1
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Yu J, Boehr DD. Regulatory mechanisms triggered by enzyme interactions with lipid membrane surfaces. Front Mol Biosci 2023; 10:1306483. [PMID: 38099197 PMCID: PMC10720463 DOI: 10.3389/fmolb.2023.1306483] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Recruitment of enzymes to intracellular membranes often modulates their catalytic activity, which can be important in cell signaling and membrane trafficking. Thus, re-localization is not only important for these enzymes to gain access to their substrates, but membrane interactions often allosterically regulate enzyme function by inducing conformational changes across different time and amplitude scales. Recent structural, biophysical and computational studies have revealed how key enzymes interact with lipid membrane surfaces, and how this membrane binding regulates protein structure and function. This review summarizes the recent progress in understanding regulatory mechanisms involved in enzyme-membrane interactions.
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Affiliation(s)
| | - David D. Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
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2
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Dhakephalkar T, Stukey G, Guan Z, Carman GM, Klein EA. Characterization of an evolutionarily distinct bacterial ceramide kinase from Caulobacter crescentus. J Biol Chem 2023:104894. [PMID: 37286040 PMCID: PMC10331486 DOI: 10.1016/j.jbc.2023.104894] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/27/2023] [Accepted: 06/01/2023] [Indexed: 06/09/2023] Open
Abstract
A common feature among nearly all Gram-negative bacteria is the requirement for lipopolysaccharide (LPS) in the outer leaflet of the outer membrane. LPS provides structural integrity to the bacterial membrane which aids bacteria in maintaining their shape and acts as a barrier from environmental stress and harmful substances such as detergents and antibiotics. Recent work has demonstrated that Caulobacter crescentus can survive without LPS due to the presence of the anionic sphingolipid ceramide-phosphoglycerate. Based on genetic evidence, we predicted that protein CpgB functions as a ceramide kinase and performs the first step in generating the phosphoglycerate head group. Here, we characterized the kinase activity of recombinantly expressed CpgB and demonstrated that it can phosphorylate ceramide to form ceramide 1-phosphate. The pH optimum for CpgB was 7.5, and the enzyme required Mg2+ as a cofactor. Mn2+, but not other divalent cations, could substitute for Mg2+. Under these conditions, the enzyme exhibited typical Michaelis-Menten kinetics with respect to NBD-C6-ceramide (Km,app=19.2 ± 5.5 μM; Vmax,app=2590 ± 230 pmol/min/mg enzyme) and ATP (Km,app=0.29 ± 0.07 mM; Vmax,app=10100 ± 996 pmol/min/mg enzyme). Phylogenetic analysis of CpgB revealed that CpgB belongs to a new class of ceramide kinases which is distinct from its eukaryotic counterpart; furthermore, the pharmacological inhibitor of human ceramide kinase (NVP-231) had no effect on CpgB. The characterization of a new bacterial ceramide kinase opens avenues for understanding the structure and function of the various microbial phosphorylated sphingolipids.
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Affiliation(s)
| | - Geordan Stukey
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food Nutrition and Health, Rutgers University, New Brunswick, NJ 08901, USA
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - George M Carman
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food Nutrition and Health, Rutgers University, New Brunswick, NJ 08901, USA
| | - Eric A Klein
- Biology Department, Rutgers University-Camden, Camden, NJ 08102, USA; Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food Nutrition and Health, Rutgers University, New Brunswick, NJ 08901, USA; Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ 08102, USA.
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3
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Elmenier FM, Lasheen DS, Abouzid KAM. Design, synthesis, and biological evaluation of new thieno[2,3- d] pyrimidine derivatives as targeted therapy for PI3K with molecular modelling study. J Enzyme Inhib Med Chem 2021; 37:315-332. [PMID: 34955086 PMCID: PMC8725920 DOI: 10.1080/14756366.2021.2010729] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Cancer is one of the most aggressive diseases characterised by abnormal growth and uncontrolled cell division. PI3K is a lipid kinase involved in cancer progression which makes it fruitful target for cancer control. 28 new morpholine based thieno[2,3-d] pyrimidine derivatives were designed and synthesised as anti-PI3K agents maintaining the common pharmacophoric features of several potent PI3K inhibitors. Their antiproliferative activity on NCI 60 cell lines as well as their enzymatic activity against PI3K isoforms were evaluated. Three compounds revealed good cytotoxic activities against breast cancer cell lines, especially T-47D. Compound VIb exhibited the best enzymatic inhibitory activity (72% & 84% on PI3Kβ & PI3Kγ), respectively and good activity on most NCI cell lines especially those with over expressed PI3K. Docking was carried out into PI3K active site which showed comparable binding mode to that of the PI-103 inhibitor. Compound VIb could be optimised to serve as a new chemical entity for discovering new anticancer agents.
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Affiliation(s)
- Fatma M Elmenier
- Faculty of Pharmacy, Pharmaceutical Chemistry Department, Ain Shams University, Cairo, Egypt
| | - Deena S Lasheen
- Faculty of Pharmacy, Pharmaceutical Chemistry Department, Ain Shams University, Cairo, Egypt
| | - Khaled A M Abouzid
- Faculty of Pharmacy, Pharmaceutical Chemistry Department, Ain Shams University, Cairo, Egypt.,Faculty of Pharmacy, Department of Organic and Medicinal Chemistry, University of Sadat City, Menoufia, Egypt
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4
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Arora GK, Palamiuc L, Emerling BM. Expanding role of PI5P4Ks in cancer: A promising druggable target. FEBS Lett 2021; 596:3-16. [PMID: 34822164 DOI: 10.1002/1873-3468.14237] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 10/01/2021] [Revised: 11/04/2021] [Accepted: 11/15/2021] [Indexed: 12/14/2022]
Abstract
Cancer cells are challenged by a myriad of microenvironmental stresses, and it is their ability to efficiently adapt to the constantly changing nutrient, energy, oxidative, and/or immune landscape that allows them to survive and proliferate. Such adaptations, however, result in distinct vulnerabilities that are attractive therapeutic targets. Phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) are a family of druggable stress-regulated phosphoinositide kinases that become conditionally essential as a metabolic adaptation, paving the way to targeting cancer cell dependencies. Further, PI5P4Ks have a synthetic lethal interaction with the tumor suppressor p53, the loss of which is one of the most prevalent genetic drivers of malignant transformation. PI5P4K's emergence as a crucial axis in the expanding landscape of phosphoinositide signaling in cancer has already stimulated the development of specific inhibitors. Thus, a better understanding of the biology of the PI5P4Ks will allow for targeted and effective therapeutic interventions. Here, we attempt to summarize the mounting roles of the PI5P4Ks in cancer, including evidence that targeting them is a therapeutic vulnerability and promising next-in-line treatment for multiple cancer subtypes.
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Affiliation(s)
- Gurpreet K Arora
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, USA
| | - Lavinia Palamiuc
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, USA
| | - Brooke M Emerling
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, USA
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5
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McLeod IX, Saxena R, Carico Z, He YW. Class I PI3K Provide Lipid Substrate in T Cell Autophagy Through Linked Activity of Inositol Phosphatases. Front Cell Dev Biol 2021; 9:709398. [PMID: 34458267 PMCID: PMC8397451 DOI: 10.3389/fcell.2021.709398] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/21/2021] [Indexed: 11/13/2022] Open
Abstract
Autophagy, a highly conserved intracellular process, has been identified as a novel mechanism regulating T lymphocyte homeostasis. Herein, we demonstrate that both starvation- and T cell receptor-mediated autophagy induction requires class I phosphatidylinositol-3 kinases to produce PI(3)P. In contrast, common gamma chain cytokines are suppressors of autophagy despite their ability to activate the PI3K pathway. T cells lacking the PI3KI regulatory subunits, p85 and p55, were almost completely unable to activate TCR-mediated autophagy and had concurrent defects in PI(3)P production. Additionally, T lymphocytes upregulate polyinositol phosphatases in response to autophagic stimuli, and the activity of the inositol phosphatases Inpp4 and SHIP are required for TCR-mediated autophagy induction. Addition of exogenous PI(3,4)P2 can supplement cellular PI(3)P and accelerate the outcome of activation-induced autophagy. TCR-mediated autophagy also requires internalization of the TCR complex, suggesting that this kinase/phosphatase activity is localized in internalized vesicles. Finally, HIV-induced bystander CD4+ T cell autophagy is dependent upon PI3KI. Overall, our data elucidate an important pathway linking TCR activation to autophagy, via induction of PI3KI activity and inositol phosphatase upregulation to produce PI(3)P.
