. Adv Biol Regul 2019; 75:100674. [PMID: 31776069 DOI: 10.1016/j.jbior.2019.100674] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 10/30/2019] [Accepted: 11/06/2019] [Indexed: 11/25/2022]
Abstract
The inositol pyrophosphates (PP-InsPs) are a unique subgroup of intracellular signals with diverse functions, many of which can be viewed as reflecting an overarching role in metabolic homeostasis. Thus, considerable attention is paid to the enzymes that synthesize and metabolize the PP-InsPs. One of these enzyme families - the diphosphoinositol pentakisphosphate kinases (PPIP5Ks) - provides an extremely rare example of separate kinase and phosphatase activities being present within the same protein. Herein, we review the current state of structure/function insight into the PPIP5Ks, the separate specialized activities of the two metazoan PPIP5K genes, and we describe a phylogenetic analysis that places PPIP5K evolutionary origin within the Excavata, the very earliest of eukaryotes. These different aspects of PPIP5K biology are placed in the context of a single, overriding question. Why are they bifunctional: i.e., what is the particular significance of the ability to turn PP-InsP signaling on or off from two separate 'switches' in a single protein?
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Affiliation(s)
- Thomas A Randall
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Chunfang Gu
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Xingyao Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Huanchen Wang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Stephen B Shears
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA.
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18
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Rowell TR, Keating JE, Zorn BT, Glish GL, Shears SB, Tarran R. Flavored e-liquids increase cytoplasmic Ca 2+ levels in airway epithelia. Am J Physiol Lung Cell Mol Physiol 2019; 318:L226-L241. [PMID: 31693394 DOI: 10.1152/ajplung.00123.2019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
E-cigarettes are noncombustible, electronic nicotine-delivery devices that aerosolize an e-liquid, i.e., nicotine, in a propylene glycol-vegetable glycerin vehicle that also contains flavors. While the effects of nicotine are relatively well understood, more information regarding the potential biological effects of the other e-liquid constituents is needed. This is a serious concern, because e-liquids are available in >7,000 distinct flavors. We previously demonstrated that many e-liquids affect cell growth/viability through an unknown mechanism. Since Ca2+ is a ubiquitous second messenger that regulates cell growth, we characterized the effects of e-liquids on cellular Ca2+ homeostasis. To better understand the extent of this effect, we screened e-liquids for their ability to alter cytosolic Ca2+ levels and found that 42 of 100 flavored e-liquids elicited a cellular Ca2+ response. Banana Pudding (BP) e-liquid, a representative e-liquid from this group, caused phospholipase C activation, endoplasmic reticulum (ER) Ca2+ release, store-operated Ca2+ entry (SOCE), and protein kinase C (PKCα) phosphorylation. However, longer exposures to BP e-liquid depleted ER Ca2+ stores and inhibited SOCE, suggesting that this e-liquid may alter Ca2+ homeostasis by short- and long-term mechanisms. Since dysregulation of Ca2+ signaling can cause chronic inflammation, ER stress, and abnormal cell growth, flavored e-cigarette products that can elicit cell Ca2+ responses should be further screened for potential toxicity.
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Affiliation(s)
- Temperance R Rowell
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina.,Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina
| | - James E Keating
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina
| | - Bryan T Zorn
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina
| | - Gary L Glish
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina
| | - Stephen B Shears
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Robert Tarran
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina.,Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina
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19
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Riley AM, Wang H, Shears SB, Potter BVL. Synthesis of an α-phosphono-α,α-difluoroacetamide analogue of the diphosphoinositol pentakisphosphate 5-InsP 7. Medchemcomm 2019; 10:1165-1172. [PMID: 31391889 PMCID: PMC6657673 DOI: 10.1039/c9md00163h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/08/2019] [Indexed: 12/16/2022]
Abstract
Diphosphoinositol phosphates (PP-InsPs) are an evolutionarily ancient group of signalling molecules that are essential to cellular and organismal homeostasis. As the detailed mechanisms of PP-InsP signalling begin to emerge, synthetic analogues of PP-InsPs containing stabilised mimics of the labile diphosphate group can provide valuable investigational tools. We synthesised 5-PCF2Am-InsP5 (1), a novel fluorinated phosphonate analogue of 5-PP-InsP5, and obtained an X-ray crystal structure of 1 in complex with diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2). 5-PCF2Am-InsP5 binds to the kinase domain of PPIP5K2 in a similar orientation to that of the natural substrate 5-PP-InsP5 and the PCF2Am structure can mimic many aspects of the diphosphate group in 5-PP-InsP5. We propose that 1, the structural and electronic properties of which are in some ways complementary to those of existing phosphonoacetate and methylenebisphosphonate analogues of 5-PP-InsP5, may be a useful addition to the expanding array of chemical tools for the investigation of signalling by PP-InsPs. The PCF2Am group may also deserve attention for wider application as a diphosphate mimic.
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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 . ; ; Tel: +44 (0)1865 271945
| | - Huanchen Wang
- Inositol Signaling Group , Laboratory of Signal Transduction , National Institute of Environmental Health Sciences , National Institutes of Health , Research Triangle Park , North Carolina , USA
| | - Stephen B Shears
- Inositol Signaling Group , Laboratory of Signal Transduction , National Institute of Environmental Health Sciences , National Institutes of Health , Research Triangle Park , North Carolina , USA
| | - Barry V L Potter
- Medicinal Chemistry and Drug Discovery , Department of Pharmacology , University of Oxford , Mansfield Road , Oxford OX1 3QT , UK . ; ; Tel: +44 (0)1865 271945
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Wang H, Jessen HJ, Shears SB. Comprehensive snapshots of an unusual reaction cycle for an atypical protein tyrosine phosphatases (PTP). FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.493.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Shears SB, Hayakawa Y. Functional Multiplicity of an Insect Cytokine Family Assists Defense Against Environmental Stress. Front Physiol 2019; 10:222. [PMID: 30967784 PMCID: PMC6439351 DOI: 10.3389/fphys.2019.00222] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 02/21/2019] [Indexed: 01/23/2023] Open
Abstract
The widespread distribution of insects over many ecological niches owes much to evolution of multiple mechanisms to defend against environmental stress, especially because their ectothermic nature and small body size render them particularly susceptible to extremes in temperature and water availability. In this review, we will summarize the latest information describing a single, multifunctional cytokine family that is deployed by six orders of insect species to combat a diverse variety of environmental stresses. The originating member of this peptide family was identified in Mythimna (formerly called Pseudaletia) separata armyworm; the cytokine was named growth-blocking peptide (GBP), reflecting its actions in combating parasitic invasion. The peptide’s name has been retained, though the list of its regulatory activities has greatly expanded. All members of this family are small peptides, 19–25 amino acid residues, whose major source is fat body. They are now known to regulate embryonic morphogenesis, larval growth rates, feeding activities, immune responses, nutrition, and aging. In this review, we will describe recent developments in our understanding of the mechanisms of action of the GBP family, but we will also highlight remaining gaps in our knowledge.
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Affiliation(s)
- Stephen B Shears
- Inositol Signalling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, United States
| | - Yoichi Hayakawa
- Department of Applied Biological Sciences, Saga University, Saga, Japan
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23
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Gu C, Stashko MA, Puhl-Rubio AC, Chakraborty M, Chakraborty A, Frye SV, Pearce KH, Wang X, Shears SB, Wang H. Inhibition of Inositol Polyphosphate Kinases by Quercetin and Related Flavonoids: A Structure-Activity Analysis. J Med Chem 2019; 62:1443-1454. [PMID: 30624931 DOI: 10.1021/acs.jmedchem.8b01593] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Dietary flavonoids inhibit certain protein kinases and phospholipid kinases by competing for their ATP-binding sites. These nucleotide pockets have structural elements that are well-conserved in two human small-molecule kinases, inositol hexakisphosphate kinase (IP6K) and inositol polyphosphate multikinase (IPMK), which synthesize multifunctional inositol phosphate cell signals. Herein, we demonstrate that both kinases are inhibited by quercetin and 16 related flavonoids; IP6K is the preferred target. Relative inhibitory activities were rationalized by X-ray analysis of kinase/flavonoid crystal structures; this detailed structure-activity analysis revealed hydrophobic and polar ligand/protein interactions, the degree of flexibility of key amino acid side chains, and the importance of water molecules. The seven most potent IP6K inhibitors were incubated with intact HCT116 cells at concentrations of 2.5 μM; diosmetin was the most selective and effective IP6K inhibitor (>70% reduction in activity). Our data can instruct on pharmacophore properties to assist the future development of inositol phosphate kinase inhibitors. Finally, we propose that dietary flavonoids may inhibit IP6K activity in cells that line the gastrointestinal tract.
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Affiliation(s)
- Chunfang Gu
- Inositol Signaling Group, Signal Transduction Laboratory , National Institute of Environmental Health Sciences , Research Triangle Park , North Carolina 27709 , United States
| | - Michael A Stashko
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Ana C Puhl-Rubio
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Molee Chakraborty
- Department of Pharmacology and Physiology , Saint Louis University School of Medicine , M370, Schwitalla Hall, 1402 South Grand Boulevard , Saint Louis , Missouri 63104 , United States
| | - Anutosh Chakraborty
- Department of Pharmacology and Physiology , Saint Louis University School of Medicine , M370, Schwitalla Hall, 1402 South Grand Boulevard , Saint Louis , Missouri 63104 , United States
| | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Kenneth H Pearce
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Xiaodong Wang
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Stephen B Shears
- Inositol Signaling Group, Signal Transduction Laboratory , National Institute of Environmental Health Sciences , Research Triangle Park , North Carolina 27709 , United States
| | - Huanchen Wang
- Inositol Signaling Group, Signal Transduction Laboratory , National Institute of Environmental Health Sciences , Research Triangle Park , North Carolina 27709 , United States
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24
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Shears SB, Wang H. Inositol phosphate kinases: Expanding the biological significance of the universal core of the protein kinase fold. Adv Biol Regul 2019; 71:118-127. [PMID: 30392847 PMCID: PMC9364425 DOI: 10.1016/j.jbior.2018.10.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/23/2018] [Accepted: 10/26/2018] [Indexed: 05/06/2023]
Abstract
The protein kinase family is characterized by substantial conservation of architectural elements that are required for both ATP binding and phosphotransferase activity. Many of these structural features have also been identified in homologous enzymes that phosphorylate a variety of alternative, non-protein substrates. A comparative structural analysis of these different kinase sub-classes is a portal to a greater understanding of reaction mechanisms, enzyme regulation, inhibitor-development strategies, and superfamily-level evolutionary relationships. To serve such advances, we review structural elements of the protein kinase fold that are conserved in the subfamily of inositol phosphate kinases (InsPKs) that share a PxxxDxKxG catalytic signature: inositol 1,4,5-trisphosphate kinase (IP3K), inositol hexakisphosphate kinase (IP6K), and inositol polyphosphate multikinase (IPMK). We describe conservation of the fundamental two-lobe kinase architecture: an N-lobe constructed upon an anti-parallel β-strand scaffold, which is coupled to a largely helical C-lobe by a single, adenine-binding hinge. This equivalency also includes a G-loop that embraces the β/γ-phosphates of ATP, a transition-state stabilizing residue (Lys/His), and a Mg-positioning aspartate residue within a catalytic triad. Furthermore, we expand this list of conserved structural features to include some not previously identified in InsPKs: a 'gatekeeper' residue in the N-lobe, and an 'αF'-like helix in the C-lobe that anchors two structurally-stabilizing, hydrophobic spines, formed from non-consecutive residues that span the two lobes. We describe how this wide-ranging structural homology can be exploited to develop lead inhibitors of IP6K and IPMK, by using strategies similar to those that have generated ATP-competing inhibitors of protein-kinases. We provide several examples to illustrate how such an approach could benefit human health.
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Affiliation(s)
- Stephen B Shears
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
| | - Huanchen Wang
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
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25
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Sung EJ, Shears SB. A genome-wide dsRNA library screen for Drosophila genes that regulate the GBP/phospholipase C signaling axis that links inflammation to aging. BMC Res Notes 2018; 11:884. [PMID: 30545410 PMCID: PMC6293519 DOI: 10.1186/s13104-018-3996-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/06/2018] [Indexed: 12/16/2022] Open
Abstract
Objective Invertebrates are productive models for understanding how inflammation, metabolism and aging are intertwined. We have deployed a dsRNA library screen to search for genes in Drosophila melanogaster—and hence identify human orthologs—that encode participants in a G-protein coupled, Ca2+-signaling pathway that regulates inflammation, metabolism and lifespan. Results We analyzed receptor-dependent, phospholipase C/Ca2+ signaling responses to the growth-blocking peptide (GBP) cytokine in Drosophila S3 cells plated in 384-well plates containing dsRNAs that target approximately 14,000 Drosophila genes. We used Z-scores of < − 3 or > + 3 to define gene hits. Filtering of ‘housekeeping’ genes from these hits yielded a total of 82 and 61 Drosophila genes that either down-regulate or up-regulate Ca2+-signaling, respectively; representatives from these two groups were validated. Human orthologs of our hits may be modulators of Ca2+ signaling in general, as well as being candidates for acting in molecular pathways that interconnect aging and inflammation.