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Affiliation(s)
- Ian X McLeod
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Ruchi Saxena
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Zachary Carico
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - You-Wen He
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
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6
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Chen S, Chandra Tjin C, Gao X, Xue Y, Jiao H, Zhang R, Wu M, He Z, Ellman J, Ha Y. Pharmacological inhibition of PI5P4Kα/β disrupts cell energy metabolism and selectively kills p53-null tumor cells. Proc Natl Acad Sci U S A 2021; 118:e2002486118. [PMID: 34001596 DOI: 10.1073/pnas.2002486118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Most human cancer cells harbor loss-of-function mutations in the p53 tumor suppressor gene. Genetic experiments have shown that phosphatidylinositol 5-phosphate 4-kinase α and β (PI5P4Kα and PI5P4Kβ) are essential for the development of late-onset tumors in mice with germline p53 deletion, but the mechanism underlying this acquired dependence remains unclear. PI5P4K has been previously implicated in metabolic regulation. Here, we show that inhibition of PI5P4Kα/β kinase activity by a potent and selective small-molecule probe disrupts cell energy homeostasis, causing AMPK activation and mTORC1 inhibition in a variety of cell types. Feedback through the S6K/insulin receptor substrate (IRS) loop contributes to insulin hypersensitivity and enhanced PI3K signaling in terminally differentiated myotubes. Most significantly, the energy stress induced by PI5P4Kαβ inhibition is selectively toxic toward p53-null tumor cells. The chemical probe, and the structural basis for its exquisite specificity, provide a promising platform for further development, which may lead to a novel class of diabetes and cancer drugs.
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7
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Abstract
Protein and phosphoinositide kinases have been successfully exploited as drug targets in various disease areas, principally in oncology. In malaria, several protein kinases are under investigation as potential drug targets, and an inhibitor of Plasmodium phosphatidylinositol 4-kinase type III beta (PI4KIIIβ) is currently in phase 2 clinical studies. In this Perspective, we review the potential of kinases as drug targets for the treatment of malaria. Kinases are known to be readily druggable, and many are essential for parasite survival. A key challenge in the design of Plasmodium kinase inhibitors is obtaining selectivity over the corresponding human orthologue(s) and other human kinases due to the highly conserved nature of the shared ATP binding site. Notwithstanding this, there are some notable differences between the Plasmodium and human kinome that may be exploitable. There is also the potential for designed polypharmacology, where several Plasmodium kinases are inhibited by the same drug. Prior to starting the drug discovery process, it is important to carefully assess potential kinase targets to ensure that the inhibition of the desired kinase will kill the parasites in the required life-cycle stages with a sufficiently fast rate of kill. Here, we highlight key target attributes and experimental approaches to consider and summarize the progress that has been made targeting Plasmodium PI4KIIIβ, cGMP-dependent protein kinase, and cyclin-dependent-like kinase 3.
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Affiliation(s)
- Lauren B. Arendse
- Drug
Discovery and Development Centre (H3D), South African Medical Research
Council Drug Discovery and Development Research Unit, Department of
Chemistry, and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town, Western Cape 7701, South Africa
| | - Susan Wyllie
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Kelly Chibale
- Drug
Discovery and Development Centre (H3D), South African Medical Research
Council Drug Discovery and Development Research Unit, Department of
Chemistry, and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town, Western Cape 7701, South Africa
| | - Ian H. Gilbert
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
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8
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Chen Z, Malia PC, Hatakeyama R, Nicastro R, Hu Z, Péli-Gulli MP, Gao J, Nishimura T, Eskes E, Stefan CJ, Winderickx J, Dengjel J, De Virgilio C, Ungermann C. TORC1 Determines Fab1 Lipid Kinase Function at Signaling Endosomes and Vacuoles. Curr Biol 2020; 31:297-309.e8. [PMID: 33157024 DOI: 10.1016/j.cub.2020.10.026] [Citation(s) in RCA: 7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/25/2020] [Accepted: 10/08/2020] [Indexed: 01/17/2023]
Abstract
Organelles of the endomembrane system maintain their identity and integrity during growth or stress conditions by homeostatic mechanisms that regulate membrane flux and biogenesis. At lysosomes and endosomes, the Fab1 lipid kinase complex and the nutrient-regulated target of rapamycin complex 1 (TORC1) control the integrity of the endolysosomal homeostasis and cellular metabolism. Both complexes are functionally connected as Fab1-dependent generation of PI(3,5)P2 supports TORC1 activity. Here, we identify Fab1 as a target of TORC1 on signaling endosomes, which are distinct from multivesicular bodies, and provide mechanistic insight into their crosstalk. Accordingly, TORC1 can phosphorylate Fab1 proximal to its PI3P-interacting FYVE domain, which causes Fab1 to shift to signaling endosomes, where it generates PI(3,5)P2. This, in turn, regulates (1) vacuole morphology, (2) recruitment of TORC1 and the TORC1-regulatory Rag GTPase-containing EGO complex to signaling endosomes, and (3) TORC1 activity. Thus, our study unravels a regulatory feedback loop between TORC1 and the Fab1 complex that controls signaling at endolysosomes.
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Affiliation(s)
- Zilei Chen
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Barbarastrasse 13, 49076 Osnabrück, Germany
| | - Pedro Carpio Malia
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Barbarastrasse 13, 49076 Osnabrück, Germany
| | - Riko Hatakeyama
- Department of Biology, University of Fribourg, Chemin du Musée, CH-1700 Fribourg, Switzerland
| | - Raffaele Nicastro
- Department of Biology, University of Fribourg, Chemin du Musée, CH-1700 Fribourg, Switzerland
| | - Zehan Hu
- Department of Biology, University of Fribourg, Chemin du Musée, CH-1700 Fribourg, Switzerland
| | - Marie-Pierre Péli-Gulli
- Department of Biology, University of Fribourg, Chemin du Musée, CH-1700 Fribourg, Switzerland
| | - Jieqiong Gao
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Barbarastrasse 13, 49076 Osnabrück, Germany
| | - Taki Nishimura
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Elja Eskes
- Functional Biology, KU Leuven, Kasteelpark Arensberg 31, 3000 Leuven, Belgium
| | - Christopher J Stefan
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Joris Winderickx
- Functional Biology, KU Leuven, Kasteelpark Arensberg 31, 3000 Leuven, Belgium
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, Chemin du Musée, CH-1700 Fribourg, Switzerland
| | - Claudio De Virgilio
- Department of Biology, University of Fribourg, Chemin du Musée, CH-1700 Fribourg, Switzerland.
| | - Christian Ungermann
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Barbarastrasse 13, 49076 Osnabrück, Germany; Center of Cellular Nanoanalytics Osnabrück (CellNanOs), University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany.