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Affiliation(s)
- Eui Jae Sung
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, 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, 111 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
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26
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Puhl-Rubio AC, Stashko MA, Wang H, Hardy PB, Tyagi V, Li B, Wang X, Kireev D, Jessen HJ, Frye SV, Shears SB, Pearce KH. Use of Protein Kinase-Focused Compound Libraries for the Discovery of New Inositol Phosphate Kinase Inhibitors. SLAS Discov 2018; 23:982-988. [PMID: 29842835 DOI: 10.1177/2472555218775323] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Inositol hexakisphosphate kinases (IP6Ks) regulate a myriad of cellular processes, not only through their catalytic activity (which synthesizes InsP7, a multifunctional inositol pyrophosphate signaling molecule) but also through protein-protein interactions. To further study the enzymatic function and distinguish between these different mechanisms, specific inhibitors that target IP6K catalytic activity are required. Only one IP6K inhibitor is commonly used: N2-( m-(trifluoromethyl)benzyl) N6-( p-nitrobenzyl)purine (TNP). TNP is, however, compromised by weak potency, inability to distinguish between IP6K isoenzymes, off-target activities, and poor pharmacokinetic properties. Herein, we describe a new inhibitor discovery strategy, based on the high degree of structural conservation of the nucleotide-binding sites of IP6Ks and protein kinases; we screened for novel IP6K2 inhibitors using a focused set of compounds with features known, or computationally predicted, to target nucleotide binding by protein kinases. We developed a time-resolved fluorescence resonance energy transfer (TR-FRET) assay of adenosine diphosphate (ADP) formation from adenosine triphosphate (ATP). Novel hit compounds for IP6K2 were identified and validated with dose-response curves and an orthogonal assay. None of these inhibitors affected another inositol pyrophosphate kinase, PPIP5K. Our screening strategy offers multiple IP6K2 inhibitors for future development and optimization. This approach will be applicable to inhibitor discovery campaigns for other inositol phosphate kinases.
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Affiliation(s)
- Ana C Puhl-Rubio
- 1 Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Michael A Stashko
- 1 Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Huanchen Wang
- 2 Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - P Brian Hardy
- 1 Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Vikas Tyagi
- 1 Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.,4 School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology (TIET), Patiala, Punjab, India
| | - Bing Li
- 1 Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Xiaodong Wang
- 1 Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Dmitri Kireev
- 1 Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Henning J Jessen
- 3 Institute of Organic Chemistry, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Stephen V Frye
- 1 Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Stephen B Shears
- 2 Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Kenneth H Pearce
- 1 Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
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27
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Rajasekaran SS, Kim J, Gaboardi GC, Gromada J, Shears SB, Dos Santos KT, Nolasco EL, de Souza Ferreira S, Illies C, Köhler M, Gu C, Ryu SH, Martins JO, Darè E, Barker CJ, Berggren PO. Corrigendum to 'Inositol hexakisphosphate kinase 1 is a metabolic sensor in pancreatic β-cells' [Cellular Signalling 46 (2018) 120-128]. Cell Signal 2018; 53:415. [PMID: 29807098 PMCID: PMC6293315 DOI: 10.1016/j.cellsig.2018.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Subu Surendran Rajasekaran
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Jaeyoon Kim
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gian-Carlo Gaboardi
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | | | - Stephen B Shears
- Signal Transduction Laboratory, Inositol Signaling Group, NIEHS, Building 101, Room F239, 111T.W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Karen Tiago Dos Santos
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden; Laboratory of Immunoendocrinology, Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Eduardo Lima Nolasco
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden; Laboratory of Immunoendocrinology, Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Sabrina de Souza Ferreira
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden; Laboratory of Immunoendocrinology, Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Christopher Illies
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Martin Köhler
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Chunfang Gu
- Signal Transduction Laboratory, Inositol Signaling Group, NIEHS, Building 101, Room F239, 111T.W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Sung Ho Ryu
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Joilson O Martins
- Laboratory of Immunoendocrinology, Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Elisabetta Darè
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Christopher J Barker
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden.
| | - Per-Olof Berggren
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.
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28
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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29
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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30
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Sahu S, Gu C, Shears SB. Role of 5‐IP
7
in the Regulation of Gene Expression. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.533.86] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Soumyadip Sahu
- Inositol Signaling GroupSignal Transduction LaboratoryThe National Institute of Environmental Health Sciences (NIEHS/NIH)Research Triangle ParkNC
| | - Chunfang Gu
- Inositol Signaling GroupSignal Transduction LaboratoryThe National Institute of Environmental Health Sciences (NIEHS/NIH)Research Triangle ParkNC
| | - Stephen B. Shears
- Inositol Signaling GroupSignal Transduction LaboratoryThe National Institute of Environmental Health Sciences (NIEHS/NIH)Research Triangle ParkNC
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31
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Yousaf R, Gu C, Ahmed ZM, Khan SN, Friedman TB, Riazuddin S, Shears SB, Riazuddin S. Mutations in Diphosphoinositol-Pentakisphosphate Kinase PPIP5K2 are associated with hearing loss in human and mouse. PLoS Genet 2018; 14:e1007297. [PMID: 29590114 PMCID: PMC5891075 DOI: 10.1371/journal.pgen.1007297] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 04/09/2018] [Accepted: 03/06/2018] [Indexed: 01/07/2023] Open
Abstract
Autosomal recessive nonsyndromic hearing loss is a genetically heterogeneous disorder. Here, we report a severe-to-profound sensorineural hearing loss locus, DFNB100 on chromosome 5q13.2-q23.2. Exome enrichment followed by massive parallel sequencing revealed a c.2510G>A transition variant in PPIP5K2 that segregated with DFNB100-associated hearing loss in two large apparently unrelated Pakistani families. PPIP5Ks enzymes interconvert 5-IP7 and IP8, two key members of the inositol pyrophosphate (PP-IP) cell-signaling family. Their actions at the interface of cell signaling and bioenergetic homeostasis can impact many biological processes. The c.2510G>A transition variant is predicted to substitute a highly invariant arginine residue with histidine (p.Arg837His) in the phosphatase domain of PPIP5K2. Biochemical studies revealed that the p.Arg837His variant reduces the phosphatase activity of PPIP5K2 and elevates its kinase activity. We found that in mouse inner ear, PPIP5K2 is expressed in the cochlear and vestibular sensory hair cells, supporting cells and spiral ganglion neurons. Mice homozygous for a targeted deletion of the Ppip5k2 phosphatase domain exhibit degeneration of cochlear outer hair cells and elevated hearing thresholds. Our demonstration that PPIP5K2 has a role in hearing in humans indicates that PP-IP signaling is important to hair cell maintenance and function within inner ear. Exome sequencing coupled with homozygosity mapping was used to identify a missense variant [c.2510G>A; p.(Arg837His)] in PPIP5K2 at the DFNB100 locus that is associated with nonsyndromic, prelingual sensorineural deafness in two large consanguineous Pakistani families. PPIP5Ks are pivotal enzymes for regulating inositol pyrophosphate (PP-IP) turnover. Biochemical analyses revealed that, compared to wild type human PPIP5K2, the PPIP5K2R837H variant exhibited lower phosphatase activity and higher kinase activity, indicating that it promotes increased metabolic flux from 5-IP7 to IP8 in vivo. In rodent inner ears, PPIP5K2 immunoreactivity was observed in the cochlear and vestibular hair cells, supporting cells, and spiral ganglion neurons. Mouse mutants homozygous for the targeted deletion of Ppip5k2 phosphatase domain exhibit degeneration of cochlear outer hair cells and progressive hearing loss. Our work provides the first description of any amino acid variant of PPIP5K2 that is both functionally-significant and associates with a human disorder. The ‘futile cycling’ of the kinase/phosphatase activity of PPIP5K2 makes inner ear function particularly susceptible to even minor changes in the phosphatase activity of PPIP5K2. We have shown that a pathogenic variant in PPIP5K2 is associated with hearing loss in humans. Thus, PPIP5K2 is given new clinical significance by our observations.
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Affiliation(s)
- Rizwan Yousaf
- Laboratory of Molecular Genetics, Department of Otorhinolaryngology-Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, United States of America
| | - Chunfang Gu
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States of America
| | - Zubair M. Ahmed
- Laboratory of Neurogenetics and Regenerative Medicine, Department of Otorhinolaryngology-Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, United States of America
| | - Shaheen N. Khan
- National Center for Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Thomas B. Friedman
- Section on Human Genetics, Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, United States of America
| | - Sheikh Riazuddin
- Shaheed Zulfiqar Ali Bhutto Medical University, Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - Stephen B. Shears
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States of America
| | - Saima Riazuddin
- Laboratory of Molecular Genetics, Department of Otorhinolaryngology-Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, United States of America
- * E-mail:
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Rajasekaran SS, Kim J, Gaboardi GC, Gromada J, Shears SB, Dos Santos KT, Nolasco EL, Ferreira SDS, Illies C, Köhler M, Gu C, Ryu SH, Martins JO, Darè E, Barker CJ, Berggren PO. Inositol hexakisphosphate kinase 1 is a metabolic sensor in pancreatic β-cells. Cell Signal 2018. [PMID: 29522819 PMCID: PMC5899964 DOI: 10.1016/j.cellsig.2018.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Diphosphoinositol pentakisphosphate (IP7) is critical for the exocytotic capacity of the pancreatic β-cell, but its regulation by the primary instigator of β-cell exocytosis, glucose, is unknown. The high Km for ATP of the IP7-generating enzymes, the inositol hexakisphosphate kinases (IP6K1 and 2) suggests that these enzymes might serve as metabolic sensors in insulin secreting β-cells and act as translators of disrupted metabolism in diabetes. We investigated this hypothesis and now show that glucose stimulation, which increases the ATP/ADP ratio, leads to an early rise in IP7 concentration in β-cells. RNAi mediated knock down of the IP6K1 isoform inhibits both glucose-mediated increase in IP7 and first phase insulin secretion, demonstrating that IP6K1 integrates glucose metabolism and insulin exocytosis. In diabetic mouse islets the deranged ATP/ADP levels under both basal and glucose-stimulated conditions are mirrored in both disrupted IP7 generation and insulin release. Thus the unique metabolic sensing properties of IP6K1 guarantees appropriate concentrations of IP7 and thereby both correct basal insulin secretion and intact first phase insulin release. In addition, our data suggest that a specific cell signaling defect, namely, inappropriate IP7 generation may be an essential convergence point integrating multiple metabolic defects into the commonly observed phenotype in diabetes. Glucose increases IP7 levels transiently through IP6K1 in pancreatic β-cells. IP6K1 decodes glucose-driven increases in ATP/ADP ratio into 1st phase insulin release. IP7 production and insulin release mirror perturbed metabolism in diabetic islets. IP6K1 acts as a β-cell metabolic sensor under normal and pathological conditions.
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Affiliation(s)
- Subu Surendran Rajasekaran
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Jaeyoon Kim
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gian-Carlo Gaboardi
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | | | - Stephen B Shears
- Signal Transduction Laboratory/Inositol Signaling Group, NIEHS, Building 101, Room F239,111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Karen Tiago Dos Santos
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden; Laboratory of Immunoendocrinology, Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Eduardo Lima Nolasco
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden; Laboratory of Immunoendocrinology, Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Sabrina de Souza Ferreira
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden; Laboratory of Immunoendocrinology, Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Christopher Illies
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Martin Köhler
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Chunfang Gu
- Signal Transduction Laboratory/Inositol Signaling Group, NIEHS, Building 101, Room F239,111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Sung Ho Ryu
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Joilson O Martins
- Laboratory of Immunoendocrinology, Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Elisabetta Darè
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Christopher J Barker
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden.
| | - Per-Olof Berggren
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.
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Shears SB, Hayakawa Y. The Drosophila cytokine, GBP: A model that illuminates the yin-yang of inflammation and longevity in humans? Cytokine 2018; 110:298-300. [PMID: 29456061 DOI: 10.1016/j.cyto.2018.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 02/09/2018] [Indexed: 01/04/2023]
Abstract
Our laboratories have determined that the Drosophila cytokine, Growth-blocking peptide (GBP), mediates its biological effects through the Mthl10 G-protein coupled receptor. In this Cytokine Stimulus, we discuss the functional plasticity of the GBP/Mthl10 axis, and we propose that conserved components of this regulatory network may be relevant to human health.
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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, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA.
| | - Yoichi Hayakawa
- Department of Applied Biological Sciences, Saga University, Saga 840-8502, Japan.
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Rajasekaran SS, Illies C, Shears SB, Wang H, Ayala TS, Martins JO, Daré E, Berggren PO, Barker CJ. Protein kinase- and lipase inhibitors of inositide metabolism deplete IP 7 indirectly in pancreatic β-cells: Off-target effects on cellular bioenergetics and direct effects on IP6K activity. Cell Signal 2017; 42:127-133. [PMID: 29042286 PMCID: PMC5765549 DOI: 10.1016/j.cellsig.2017.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 10/11/2017] [Accepted: 10/13/2017] [Indexed: 12/22/2022]
Abstract
Inositol pyrophosphates have emerged as important regulators of many critical cellular processes from vesicle trafficking and cytoskeletal rearrangement to telomere length regulation and apoptosis. We have previously demonstrated that 5-di-phosphoinositol pentakisphosphate, IP7, is at a high level in pancreatic β-cells and is important for insulin exocytosis. To better understand IP7 regulation in β-cells, we used an insulin secreting cell line, HIT-T15, to screen a number of different pharmacological inhibitors of inositide metabolism for their impact on cellular IP7. Although the inhibitors have diverse targets, they all perturbed IP7 levels. This made us suspicious that indirect, off-target effects of the inhibitors could be involved. It is known that IP7 levels are decreased by metabolic poisons. The fact that the inositol hexakisphosphate kinases (IP6Ks) have a high Km for ATP makes IP7 synthesis potentially vulnerable to ATP depletion. Furthermore, many kinase inhibitors are targeted to the ATP binding site of kinases, but given the similarity of such sites, high specificity is difficult to achieve. Here, we show that IP7 concentrations in HIT-T15 cells were reduced by inhibitors of PI3K (wortmannin, LY294002), PI4K (Phenylarsine Oxide, PAO), PLC (U73122) and the insulin receptor (HNMPA). Each of these inhibitors also decreased the ATP/ADP ratio. Thus reagents that compromise energy metabolism reduce IP7 indirectly. Additionally, PAO, U73122 and LY294002 also directly inhibited the activity of purified IP6K. These data are of particular concern for those studying signal transduction in pancreatic β-cells, but also highlight the fact that employment of these inhibitors could have erroneously suggested the involvement of key signal transduction pathways in various cellular processes. Conversely, IP7’s role in cellular signal transduction is likely to have been underestimated. In pancreatic β-cells several inhibitors of signal transduction reduce IP7 levels. There is a positive correlation between IP7 reduction and decrease in ATP/ADP. Inhibitors deplete IP7 levels indirectly by decreasing ATP/ADP levels. Some purportedly specific cell-signaling inhibitors directly target IP6K activity. Caution is required in interpreting data obtained using inhibitors of inositide metabolism.