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9
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Lees JA, Li P, Kumar N, Weisman LS, Reinisch KM. Insights into Lysosomal PI(3,5)P 2 Homeostasis from a Structural-Biochemical Analysis of the PIKfyve Lipid Kinase Complex. Mol Cell 2020; 80:736-743.e4. [PMID: 33098764 DOI: 10.1016/j.molcel.2020.10.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [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: 07/21/2020] [Revised: 09/11/2020] [Accepted: 10/01/2020] [Indexed: 11/30/2022]
Abstract
The phosphoinositide PI(3,5)P2, generated exclusively by the PIKfyve lipid kinase complex, is key for lysosomal biology. Here, we explore how PI(3,5)P2 levels within cells are regulated. We find the PIKfyve complex comprises five copies of the scaffolding protein Vac14 and one copy each of the lipid kinase PIKfyve, generating PI(3,5)P2 from PI3P and the lipid phosphatase Fig4, reversing the reaction. Fig4 is active as a lipid phosphatase in the ternary complex, whereas PIKfyve within the complex cannot access membrane-incorporated phosphoinositides due to steric constraints. We find further that the phosphoinositide-directed activities of both PIKfyve and Fig4 are regulated by protein-directed activities within the complex. PIKfyve autophosphorylation represses its lipid kinase activity and stimulates Fig4 lipid phosphatase activity. Further, Fig4 is also a protein phosphatase acting on PIKfyve to stimulate its lipid kinase activity, explaining why catalytically active Fig4 is required for maximal PI(3,5)P2 production by PIKfyve in vivo.
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Affiliation(s)
- Joshua A Lees
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - PeiQi Li
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Nikit Kumar
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Lois S Weisman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karin M Reinisch
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
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10
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Strätker K, Haidar S, Amesty Á, El-Awaad E, Götz C, Estévez-Braun A, Jose J. Development of an in vitro screening assay for PIP5K1α lipid kinase and identification of potent inhibitors. FEBS J 2020; 287:3042-3064. [PMID: 31876381 DOI: 10.1111/febs.15194] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/28/2019] [Accepted: 12/22/2019] [Indexed: 12/17/2022]
Abstract
The human phosphatidylinositol 4-phosphate 5-kinase type I α (hPIP5K1α) participates in the phosphoinositide-3-kinase/protein kinase B/mammalian target of rapamycin signaling pathway. Despite the evidence that hPIP5K1α plays a role in the development of prostate cancer (PCa), only one inhibitor is known to date. With the aim of identifying new inhibitors, a nonradiometric assay for measurement of the hPIP5K1α enzyme activity was developed. The assay is based on the separation of the fluorescently labeled substrate phosphatidylinositol-4-phosphate (PI(4)P) and the resulting product phosphatidylinositol-4,5-bisphosphate (PIP2 ) by capillary electrophoresis (CE). Furthermore, an inactive mutant K261A of hPIP5K1α was generated by site-directed mutagenesis and used as a control. Michaelis-Menten analysis revealed a Km value of 21.6 µm and Vmax of 0.65 pmol·min-1 for the cosubstrate ATP. The average Z' value was determined to be 0.86, indicating a high reliability of the assay. An in silico screening of an in-house compound library was performed employing the crystal structure of zebrafish PIP5K1α. By applying this strategy, three compounds with a 2-amino-3-cyano-4H-pyranobenzoquinone scaffold were identified and tested using the CE-based assay. These compounds inhibited hPIP5K1α to > 90% at a concentration of 50 µm. Subsequently, the inhibitory activity of all compounds with a pyranobenzoquinone scaffold (29) was tested on hPIP5K1α. Compound 4-(2-amino-3-cyano-6-hydroxy-5,8-dioxo-7-undecyl-5,8-dihydro-4H-chromen-4-yl)benzoic acid appeared to be the most potent inhibitor of hPIP5K1α identified so far with an IC50 value of 1.55 µm, exhibiting a substrate-competitive mode of action. The effects of this compound on cell viability and the induction of apoptosis were investigated in LNCaP, DU145, and PC3 PCa cells.
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Affiliation(s)
- Katja Strätker
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Germany
| | - Samer Haidar
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Germany.,Faculty of Pharmacy, Damascus University, Syria
| | - Ángel Amesty
- Departamento de Química Orgánica, Instituto Universitario de Bio-Orgánica Antonio González (CIBICAN), Universidad de La Laguna, Spain
| | - Ehab El-Awaad
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Germany.,Department of Pharmacology, Faculty of Medicine, Assiut University, Egypt
| | - Claudia Götz
- Universität des Saarlandes Medizinische Biochemie und Molekularbiologie Geb, Homburg, Germany
| | - Ana Estévez-Braun
- Departamento de Química Orgánica, Instituto Universitario de Bio-Orgánica Antonio González (CIBICAN), Universidad de La Laguna, Spain
| | - Joachim Jose
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Germany
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11
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Baldanzi G, Malerba M. DGKα in Neutrophil Biology and Its Implications for Respiratory Diseases. Int J Mol Sci 2019; 20:E5673. [PMID: 31766109 DOI: 10.3390/ijms20225673] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 12/21/2022] Open
Abstract
Diacylglycerol kinases (DGKs) play a key role in phosphoinositide signaling by removing diacylglycerol and generating phosphatidic acid. Besides the well-documented role of DGKα and DGKζ as negative regulators of lymphocyte responses, a robust body of literature points to those enzymes, and specifically DGKα, as crucial regulators of leukocyte function. Upon neutrophil stimulation, DGKα activation is necessary for migration and a productive response. The role of DGKα in neutrophils is evidenced by its aberrant behavior in juvenile periodontitis patients, which express an inactive DGKα transcript. Together with in vitro experiments, this suggests that DGKs may represent potential therapeutic targets for disorders where inflammation, and neutrophils in particular, plays a major role. In this paper we focus on obstructive respiratory diseases, including asthma and chronic obstructive pulmonary disease (COPD), but also rare genetic diseases such as alpha-1-antitrypsin deficiency. Indeed, the biological role of DGKα is understudied outside the T lymphocyte field. The recent wave of research aiming to develop novel and specific inhibitors as well as KO mice will allow a better understanding of DGK's role in neutrophilic inflammation. Better knowledge and pharmacologic tools may also allow DGK to move from the laboratory bench to clinical trials.
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12
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Ghosh A, Sharma S, Shinde D, Ramya V, Raghu P. A novel mass assay to measure phosphatidylinositol-5-phosphate from cells and tissues. Biosci Rep 2019; 39:BSR20192502. [PMID: 31652444 PMCID: PMC6822513 DOI: 10.1042/bsr20192502] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 07/25/2019] [Revised: 09/19/2019] [Accepted: 09/27/2019] [Indexed: 12/23/2022] Open
Abstract
Phosphatidylinositol-5-phosphate (PI5P) is a low abundance lipid proposed to have functions in cell migration, DNA damage responses, receptor trafficking and insulin signalling in metazoans. However, studies of PI5P function are limited by the lack of scalable techniques to quantify its level from cells and tissues in multicellular organisms. Currently, PI5P measurement requires the use of radionuclide labelling approaches that are not easily applicable in tissues or in vivo samples. In the present study, we describe a simple and reliable, non-radioactive mass assay to measure total PI5P levels from cells and tissues of Drosophila, a genetically tractable multicellular model. We use heavy oxygen-labelled ATP (18O-ATP) to label PI5P from tissue extracts while converting it into PI(4,5)P2 using an in vitro kinase reaction. The product of this reaction can be selectively detected and quantified with high sensitivity using a liquid chromatography-tandem mass spectrometry (LC-MS/MS) platform. Further, using this method, we capture and quantify the unique acyl chain composition of PI5P from Drosophila cells and tissues. Finally, we demonstrate the use of this technique to quantify elevations in PI5P levels, from Drosophila larval tissues and cultured cells depleted of phosphatidylinositol 5 phosphate 4-kinase (PIP4K), that metabolizes PI5P into PI(4,5)P2 thus regulating its levels. Thus, we demonstrate the potential of our method to quantify PI5P levels with high sensitivity from cells and tissues of multicellular organisms thus accelerating understanding of PI5P functions in vivo.