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Affiliation(s)
- Subu Surendran Rajasekaran
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Christopher Illies
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Stephen B Shears
- Signal Transduction Laboratory/Inositol Signaling Group, NIEHS, Building 101, Room F239, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Huanchen Wang
- Signal Transduction Laboratory/Inositol Signaling Group, NIEHS, Building 101, Room F239, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Thais S Ayala
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden; Laboratory of Immunoendocrinology, Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Joilson O Martins
- Laboratory of Immunoendocrinology, Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Elisabetta Daré
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Per-Olof Berggren
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden.
| | - Christopher J Barker
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden.
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Wang H, Shears SB. Structural features of human inositol phosphate multikinase rationalize its inositol phosphate kinase and phosphoinositide 3-kinase activities. J Biol Chem 2017; 292:18192-18202. [PMID: 28882892 DOI: 10.1074/jbc.m117.801845] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 09/01/2017] [Indexed: 01/17/2023] Open
Abstract
Human inositol phosphate multikinase (HsIPMK) critically contributes to intracellular signaling through its inositol-1,4,5-trisphosphate (Ins(1,4,5)P3) 3-kinase and phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) 3-kinase activities. This catalytic profile is not conserved; orthologs from Arabidopsis thaliana and Saccharomyces cerevisiae are predominantly Ins(1,4,5)P3 6-kinases, and the plant enzyme cannot phosphorylate PtdIns(4,5)P2 Therefore, crystallographic analysis of the yeast and plant enzymes, without bound inositol phosphates, do not structurally rationalize HsIPMK activities. Here, we present 1.6-Å resolution crystal structures of HsIPMK in complex with either Ins(1,4,5)P3 or PtdIns(4,5)P2 The Ins(1,4,5)P3 headgroup of PtdIns(4,5)P2 binds in precisely the same orientation as free Ins(1,4,5)P3 itself, indicative of evolutionary optimization of 3-kinase activities against both substrates. We report on nucleotide binding between the separate N- and C-lobes of HsIPMK. The N-lobe exhibits a remarkable degree of conservation with protein kinase A (root mean square deviation = 1.8 Å), indicating common ancestry. We also describe structural features unique to HsIPMK. First, we observed a constrained, horseshoe-shaped substrate pocket, formed from an α-helix, a 310 helix, and a recently evolved tri-proline loop. We further found HsIPMK activities rely on a preponderance of Gln residues, in contrast to the larger Lys and Arg residues in yeast and plant orthologs. These conclusions are supported by analyzing 14 single-site HsIPMK mutants, some of which differentially affect 3-kinase and 6-kinase activities. Overall, we structurally rationalize phosphorylation of Ins(1,4,5)P3 and PtdIns(4,5)P2 by HsIPMK.
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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
| | - 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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Baughman BM, Wang H, An Y, Kireev D, Stashko MA, Jessen HJ, Pearce KH, Frye SV, Shears SB. Retraction: A High-Throughput Screening-Compatible Strategy for the Identification of Inositol Pyrophosphate Kinase Inhibitors. PLoS One 2017. [PMID: 28636659 PMCID: PMC5479587 DOI: 10.1371/journal.pone.0180272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Gu C, Nguyen HN, Hofer A, Jessen HJ, Dai X, Wang H, Shears SB. The Significance of the Bifunctional Kinase/Phosphatase Activities of Diphosphoinositol Pentakisphosphate Kinases (PPIP5Ks) for Coupling Inositol Pyrophosphate Cell Signaling to Cellular Phosphate Homeostasis. J Biol Chem 2017; 292:4544-4555. [PMID: 28126903 PMCID: PMC5377771 DOI: 10.1074/jbc.m116.765743] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/25/2017] [Indexed: 12/31/2022] Open
Abstract
Proteins responsible for Pi homeostasis are critical for all life. In Saccharomyces cerevisiae, extracellular [Pi] is "sensed" by the inositol-hexakisphosphate kinase (IP6K) that synthesizes the intracellular inositol pyrophosphate 5-diphosphoinositol 1,2,3,4,6-pentakisphosphate (5-InsP7) as follows: during a period of Pi starvation, there is a decline in cellular [ATP]; the unusually low affinity of IP6Ks for ATP compels 5-InsP7 levels to fall in parallel (Azevedo, C., and Saiardi, A. (2017) Trends. Biochem. Sci. 42, 219-231. Hitherto, such Pi sensing has not been documented in metazoans. Here, using a human intestinal epithelial cell line (HCT116), we show that levels of both 5-InsP7 and ATP decrease upon [Pi] starvation and subsequently recover during Pi replenishment. However, a separate inositol pyrophosphate, 1,5-bisdiphosphoinositol 2,3,4,6-tetrakisphosphate (InsP8), reacts more dramatically (i.e. with a wider dynamic range and greater sensitivity). To understand this novel InsP8 response, we characterized kinetic properties of the bifunctional 5-InsP7 kinase/InsP8 phosphatase activities of full-length diphosphoinositol pentakisphosphate kinases (PPIP5Ks). These data fulfil previously published criteria for any bifunctional kinase/phosphatase to exhibit concentration robustness, permitting levels of the kinase product (InsP8 in this case) to fluctuate independently of varying precursor (i.e. 5-InsP7) pool size. Moreover, we report that InsP8 phosphatase activities of PPIP5Ks are strongly inhibited by Pi (40-90% within the 0-1 mm range). For PPIP5K2, Pi sensing by InsP8 is amplified by a 2-fold activation of 5-InsP7 kinase activity by Pi within the 0-5 mm range. Overall, our data reveal mechanisms that can contribute to specificity in inositol pyrophosphate signaling, regulating InsP8 turnover independently of 5-InsP7, in response to fluctuations in extracellular supply of a key nutrient.
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Affiliation(s)
- Chunfang Gu
- From the Laboratory of Signal Transduction, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, 27709
| | - Hoai-Nghia Nguyen
- From the Laboratory of Signal Transduction, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, 27709
| | - Alexandre Hofer
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Henning J Jessen
- Institute of Organic Chemistry, Albert Ludwigs University, Albertstrasse 21, 79104 Freiburg, Germany, and
| | - Xuming Dai
- Division of Cardiology, McAllister Heart Institute, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Huanchen Wang
- From the Laboratory of Signal Transduction, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, 27709
| | - Stephen B Shears
- From the Laboratory of Signal Transduction, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, 27709,
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Shears SB, Baughman BM, Gu C, Nair VS, Wang H. The significance of the 1-kinase/1-phosphatase activities of the PPIP5K family. Adv Biol Regul 2016; 63:98-106. [PMID: 27776974 DOI: 10.1016/j.jbior.2016.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 10/13/2016] [Accepted: 10/15/2016] [Indexed: 01/29/2023]
Abstract
The inositol pyrophosphates (diphosphoinositol polyphosphates), which include 1-InsP7, 5-InsP7, and InsP8, are highly 'energetic' signaling molecules that play important roles in many cellular processes, particularly with regards to phosphate and bioenergetic homeostasis. Two classes of kinases synthesize the PP-InsPs: IP6Ks and PPIP5Ks. The significance of the IP6Ks - and their 5-InsP7 product - has been widely reported. However, relatively little is known about the biological significance of the PPIP5Ks. The purpose of this review is to provide an update on developments in our understanding of key features of the PPIP5Ks, which we believe strengthens the hypothesis that their catalytic activities serve important cellular functions. Central to this discussion is the recent discovery that the PPIP5K is a rare example of a single protein that catalyzes a kinase/phosphatase futile cycle.
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Affiliation(s)
- 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, NC, 27709, USA.
| | - Brandi M Baughman
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Chunfang Gu
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Vasudha S Nair
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Huanchen Wang
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
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Baughman BM, Wang H, An Y, Kireev D, Stashko MA, Jessen HJ, Pearce KH, Frye SV, Shears SB. A High-Throughput Screening-Compatible Strategy for the Identification of Inositol Pyrophosphate Kinase Inhibitors. PLoS One 2016; 11:e0164378. [PMID: 27736936 PMCID: PMC5063353 DOI: 10.1371/journal.pone.0164378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/24/2016] [Indexed: 11/22/2022] Open
Abstract
Pharmacological tools-'chemical probes'-that intervene in cell signaling cascades are important for complementing genetically-based experimental approaches. Probe development frequently begins with a high-throughput screen (HTS) of a chemical library. Herein, we describe the design, validation, and implementation of the first HTS-compatible strategy against any inositol phosphate kinase. Our target enzyme, PPIP5K, synthesizes 'high-energy' inositol pyrophosphates (PP-InsPs), which regulate cell function at the interface between cellular energy metabolism and signal transduction. We optimized a time-resolved, fluorescence resonance energy transfer ADP-assay to record PPIP5K-catalyzed, ATP-driven phosphorylation of 5-InsP7 to 1,5-InsP8 in 384-well format (Z' = 0.82 ± 0.06). We screened a library of 4745 compounds, all anticipated to be membrane-permeant, which are known-or conjectured based on their structures-to target the nucleotide binding site of protein kinases. At a screening concentration of 13 μM, fifteen compounds inhibited PPIP5K >50%. The potency of nine of these hits was confirmed by dose-response analyses. Three of these molecules were selected from different structural clusters for analysis of binding to PPIP5K, using isothermal calorimetry. Acceptable thermograms were obtained for two compounds, UNC10112646 (Kd = 7.30 ± 0.03 μM) and UNC10225498 (Kd = 1.37 ± 0.03 μM). These Kd values lie within the 1-10 μM range generally recognized as suitable for further probe development. In silico docking data rationalizes the difference in affinities. HPLC analysis confirmed that UNC10225498 and UNC10112646 directly inhibit PPIP5K-catalyzed phosphorylation of 5-InsP7 to 1,5-InsP8; kinetic experiments showed inhibition to be competitive with ATP. No other biological activity has previously been ascribed to either UNC10225498 or UNC10112646; moreover, at 10 μM, neither compound inhibits IP6K2, a structurally-unrelated PP-InsP kinase. Our screening strategy may be generally applicable to inhibitor discovery campaigns for other inositol phosphate kinases.
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Affiliation(s)
- Brandi M. Baughman
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Huanchen Wang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Yi An
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Michael A. Stashko
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Henning J. Jessen
- Institute of Organic Chemistry, Albert-Ludwigs-University of Freiburg, Freiburg 79104, Germany
| | - Kenneth H. Pearce
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Stephen B. Shears
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Wang H, Nair VS, Holland AA, Capolicchio S, Jessen HJ, Johnson MK, Shears SB. Asp1 from Schizosaccharomyces pombe binds a [2Fe-2S](2+) cluster which inhibits inositol pyrophosphate 1-phosphatase activity. Biochemistry 2015; 54:6462-74. [PMID: 26422458 DOI: 10.1021/acs.biochem.5b00532] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iron-sulfur (Fe-S) clusters are widely distributed protein cofactors that are vital to cellular biochemistry and the maintenance of bioenergetic homeostasis, but to our knowledge, they have never been identified in any phosphatase. Here, we describe an iron-sulfur cluster in Asp1, a dual-function kinase/phosphatase that regulates cell morphogenesis in Schizosaccharomyces pombe. Full-length Asp1, and its phosphatase domain (Asp1(371-920)), were each heterologously expressed in Escherichia coli. The phosphatase activity is exquisitely specific: it hydrolyzes the 1-diphosphate from just two members of the inositol pyrophosphate (PP-InsP) signaling family, namely, 1-InsP7 and 1,5-InsP8. We demonstrate that Asp1 does not hydrolyze either InsP6, 2-InsP7, 3-InsP7, 4-InsP7, 5-InsP7, 6-InsP7, or 3,5-InsP8. We also recorded 1-phosphatase activity in a human homologue of Asp1, hPPIP5K1, which was heterologously expressed in Drosophila S3 cells with a biotinylated N-terminal tag, and then isolated from cell lysates with avidin beads. Purified, recombinant Asp1(371-920) contained iron and acid-labile sulfide, but the stoichiometry (0.8 atoms of each per protein molecule) indicates incomplete iron-sulfur cluster assembly. We reconstituted the Fe-S cluster in vitro under anaerobic conditions, which increased the stoichiometry to approximately 2 atoms of iron and acid-labile sulfide per Asp1 molecule. The presence of a [2Fe-2S](2+) cluster in Asp1(371-920) was demonstrated by UV-visible absorption, resonance Raman spectroscopy, and electron paramagnetic resonance spectroscopy. We determined that this [2Fe-2S](2+) cluster is unlikely to participate in redox chemistry, since it rapidly degraded upon reduction by dithionite. Biochemical and mutagenic studies demonstrated that the [2Fe-2S](2+) cluster substantially inhibits the phosphatase activity of Asp1, thereby increasing its net kinase activity.