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Affiliation(s)
- Avishek Ghosh
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Sanjeev Sharma
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Dhananjay Shinde
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Visvanathan Ramya
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Padinjat Raghu
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore 560065, India
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13
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Young LN, Goerdeler F, Hurley JH. Structural pathway for allosteric activation of the autophagic PI 3-kinase complex I. Proc Natl Acad Sci U S A 2019; 116:21508-13. [PMID: 31591221 DOI: 10.1073/pnas.1911612116] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Autophagy induction by starvation and stress involves the enzymatic activation of the class III phosphatidylinositol (PI) 3-kinase complex I (PI3KC3-C1). The inactive basal state of PI3KC3-C1 is maintained by inhibitory contacts between the VPS15 protein kinase and VPS34 lipid kinase domains that restrict the conformation of the VPS34 activation loop. Here, the proautophagic MIT domain-containing protein NRBF2 was used to map the structural changes leading to activation. Cryoelectron microscopy was used to visualize a 2-step PI3KC3-C1 activation pathway driven by NRFB2 MIT domain binding. Binding of a single NRBF2 MIT domain bends the helical solenoid of the VPS15 scaffold, displaces the protein kinase domain of VPS15, and releases the VPS34 kinase domain from the inhibited conformation. Binding of a second MIT stabilizes the VPS34 lipid kinase domain in an active conformation that has an unrestricted activation loop and is poised for access to membranes.
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14
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Fiume R, Faenza I, Sheth B, Poli A, Vidalle MC, Mazzetti C, Abdul SH, Campagnoli F, Fabbrini M, Kimber ST, Mariani GA, Xian J, Marvi MV, Mongiorgi S, Shah Z, Divecha N. Nuclear Phosphoinositides: Their Regulation and Roles in Nuclear Functions. Int J Mol Sci 2019; 20:E2991. [PMID: 31248120 DOI: 10.3390/ijms20122991] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/22/2019] [Accepted: 06/17/2019] [Indexed: 12/29/2022] Open
Abstract
Polyphosphoinositides (PPIns) are a family of seven lipid messengers that regulate a vast array of signalling pathways to control cell proliferation, migration, survival and differentiation. PPIns are differentially present in various sub-cellular compartments and, through the recruitment and regulation of specific proteins, are key regulators of compartment identity and function. Phosphoinositides and the enzymes that synthesise and degrade them are also present in the nuclear membrane and in nuclear membraneless compartments such as nuclear speckles. Here we discuss how PPIns in the nucleus are modulated in response to external cues and how they function to control downstream signalling. Finally we suggest a role for nuclear PPIns in liquid phase separations that are involved in the formation of membraneless compartments within the nucleus.
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15
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Amos SBTA, Kalli AC, Shi J, Sansom MSP. Membrane Recognition and Binding by the Phosphatidylinositol Phosphate Kinase PIP5K1A: A Multiscale Simulation Study. Structure 2019; 27:1336-1346.e2. [PMID: 31204251 PMCID: PMC6688827 DOI: 10.1016/j.str.2019.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 11/28/2018] [Revised: 03/07/2019] [Accepted: 05/14/2019] [Indexed: 11/28/2022]
Abstract
Phosphatidylinositol phosphates (PIPs) are lipid signaling molecules that play key roles in many cellular processes. PIP5K1A kinase catalyzes phosphorylation of PI4P to form PIP2, which in turn interacts with membrane and membrane-associated proteins. We explore the mechanism of membrane binding by the PIP5K1A kinase using a multiscale molecular dynamics approach. Coarse-grained simulations show binding of monomeric PIP5K1A to a model cell membrane containing PI4P. PIP5K1A did not bind to zwitterionic or anionic membranes lacking PIP molecules. Initial encounter of kinase and bilayer was followed by reorientation to enable productive binding to the PI4P-containing membrane. The simulations suggest that unstructured regions may be important for the preferred orientation for membrane binding. Atomistic simulations indicated that the dimeric kinase could not bind to the membrane via both active sites at the same time, suggesting a conformational change in the protein and/or bilayer distortion may be needed for dual-site binding to occur. PIP5K1A kinase interacts with PIP-containing membranes via its activation loop PIP5K1A does not bind to zwitterionic or anionic membranes lacking PIP molecules Initial encounter of protein and bilayer is followed by reorientation and binding Dimeric PIP5K1A binds with membrane contacts via only one catalytic site at a time
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Affiliation(s)
- Sarah-Beth T A Amos
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Antreas C Kalli
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jiye Shi
- UCB Pharma, 208 Bath Road, Slough SL1 3WE, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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16
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Ziyad S, Riordan JD, Cavanaugh AM, Su T, Hernandez GE, Hilfenhaus G, Morselli M, Huynh K, Wang K, Chen JN, Dupuy AJ, Iruela-Arispe ML. A Forward Genetic Screen Targeting the Endothelium Reveals a Regulatory Role for the Lipid Kinase Pi4ka in Myelo- and Erythropoiesis. Cell Rep 2019; 22:1211-1224. [PMID: 29386109 PMCID: PMC5828030 DOI: 10.1016/j.celrep.2018.01.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 11/05/2017] [Accepted: 01/05/2018] [Indexed: 11/19/2022] Open
Abstract
Given its role as the source of definitive hematopoietic cells, we sought to determine whether mutations initiated in the hemogenic endothelium would yield hematopoietic abnormalities or malignancies. Here, we find that endothelium-specific transposon mutagenesis in mice promotes hematopoietic pathologies that are both myeloid and lymphoid in nature. Frequently mutated genes included previously recognized cancer drivers and additional candidates, such as Pi4ka, a lipid kinase whose mutation was found to promote myeloid and erythroid dysfunction. Subsequent validation experiments showed that targeted inactivation of the Pi4ka catalytic domain or reduction in mRNA expression inhibited myeloid and erythroid cell differentiation in vitro and promoted anemia in vivo through a mechanism involving deregulation of AKT, MAPK, SRC, and JAK-STAT signaling. Finally, we provide evidence linking PI4KAP2, previously considered a pseudogene, to human myeloid and erythroid leukemia.
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Affiliation(s)
- Safiyyah Ziyad
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jesse D Riordan
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Ann M Cavanaugh
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Trent Su
- Institute for Quantitative and Computational Biology and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gloria E Hernandez
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Georg Hilfenhaus
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marco Morselli
- Institute for Quantitative and Computational Biology and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kristine Huynh
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kevin Wang
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jau-Nian Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - M Luisa Iruela-Arispe
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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17
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Lundquist MR, Goncalves MD, Loughran RM, Possik E, Vijayaraghavan T, Yang A, Pauli C, Ravi A, Verma A, Yang Z, Johnson JL, Wong JCY, Ma Y, Hwang KSK, Weinkove D, Divecha N, Asara JM, Elemento O, Rubin MA, Kimmelman AC, Pause A, Cantley LC, Emerling BM. Phosphatidylinositol-5-Phosphate 4-Kinases Regulate Cellular Lipid Metabolism By Facilitating Autophagy. Mol Cell 2019; 70:531-544.e9. [PMID: 29727621 DOI: 10.1016/j.molcel.2018.03.037] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [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: 09/18/2017] [Revised: 02/13/2018] [Accepted: 03/29/2018] [Indexed: 01/21/2023]
Abstract
While the majority of phosphatidylinositol-4, 5-bisphosphate (PI-4, 5-P2) in mammalian cells is generated by the conversion of phosphatidylinositol-4-phosphate (PI-4-P) to PI-4, 5-P2, a small fraction can be made by phosphorylating phosphatidylinositol-5-phosphate (PI-5-P). The physiological relevance of this second pathway is not clear. Here, we show that deletion of the genes encoding the two most active enzymes in this pathway, Pip4k2a and Pip4k2b, in the liver of mice causes a large enrichment in lipid droplets and in autophagic vesicles during fasting. These changes are due to a defect in the clearance of autophagosomes that halts autophagy and reduces the supply of nutrients salvaged through this pathway. Similar defects in autophagy are seen in nutrient-starved Pip4k2a-/-Pip4k2b-/- mouse embryonic fibroblasts and in C. elegans lacking the PI5P4K ortholog. These results suggest that this alternative pathway for PI-4, 5-P2 synthesis evolved, in part, to enhance the ability of multicellular organisms to survive starvation.