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Affiliation(s)
- Huanchen Wang
- 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
| | - Vasudha S Nair
- 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
| | - Ashley A Holland
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia , Athens, Georgia 30602, United States
| | - Samanta Capolicchio
- Department of Chemistry, University of Zurich (UZH) , Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Henning J Jessen
- Department of Chemistry, University of Zurich (UZH) , Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Michael K Johnson
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia , Athens, Georgia 30602, United States
| | - 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
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Riley AM, Wang H, Shears SB, L. Potter BV. Synthetic tools for studying the chemical biology of InsP8. Chem Commun (Camb) 2015; 51:12605-8. [PMID: 26153667 PMCID: PMC4643724 DOI: 10.1039/c5cc05017k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 07/03/2015] [Indexed: 12/28/2022]
Abstract
To synthesise stabilised mimics of InsP8, the most phosphorylated inositol phosphate signalling molecule in Nature, we replaced its two diphosphate (PP) groups with either phosphonoacetate (PA) or methylenebisphosphonate (PCP) groups. Utility of the PA and PCP analogues was verified by structural and biochemical analyses of their interactions with enzymes of InsP8 metabolism.
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Affiliation(s)
- Andrew M. Riley
- Wolfson Laboratory of Medicinal Chemistry , Department of Pharmacy and Pharmacology , University of Bath , Claverton Down , Bath , BA2 7AY , UK
| | - Huanchen Wang
- Inositol Signaling Group , Laboratory of Signal Transduction , National Institute of Environmental Health Sciences , National Institutes of Health , Research Triangle Park , North Carolina , USA
| | - Stephen B. Shears
- Inositol Signaling Group , Laboratory of Signal Transduction , National Institute of Environmental Health Sciences , National Institutes of Health , Research Triangle Park , North Carolina , USA
| | - Barry V. L. Potter
- Wolfson Laboratory of Medicinal Chemistry , Department of Pharmacy and Pharmacology , University of Bath , Claverton Down , Bath , BA2 7AY , UK
- Department of Pharmacology , University of Oxford , Mansfield Road , Oxford , OX1 3QT , UK . ; Fax: +44-1865-271853 ; Tel: +44-1865-271945
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Yong ST, Nguyen HN, Choi JH, Bortner CD, Williams J, Pulloor NK, Krishnan MN, Shears SB. Identification of a functional nuclear translocation sequence in hPPIP5K2. BMC Cell Biol 2015; 16:17. [PMID: 26084399 PMCID: PMC4472268 DOI: 10.1186/s12860-015-0063-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 05/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cells contain several inositol pyrophosphates (PP-InsPs; also known as diphosphoinositol polyphosphates), which play pivotal roles in cellular and organismic homeostasis. It has been proposed that determining mechanisms of compartmentation of the synthesis of a particular PP-InsP is key to understanding how each of them may exert a specific function. Human PPIP5K2 (hPPIP5K2), one of the key enzymes that synthesizes PP-InsPs, contains a putative consensus sequence for a nuclear localization signal (NLS). However, such in silico analysis has limited predictive power, and may be complicated by phosphorylation events that can dynamically modulate NLS function. We investigated if this candidate NLS is functional and regulated, using the techniques of cell biology, mutagenesis and mass spectrometry. RESULTS Multiple sequence alignments revealed that the metazoan PPIP5K2 family contains a candidate NLS within a strikingly well-conserved 63 amino-acid domain. By analyzing the distribution of hPPIP5K2-GFP in HEK293T cells with the techniques of confocal microscopy and imaging flow cytometry, we found that a distinct pool of hPPIP5K2 is present in the nucleus. Imaging flow cytometry yielded particular insight into the characteristics of the nuclear hPPIP5K2 sub-pool, through a high-throughput, statistically-robust analysis of many hundreds of cells. Mutagenic disruption of the candidate NLS in hPPIP5K2 reduced its degree of nuclear localization. Proximal to the NLS is a Ser residue (S1006) that mass spectrometry data indicate is phosphorylated inside cells. The degree of nuclear localization of hPPIP5K2 was increased when S1006 was rendered non-phosphorylatable by its mutation to Ala. Conversely, a S1006D phosphomimetic mutant of hPPIP5K2 exhibited a lower degree of nuclear localization. CONCLUSIONS The current study describes for the first time the functional significance of an NLS in the conserved PPIP5K2 family. We have further demonstrated that there is phosphorylation of a Ser residue that is proximal to the NLS of hPPIP5K2. These conclusions draw attention to nuclear compartmentation of PPIP5K2 as being a physiologically relevant and covalently-regulated event. Our study also increases general insight into the consensus sequences of other NLSs, the functions of which might be similarly regulated.
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Affiliation(s)
- Sheila T Yong
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
| | - Hoai-Nghia Nguyen
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
| | - Jae H Choi
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA. .,Current address: Thermo Fisher Scientific, LSG/Biosciences Division, 3747 N. Meridian Drive, Rockford, IL, 61101, USA.
| | - Carl D Bortner
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
| | - Jason Williams
- Protein Microcharacterization Core Facility, Mass Spectrometry Group, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
| | - Niyas K Pulloor
- Program on Emerging Infectious Diseases, DUKE-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Republic of Singapore.
| | - Manoj N Krishnan
- Program on Emerging Infectious Diseases, DUKE-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Republic of Singapore.
| | - 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, NC, 27709, USA.
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Abstract
The inositol pyrophosphates (PP-InsPs) are a specialized group of "energetic" signaling molecules found in yeasts, plants and animals. PP-InsPs boast the most crowded three dimensional phosphate arrays found in Nature; multiple phosphates and diphosphates are crammed around the six-carbon, inositol ring. Yet, phosphate esters are also a major energy currency in cells. So the synthesis of PP-InsPs, and the maintenance of their levels in the face of a high rate of ongoing turnover, all requires significant bioenergetic input. What are the particular properties of PP-InsPs that repay this investment of cellular energy? Potential answers to that question are discussed here, against the backdrop of a recent hypothesis that signaling by PP-InsPs is evolutionarily ancient. The latter idea is extended herein, with the proposal that the primordial origins of PP-InsPs is reflected in the apparent lack of isomeric specificity of certain of their actions. Nevertheless, there are other aspects of signaling by these polyphosphates that are more selective for a particular PP-InsP isomer. Consideration of the nature of both specific and non-specific effects of PP-InsPs can help rationalize why such molecules possess so many phosphates.
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Affiliation(s)
- Stephen B Shears
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, NIH, DHHS, PO Box 12233, Research Triangle Park, NC 27709, USA.