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Affiliation(s)
- Mark R Lundquist
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Marcus D Goncalves
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ryan M Loughran
- Sanford Burnham Prebys Medical Discovery Institute, Cancer Metabolism and Signaling Networks Program, La Jolla, CA 92037, USA
| | - Elite Possik
- Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada; Department of Biochemistry, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Tarika Vijayaraghavan
- Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada; Department of Biochemistry, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Annan Yang
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Chantal Pauli
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine-New York Presbyterian Hospital, New York, NY 10065, USA
| | - Archna Ravi
- Sanford Burnham Prebys Medical Discovery Institute, Cancer Metabolism and Signaling Networks Program, La Jolla, CA 92037, USA
| | - Akanksha Verma
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Zhiwei Yang
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jared L Johnson
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jenny C Y Wong
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Yilun Ma
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Katie Seo-Kyoung Hwang
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - David Weinkove
- School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, UK
| | - Nullin Divecha
- The Inositide Laboratory, Centre for Biological Sciences, Southampton University, Southampton, SO17 1BJ, UK
| | - John M Asara
- Department of Medicine, Division of Signal Transduction, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Olivier Elemento
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Mark A Rubin
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine-New York Presbyterian Hospital, New York, NY 10065, USA
| | - Alec C Kimmelman
- Perlmutter Cancer Center, Department of Radiation Oncology, NYU Medical School, New York, NY 10016, USA
| | - Arnim Pause
- Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada; Department of Biochemistry, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Lewis C Cantley
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Brooke M Emerling
- Sanford Burnham Prebys Medical Discovery Institute, Cancer Metabolism and Signaling Networks Program, La Jolla, CA 92037, USA.
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18
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Roulin PS, Murer LP, Greber UF. A Single Point Mutation in the Rhinovirus 2B Protein Reduces the Requirement for Phosphatidylinositol 4-Kinase Class III Beta in Viral Replication. J Virol 2018; 92:e01462-18. [PMID: 30209171 DOI: 10.1128/JVI.01462-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 08/31/2018] [Indexed: 01/31/2023] Open
Abstract
Rhinoviruses (RVs) replicate on cytoplasmic membranes derived from the Golgi apparatus. They encode membrane-targeted proteins 2B, 2C, and 3A, which control trafficking and lipid composition of the replication membrane. The virus recruits host factors for replication, such as phosphatidylinositol 4 (PI4)-kinase 3beta (PI4K3b), which boosts PI4-phosphate (PI4P) levels and drives lipid countercurrent exchange of PI4P against cholesterol at endoplasmic reticulum-Golgi membrane contact sites through the lipid shuttling protein oxysterol binding protein 1 (OSBP1). We identified a PI4K3b inhibitor-resistant RV-A16 variant with a single point mutation in the conserved 2B protein near the cytosolic carboxy terminus, isoleucine 92 to threonine (termed 2B[I92T]). The mutation did not confer resistance to cholesterol-sequestering compounds or OSBP1 inhibition, suggesting invariant dependency on the PI4P/cholesterol lipid countercurrents. In the presence of PI4K3b inhibitor, Golgi reorganization and PI4P lipid induction occurred in RV-A16 2B[I92] but not in wild-type infection. The knockout of PI4K3b abolished the replication of both the 2B[I92T] mutant and the wild type. Doxycycline-inducible expression of PI4K3b in PI4K3b knockout cells efficiently rescued the 2B[I92T] mutant and, less effectively, wild-type virus infection. Ectopic expression of 2B[I92T] or 2B was less efficient than that of 3A in recruiting PI4K3b to perinuclear membranes, suggesting a supportive rather than decisive role of 2B in recruiting PI4K3b. The data suggest that 2B tunes the recruitment of PI4K3b to the replication membrane and allows the virus to adapt to cells with low levels of PI4K3b while still maintaining the PI4P/cholesterol countercurrent for establishing Golgi-derived RV replication membranes.IMPORTANCE Human rhinoviruses (RVs) are the major cause of the common cold worldwide. They cause asthmatic exacerbations and chronic obstructive pulmonary disease. Despite recent advances, the development of antivirals and vaccines has proven difficult due to the high number and variability of RV types. The identification of critical host factors and their interactions with viral proteins and membrane lipids for the establishment of viral replication is a basis for drug development strategies. Our findings here shed new light on the interactions between nonstructural viral membrane proteins and class III phosphatidylinositol 4 kinases from the host and highlight the importance of phosphatidylinositol 4 phosphate for RV replication.
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19
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Fogarty K, Kashem M, Bauer A, Bernardino A, Brennan D, Cook B, Farrow N, Molinaro T, Nelson R. Development of Three Orthogonal Assays Suitable for the Identification and Qualification of PIKfyve Inhibitors. Assay Drug Dev Technol 2018; 15:210-219. [PMID: 28723271 DOI: 10.1089/adt.2017.790] [Citation(s) in RCA: 5] [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] [Indexed: 12/18/2022] Open
Abstract
FYVE-type zinc finger-containing phosphoinositide kinase (PIKfyve) catalyzes the formation of phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) from phosphatidylinositol 3-phosphate (PI(3)P). PIKfyve has been implicated in multiple cellular processes, and its role in the regulation of toll-like receptor (TLR) pathways and the production of proinflammatory cytokines has sparked interest in developing small-molecule PIKfyve inhibitors as potential therapeutics to treat autoimmune and inflammatory diseases. We developed three orthogonal assays to identify and qualify small-molecule inhibitors of PIKfyve: (1) a purified component microfluidic enzyme assay that measures the conversion of fluorescently labeled PI(3)P to PI(3,5)P2 by purified recombinant full-length human 6His-PIKfyve (rPIKfyve); (2) an intracellular protein stabilization assay using the kinase domain of PIKfyve expressed in HEK293 cells; and (3) a cell-based functional assay that measures the production of interleukin (IL)-12p70 in human peripheral blood mononuclear cells stimulated with TLR agonists lipopolysaccharide and R848. We determined apparent Km values for both ATP and labeled PI(3)P in the rPIKfyve enzyme assay and evaluated the enzyme's ability to use phosphatidylinositol as a substrate. We also tested four reference compounds in the three assays and showed that together these assays provide a platform that is suitable to select promising inhibitors having appropriate functional activity and confirmed cellular target engagement to advance into preclinical models of inflammation.
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Affiliation(s)
- Kylie Fogarty
- 1 Department of Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc. , Ridgefield, Connecticut
| | - Mohammed Kashem
- 1 Department of Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc. , Ridgefield, Connecticut
| | - Andras Bauer
- 2 Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc. , Ridgefield, Connecticut
| | - Alexandra Bernardino
- 2 Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc. , Ridgefield, Connecticut
| | - Debra Brennan
- 1 Department of Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc. , Ridgefield, Connecticut
| | - Brian Cook
- 1 Department of Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc. , Ridgefield, Connecticut
| | - Neil Farrow
- 1 Department of Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc. , Ridgefield, Connecticut
| | - Teresa Molinaro
- 1 Department of Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc. , Ridgefield, Connecticut
| | - Richard Nelson
- 1 Department of Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc. , Ridgefield, Connecticut
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20
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Gao T, Mu C, Shi H, Shi L, Mao X, Li G. Embedding Capture-Magneto-Catalytic Activity into a Nanocatalyst for the Determination of Lipid Kinase. ACS Appl Mater Interfaces 2018; 10:59-65. [PMID: 29231711 DOI: 10.1021/acsami.7b10857] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The use of emerging nanocatalysts to investigate the activity of biocatalysts (protein enzymes, catalytic RNAs, etc.) is increasingly receiving attention from material, analytic, and biomedical scientists. Here, we have first fabricated a three-in-one nanocatalyst, the nitrilotriacetic acid (NTA)-modified magnetite nanoparticle (NTA-MNP), to develop an integrated magneto-colorimetric (MagColor) assay for lipid kinase activity so as to solve the inherent problems in a lipid kinase assay. On the basis of three integrated functions of the NTA-MNPs (capture, magnetic separation, and peroxidase activity), the catalytic activity of lipid kinase is directly converted to colorimetric signals. Therefore, the assay procedure is significantly simplified such that in one step the visual detection of lipid kinase activity is possible. Moreover, the whole system responds sensitively in the case that NTA-MNPs recognize a few numbers of the reaction sites, which efficiently initiates the chromogenic reaction of a large amount of chromogens; thus, the detection limit decreases to 6.5 ± 5.8 fM, about three orders of magnitude lower as compared to that of enzyme-linked immune-sorbent assay. So, by embedding desired functions into nanocatalysts, the assay for biocatalysts becomes easy, which may promisingly provide useful tools for biomedical and clinical research in the future.
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Affiliation(s)
| | - Chaoli Mu
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, P. R. China
| | - Hai Shi
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, P. R. China
| | - Liu Shi
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, P. R. China
| | | | - Genxi Li
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, P. R. China
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21
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Al-Ramahi I, Giridharan SSP, Chen YC, Patnaik S, Safren N, Hasegawa J, de Haro M, Wagner Gee AK, Titus SA, Jeong H, Clarke J, Krainc D, Zheng W, Irvine RF, Barmada S, Ferrer M, Southall N, Weisman LS, Botas J, Marugan JJ. Inhibition of PIP4Kγ ameliorates the pathological effects of mutant huntingtin protein. eLife 2017; 6:29123. [PMID: 29256861 PMCID: PMC5743427 DOI: 10.7554/elife.29123] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [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: 05/30/2017] [Accepted: 11/13/2017] [Indexed: 12/15/2022] Open
Abstract
The discovery of the causative gene for Huntington’s disease (HD) has promoted numerous efforts to uncover cellular pathways that lower levels of mutant huntingtin protein (mHtt) and potentially forestall the appearance of HD-related neurological defects. Using a cell-based model of pathogenic huntingtin expression, we identified a class of compounds that protect cells through selective inhibition of a lipid kinase, PIP4Kγ. Pharmacological inhibition or knock-down of PIP4Kγ modulates the equilibrium between phosphatidylinositide (PI) species within the cell and increases basal autophagy, reducing the total amount of mHtt protein in human patient fibroblasts and aggregates in neurons. In two Drosophila models of Huntington’s disease, genetic knockdown of PIP4K ameliorated neuronal dysfunction and degeneration as assessed using motor performance and retinal degeneration assays respectively. Together, these results suggest that PIP4Kγ is a druggable target whose inhibition enhances productive autophagy and mHtt proteolysis, revealing a useful pharmacological point of intervention for the treatment of Huntington’s disease, and potentially for other neurodegenerative disorders.
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Affiliation(s)
- Ismael Al-Ramahi
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Baylor College of Medicine, Texas Medical Center, Houston, United States
| | | | - Yu-Chi Chen
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, United States
| | - Samarjit Patnaik
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, United States
| | - Nathaniel Safren
- Department of Neurology, University of Michigan, Ann Arbor, United States
| | - Junya Hasegawa
- Department of Cell and Developmental Biology, Life Sciences Institute, University of Michigan, Ann Arbor, United States
| | - Maria de Haro
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Baylor College of Medicine, Texas Medical Center, Houston, United States
| | - Amanda K Wagner Gee
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, United States
| | - Steven A Titus
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, United States
| | - Hyunkyung Jeong
- The Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Jonathan Clarke
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Dimitri Krainc
- The Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Wei Zheng
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, United States
| | - Robin F Irvine
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Sami Barmada
- Department of Neurology, University of Michigan, Ann Arbor, United States
| | - Marc Ferrer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, United States
| | - Noel Southall
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, United States
| | - Lois S Weisman
- Department of Cell and Developmental Biology, Life Sciences Institute, University of Michigan, Ann Arbor, United States
| | - Juan Botas
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Baylor College of Medicine, Texas Medical Center, Houston, United States
| | - Juan Jose Marugan
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, United States
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22
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Lees JA, Zhang Y, Oh MS, Schauder CM, Yu X, Baskin JM, Dobbs K, Notarangelo LD, De Camilli P, Walz T, Reinisch KM. Architecture of the human PI4KIIIα lipid kinase complex. Proc Natl Acad Sci U S A 2017; 114:13720-5. [PMID: 29229838 DOI: 10.1073/pnas.1718471115] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Plasma membrane (PM) phosphoinositides play essential roles in cell physiology, serving as both markers of membrane identity and signaling molecules central to the cell's interaction with its environment. The first step in PM phosphoinositide synthesis is the conversion of phosphatidylinositol (PI) to PI4P, the precursor of PI(4,5)P2 and PI(3,4,5)P3 This conversion is catalyzed by the PI4KIIIα complex, comprising a lipid kinase, PI4KIIIα, and two regulatory subunits, TTC7 and FAM126. We here report the structure of this complex at 3.6-Å resolution, determined by cryo-electron microscopy. The proteins form an obligate ∼700-kDa superassembly with a broad surface suitable for membrane interaction, toward which the kinase active sites are oriented. The structural complexity of the assembly highlights PI4P synthesis as a major regulatory junction in PM phosphoinositide homeostasis. Our studies provide a framework for further exploring the mechanisms underlying PM phosphoinositide regulation.
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23
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Stjepanovic G, Baskaran S, Lin MG, Hurley JH. Unveiling the role of VPS34 kinase domain dynamics in regulation of the autophagic PI3K complex. Mol Cell Oncol 2017; 4:e1367873. [PMID: 29209653 DOI: 10.1080/23723556.2017.1367873] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 08/10/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 10/18/2022]
Abstract
The class III PI 3-kinase, VPS34 forms distinct complexes essential for cargo sorting and membrane trafficking in endocytosis as well as for autophagosome nucleation and maturation. We used integrative structural biology approach to provide insights into the conformational dynamics of the complex and mechanisms that regulate VPS34 activity at the membrane.
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Affiliation(s)
- Goran Stjepanovic
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sulochanadevi Baskaran
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Mary G Lin
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - James H Hurley
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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24
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Stjepanovic G, Baskaran S, Lin MG, Hurley JH. Vps34 Kinase Domain Dynamics Regulate the Autophagic PI 3-Kinase Complex. Mol Cell 2017; 67:528-534.e3. [PMID: 28757208 DOI: 10.1016/j.molcel.2017.07.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/16/2017] [Accepted: 06/30/2017] [Indexed: 12/29/2022]
Abstract
The class III phosphatidylinositol 3-kinase complex I (PI3KC3-C1) is required for the initiation of essentially all macroautophagic processes. PI3KC3-C1 consists of the lipid kinase catalytic subunit VPS34, the VPS15 scaffold, and the regulatory BECN1 and ATG14 subunits. The VPS34 catalytic domain and BECN1:ATG14 subcomplex do not touch, and it is unclear how allosteric signals are transmitted to VPS34. We used EM and crosslinking mass spectrometry to dissect five conformational substates of the complex, including one in which the VPS34 catalytic domain is dislodged from the complex but remains tethered by an intrinsically disordered linker. A "leashed" construct prevented dislodging without interfering with the other conformations, blocked enzyme activity in vitro, and blocked autophagy induction in yeast cells. This pinpoints the dislodging and tethering of the VPS34 catalytic domain, and its regulation by VPS15, as a master allosteric switch in autophagy induction.