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47
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Capolicchio S, Wang H, Thakor DT, Shears SB, Jessen HJ. Synthesis of densely phosphorylated bis-1,5-diphospho-myo-inositol tetrakisphosphate and its enantiomer by bidirectional P-anhydride formation. Angew Chem Int Ed Engl 2014; 53:9508-11. [PMID: 25044992 PMCID: PMC4153399 DOI: 10.1002/anie.201404398] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 05/23/2014] [Indexed: 11/06/2022]
Abstract
The ubiquitous mammalian signaling molecule bis-diphosphoinositol tetrakisphosphate (1,5-(PP)2 -myo-InsP4 , or InsP8 ) displays the most congested three-dimensional array of phosphate groups found in nature. The high charge density, the accumulation of unstable P-anhydrides and P-esters, the lack of UV absorbance, and low levels of optical rotation constitute severe obstacles to its synthesis, characterization, and purification. Herein, we describe the first procedure for the synthesis of enantiopure 1,5-(PP)2 -myo-InsP4 and 3,5-(PP)2 -myo-InsP4 utilizing a C2 -symmetric P-amidite for desymmetrization and concomitant phosphitylation followed by a one-pot bidirectional P-anhydride-forming reaction that combines sixteen chemical transformations with high efficiency. The configuration of these materials is unambiguously shown by subsequent X-ray analyses of both enantiomers after being individually soaked into crystals of the kinase domain of human diphosphoinositol pentakisphosphate kinase 2.
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Affiliation(s)
- Samanta Capolicchio
- Department of Chemistry, University of Zürich (UZH), Winterthurerstrasse 190, 8057 Zürich (Switzerland)
| | - Huanchen Wang
- Inositol Signaling Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC (USA)
| | - Divyeshsinh T. Thakor
- Department of Chemistry University of Zürich (UZH) Winterthurerstrasse 190, 8057 Zürich (Switzerland)
| | - Stephen B. Shears
- Inositol Signaling Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC (USA)
| | - Henning J. Jessen
- Department of Chemistry University of Zürich (UZH) Winterthurerstrasse 190, 8057 Zürich (Switzerland)
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48
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Tsuzuki S, Matsumoto H, Furihata S, Ryuda M, Tanaka H, Sung EJ, Bird GS, Zhou Y, Shears SB, Hayakawa Y. Switching between humoral and cellular immune responses in Drosophila is guided by the cytokine GBP. Nat Commun 2014; 5:4628. [PMID: 25130174 DOI: 10.1038/ncomms5628] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 07/08/2014] [Indexed: 11/09/2022] Open
Abstract
Insects combat infection through carefully measured cellular (for example, phagocytosis) and humoral (for example, secretion of antimicrobial peptides (AMPs)) innate immune responses. Little is known concerning how these different defense mechanisms are coordinated. Here, we use insect plasmatocytes and hemocyte-like Drosophila S2 cells to characterize mechanisms of immunity that operate in the haemocoel. We demonstrate that a Drosophila cytokine, growth-blocking peptides (GBP), acts through the phospholipase C (PLC)/Ca(2+) signalling cascade to mediate the secretion of Pvf, a ligand for platelet-derived growth factor- and vascular endothelial growth factor-receptor (Pvr) homologue. Activated Pvr recruits extracellular signal-regulated protein kinase to inhibit humoral immune responses, while stimulating cell 'spreading', an initiating event in cellular immunity. The double-stranded RNA (dsRNA)-targeted knockdown of either Pvf2 or Pvr inhibits GBP-mediated cell spreading and activates AMP expression. Conversely, Pvf2 overexpression enhances cell spreading but inhibits AMP expression. Thus, we describe mechanisms to initiate immune programs that are either humoral or cellular in nature, but not both; such immunophysiological polarization may minimize homeostatic imbalance during infection.
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Affiliation(s)
- Seiji Tsuzuki
- 1] Department of Applied Biological Sciences, Saga University, Saga 840-8502, Japan [2]
| | - Hitoshi Matsumoto
- 1] Department of Applied Biological Sciences, Saga University, Saga 840-8502, Japan [2]
| | - Shunsuke Furihata
- Department of Applied Biological Sciences, Saga University, Saga 840-8502, Japan
| | - Masasuke Ryuda
- Department of Applied Biological Sciences, Saga University, Saga 840-8502, Japan
| | - Hirotoshi Tanaka
- Department of Applied Biological Sciences, Saga University, Saga 840-8502, Japan
| | - Eui Jae Sung
- Inositol Signaling Section, NIEHS, NIH, DHHS, Research Triangle Park, North Carolina 27709, USA
| | - Gary S Bird
- 1] Inositol Signaling Section, NIEHS, NIH, DHHS, Research Triangle Park, North Carolina 27709, USA [2] Calcium Regulation Section, NIEHS, NIH, DHHS, Research Triangle Park, North Carolina 27709, USA
| | - Yixing Zhou
- Inositol Signaling Section, NIEHS, NIH, DHHS, Research Triangle Park, North Carolina 27709, USA
| | - Stephen B Shears
- Inositol Signaling Section, NIEHS, NIH, DHHS, Research Triangle Park, North Carolina 27709, USA
| | - Yoichi Hayakawa
- Department of Applied Biological Sciences, Saga University, Saga 840-8502, Japan
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49
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Capolicchio S, Wang H, Thakor DT, Shears SB, Jessen HJ. Synthesis of Densely Phosphorylated Bis-1,5-Diphospho-myo-Inositol Tetrakisphosphate and its Enantiomer by Bidirectional P-Anhydride Formation. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404398] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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50
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Wang H, Godage HY, Riley AM, Weaver JD, Shears SB, Potter BVL. Synthetic inositol phosphate analogs reveal that PPIP5K2 has a surface-mounted substrate capture site that is a target for drug discovery. ACTA ACUST UNITED AC 2014; 21:689-99. [PMID: 24768307 PMCID: PMC4085797 DOI: 10.1016/j.chembiol.2014.03.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/28/2014] [Accepted: 03/17/2014] [Indexed: 11/17/2022]
Abstract
Diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) is one of the mammalian PPIP5K isoforms responsible for synthesis of diphosphoinositol polyphosphates (inositol pyrophosphates; PP-InsPs), regulatory molecules that function at the interface of cell signaling and organismic homeostasis. The development of drugs that inhibit PPIP5K2 could have both experimental and therapeutic applications. Here, we describe a synthetic strategy for producing naturally occurring 5-PP-InsP4, as well as several inositol polyphosphate analogs, and we study their interactions with PPIP5K2 using biochemical and structural approaches. These experiments uncover an additional ligand-binding site on the surface of PPIP5K2, adjacent to the catalytic pocket. This site facilitates substrate capture from the bulk phase, prior to transfer into the catalytic pocket. In addition to demonstrating a “catch-and-pass” reaction mechanism in a small molecule kinase, we demonstrate that binding of our analogs to the substrate capture site inhibits PPIP5K2. This work suggests that the substrate-binding site offers new opportunities for targeted drug design. Chemical synthesis of 5-PP-InsP4 and a diphosphorylated analog Chemical synthesis of inositol polyphosphate analogs with hydrophobic groups An inositol pyrophosphate kinase has a surface-mounted, substrate capture site Structural and biochemical characterization of a catch-and-pass catalytic cycle
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Affiliation(s)
- Huanchen Wang
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Himali Y Godage
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath, Somerset BA2 7AY, UK
| | - Andrew M Riley
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath, Somerset BA2 7AY, UK
| | - Jeremy D Weaver
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Stephen B Shears
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
| | - Barry V L Potter
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath, Somerset BA2 7AY, UK.
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