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Affiliation(s)
- Goran Stjepanovic
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sulochanadevi Baskaran
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mary G Lin
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James H Hurley
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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25
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Maheshwari S, Miller MS, O'Meally R, Cole RN, Amzel LM, Gabelli SB. Kinetic and structural analyses reveal residues in phosphoinositide 3-kinase α that are critical for catalysis and substrate recognition. J Biol Chem 2017; 292:13541-13550. [PMID: 28676499 DOI: 10.1074/jbc.m116.772426] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 06/30/2017] [Indexed: 12/26/2022] Open
Abstract
Phosphoinositide 3-kinases (PI3Ks) are ubiquitous lipid kinases that activate signaling cascades controlling cell survival, proliferation, protein synthesis, and vesicle trafficking. PI3Ks have dual kinase specificity: a lipid kinase activity that phosphorylates the 3'-hydroxyl of phosphoinositides and a protein-kinase activity that includes autophosphorylation. Despite the wealth of biochemical and structural information on PI3Kα, little is known about the identity and roles of individual active-site residues in catalysis. To close this gap, we explored the roles of residues of the catalytic domain and the regulatory subunit of human PI3Kα in lipid and protein phosphorylation. Using site-directed mutagenesis, kinetic assays, and quantitative mass spectrometry, we precisely mapped key residues involved in substrate recognition and catalysis by PI3Kα. Our results revealed that Lys-776, located in the P-loop of PI3Kα, is essential for the recognition of lipid and ATP substrates and also plays an important role in PI3Kα autophosphorylation. Replacement of the residues His-936 and His-917 in the activation and catalytic loops, respectively, with alanine dramatically changed PI3Kα kinetics. Although H936A inactivated the lipid kinase activity without affecting autophosphorylation, H917A abolished both the lipid and protein kinase activities of PI3Kα. On the basis of these kinetic and structural analyses, we propose possible mechanistic roles of these critical residues in PI3Kα catalysis.
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Affiliation(s)
- Sweta Maheshwari
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Michelle S Miller
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Robert O'Meally
- Mass Spectrometry and Proteomics Facility, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, and
| | - Robert N Cole
- Mass Spectrometry and Proteomics Facility, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, and
| | - L Mario Amzel
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205,
| | - Sandra B Gabelli
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, .,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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26
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Chiu H, Mallya S, Nguyen P, Mai A, Jackson LV, Winkler DG, DiNitto JP, Brophy EE, McGovern K, Kutok JL, Fruman DA. The Selective Phosphoinoside-3-Kinase p110δ Inhibitor IPI-3063 Potently Suppresses B Cell Survival, Proliferation, and Differentiation. Front Immunol 2017; 8:747. [PMID: 28713374 PMCID: PMC5491903 DOI: 10.3389/fimmu.2017.00747] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 11/30/2016] [Accepted: 06/12/2017] [Indexed: 12/02/2022] Open
Abstract
The class I phosphoinoside-3-kinases (PI3Ks) are important enzymes that relay signals from cell surface receptors to downstream mediators driving cellular functions. Elevated PI3K signaling is found in B cell malignancies and lymphocytes of patients with autoimmune disease. The p110δ catalytic isoform of PI3K is a rational target since it is critical for B lymphocyte development, survival, activation, and differentiation. In addition, activating mutations in PIK3CD encoding p110δ cause a human immunodeficiency known as activated PI3K delta syndrome. Currently, idelalisib is the only selective p110δ inhibitor that has been FDA approved to treat certain B cell malignancies. p110δ inhibitors can suppress autoantibody production in mouse models, but limited clinical trials in human autoimmunity have been performed with PI3K inhibitors to date. Thus, there is a need for additional tools to understand the effect of pharmacological inhibition of PI3K isoforms in lymphocytes. In this study, we tested the effects of a potent and selective p110δ inhibitor, IPI-3063, in assays of B cell function. We found that IPI-3063 potently reduced mouse B cell proliferation, survival, and plasmablast differentiation while increasing antibody class switching to IgG1, almost to the same degree as a pan-PI3K inhibitor. Similarly, IPI-3063 potently inhibited human B cell proliferation in vitro. The p110γ isoform has partially overlapping roles with p110δ in B cell development, but little is known about its role in B cell function. We found that the p110γ inhibitor AS-252424 had no significant impact on B cell responses. A novel dual p110δ/γ inhibitor, IPI-443, had comparable effects to p110δ inhibition alone. These findings show that p110δ is the dominant isoform mediating B cell responses and establish that IPI-3063 is a highly potent molecule useful for studying p110δ function in immune cells.
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Affiliation(s)
- Honyin Chiu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Sharmila Mallya
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Phuongthao Nguyen
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Annie Mai
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Leandra V Jackson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - David G Winkler
- Infinity Pharmaceuticals, Inc., Cambridge, MA, United States
| | | | - Erin E Brophy
- Infinity Pharmaceuticals, Inc., Cambridge, MA, United States
| | - Karen McGovern
- Infinity Pharmaceuticals, Inc., Cambridge, MA, United States
| | - Jeffery L Kutok
- Infinity Pharmaceuticals, Inc., Cambridge, MA, United States
| | - David A Fruman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
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27
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Kawasaki T, Ito K, Miyata H, Akira S, Kawai T. Deletion of PIKfyve alters alveolar macrophage populations and exacerbates allergic inflammation in mice. EMBO J 2017; 36:1707-1718. [PMID: 28533230 DOI: 10.15252/embj.201695528] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 03/14/2017] [Accepted: 04/07/2017] [Indexed: 11/09/2022] Open
Abstract
Alveolar macrophages (AMs) are specialized tissue-resident macrophages that orchestrate the immune responses to inhaled pathogens and maintain organ homeostasis of the lung. Dysregulation of AMs is associated with allergic inflammation and asthma. Here, we examined the role of a phosphoinositide kinase PIKfyve in AM development and function. Mice with conditionally deleted PIKfyve in macrophages have altered AM populations. PIKfyve deficiency results in a loss of AKT activation in response to GM-CSF, a cytokine critical for AM development. Upon exposure to house dust mite extract, mutant mice display severe lung inflammation and allergic asthma accompanied by infiltration of eosinophils and lymphoid cells. Moreover, they have defects in production of retinoic acid and fail to support incorporation of Foxp3+ Treg cells in the lung, resulting in exacerbation of lung inflammation. Thus, PIKfyve plays a role in preventing excessive lung inflammation through regulating AM function.
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Affiliation(s)
- Takumi Kawasaki
- Laboratory of Molecular Immunobiology, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Nara, Japan
| | - Kosuke Ito
- Laboratory of Molecular Immunobiology, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Nara, Japan
| | - Haruhiko Miyata
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shizuo Akira
- Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Laboratory of Host Defense, Immunology Frontier Research Center (IFReC), Osaka University, Osaka, Japan
| | - Taro Kawai
- Laboratory of Molecular Immunobiology, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Nara, Japan
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28
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Mannerås-Holm L, Schönke M, Brozinick JT, Vetterli L, Bui HH, Sanders P, Nascimento EBM, Björnholm M, Chibalin AV, Zierath JR. Diacylglycerol kinase ε deficiency preserves glucose tolerance and modulates lipid metabolism in obese mice. J Lipid Res 2017; 58:907-915. [PMID: 28246337 DOI: 10.1194/jlr.m074443] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 12/21/2016] [Revised: 02/13/2017] [Indexed: 12/19/2022] Open
Abstract
Diacylglycerol kinases (DGKs) catalyze the phosphorylation and conversion of diacylglycerol (DAG) into phosphatidic acid. DGK isozymes have unique primary structures, expression patterns, subcellular localizations, regulatory mechanisms, and DAG preferences. DGKε has a hydrophobic segment that promotes its attachment to membranes and shows substrate specificity for DAG with an arachidonoyl acyl chain in the sn-2 position of the substrate. We determined the role of DGKε in the regulation of energy and glucose homeostasis in relation to diet-induced insulin resistance and obesity using DGKε-KO and wild-type mice. Lipidomic analysis revealed elevated unsaturated and saturated DAG species in skeletal muscle of DGKε KO mice, which was paradoxically associated with increased glucose tolerance. Although skeletal muscle insulin sensitivity was unaltered, whole-body respiratory exchange ratio was reduced, and abundance of mitochondrial markers was increased, indicating a greater reliance on fat oxidation and intracellular lipid metabolism in DGKε KO mice. Thus, the increased intracellular lipids in skeletal muscle from DGKε KO mice may undergo rapid turnover because of increased mitochondrial function and lipid oxidation, rather than storage, which in turn may preserve insulin sensitivity. In conclusion, DGKε plays a role in glucose and energy homeostasis by modulating lipid metabolism in skeletal muscle.
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Affiliation(s)
- Louise Mannerås-Holm
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery and Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Milena Schönke
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery and Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | | | - Laurène Vetterli
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery and Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Hai-Hoang Bui
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN
| | - Philip Sanders
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN
| | - Emmani B M Nascimento
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery and Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Marie Björnholm
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery and Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Alexander V Chibalin
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery and Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Juleen R Zierath
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery and Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
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29
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Abstract
Phosphoinositides are a family of phospholipid messenger molecules that control various aspects of cell biology in part by interacting with and regulating downstream protein partners. Importantly, phosphoinositides are present in the nucleus. They form part of the nuclear envelope and are present within the nucleus in nuclear speckles, intra nuclear chromatin domains, the nuclear matrix and in chromatin. What their exact role is within these compartments is not completely clear, but the identification of nuclear specific proteins that contain phosphoinositide interaction domains suggest that they are important regulators of DNA topology, chromatin conformation and RNA maturation and export. The plant homeo domain (PHD) finger is a phosphoinositide binding motif that is largely present in nuclear proteins that regulate chromatin conformation. In the present study I outline how changes in the levels of the nuclear phosphoinositide PtdIns5P impact on muscle cell differentiation through the PHD finger of TAF3 (TAF, TATA box binding protein (TBP)-associated factor), which is a core component of a number of different basal transcription complexes.
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30
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Martens S, Nakamura S, Yoshimori T. Phospholipids in Autophagosome Formation and Fusion. J Mol Biol 2016; 428:S0022-2836(16)30455-7. [PMID: 27984040 PMCID: PMC7610884 DOI: 10.1016/j.jmb.2016.10.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [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: 09/06/2016] [Revised: 10/20/2016] [Accepted: 10/24/2016] [Indexed: 12/29/2022]
Abstract
Autophagosomes are double membrane organelles that are formed during a process referred to as macroautophagy. They serve to deliver cytoplasmic material into the lysosome for degradation. Autophagosomes are formed in a de novo manner and are the result of substantial membrane remodeling processes involving numerous protein-lipid interactions. While most studies focus on the proteins involved in autophagosome formation it is obvious that lipids including phospholipids, sphingolipids and sterols play an equally important role. Here we summarize the current knowledge about the role of lipids, especially focusing on phospholipids and their interplay with the autophagic protein machinery during autophagosome formation and fusion.
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Affiliation(s)
- Sascha Martens
- Max F. Perutz Laboratories, University of Vienna, Dr Bohr-Gasse 9/3, 1030 Vienna, Austria.
| | - Shuhei Nakamura
- Department of Genetics, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan.
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31
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Kolay S, Basu U, Raghu P. Control of diverse subcellular processes by a single multi-functional lipid phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]. Biochem J 2016; 473:1681-92. [PMID: 27288030 PMCID: PMC6609453 DOI: 10.1042/bcj20160069] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [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: 02/04/2016] [Accepted: 03/07/2016] [Indexed: 12/16/2022]
Abstract
Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is a multi-functional lipid that regulates several essential subcellular processes in eukaryotic cells. In addition to its well-established function as a substrate for receptor-activated signalling at the plasma membrane (PM), it is now recognized that distinct PI(4,5)P2 pools are present at other organelle membranes. However, a long-standing question that remains unresolved is the mechanism by which a single lipid species, with an invariant functional head group, delivers numerous functions without loss of fidelity. In the present review, we summarize studies that have examined the molecular processes that shape the repertoire of PI(4,5)P2 pools in diverse eukaryotes. Collectively, these studies indicate a conserved role for lipid kinase isoforms in generating functionally distinct pools of PI(4,5)P2 in diverse metazoan species. The sophistication underlying the regulation of multiple functions by PI(4,5)P2 is also shaped by mechanisms that regulate its availability to enzymes involved in its metabolism as well as molecular processes that control its diffusion at nanoscales in the PM. Collectively, these mechanisms ensure the specificity of PI(4,5)P2 mediated signalling at eukaryotic membranes.
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Affiliation(s)
- Sourav Kolay
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore 560065, India Manipal University, Madhav Nagar, Manipal 576104, Karnataka, India
| | - Urbashi Basu
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Padinjat Raghu
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore 560065, India
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32
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Wu P, Nielsen TE, Clausen MH. FDA-approved small-molecule kinase inhibitors. Trends Pharmacol Sci 2015; 36:422-39. [PMID: 25975227 DOI: 10.1016/j.tips.2015.04.005] [Citation(s) in RCA: 683] [Impact Index Per Article: 75.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 02/07/2023]
Abstract
Kinases have emerged as one of the most intensively pursued targets in current pharmacological research, especially for cancer, due to their critical roles in cellular signaling. To date, the US FDA has approved 28 small-molecule kinase inhibitors, half of which were approved in the past 3 years. While the clinical data of these approved molecules are widely presented and structure-activity relationship (SAR) has been reported for individual molecules, an updated review that analyzes all approved molecules and summarizes current achievements and trends in the field has yet to be found. Here we present all approved small-molecule kinase inhibitors with an emphasis on binding mechanism and structural features, summarize current challenges, and discuss future directions in this field.
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33
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Lacalle RA, de Karam JC, Martínez-Muñoz L, Artetxe I, Peregil RM, Sot J, Rojas AM, Goñi FM, Mellado M, Mañes S. Type I phosphatidylinositol 4-phosphate 5-kinase homo- and heterodimerization determines its membrane localization and activity. FASEB J 2015; 29:2371-85. [PMID: 25713054 DOI: 10.1096/fj.14-264606] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 02/03/2015] [Indexed: 11/11/2022]
Abstract
Type I phosphatidylinositol 4-phosphate 5-kinases (PIP5KIs; α, β, and γ) are a family of isoenzymes that produce phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] using phosphatidylinositol 4-phosphate as substrate. Their structural homology with the class II lipid kinases [type II phosphatidylinositol 5-phosphate 4-kinase (PIP4KII)] suggests that PIP5KI dimerizes, although this has not been formally demonstrated. Neither the hypothetical structural dimerization determinants nor the functional consequences of dimerization have been studied. Here, we used Förster resonance energy transfer, coprecipitation, and ELISA to show that PIP5KIβ forms homo- and heterodimers with PIP5KIγ_i2 in vitro and in live human cells. Dimerization appears to be a general phenomenon for PIP5KI isoenzymes because PIP5KIβ/PIP5KIα heterodimers were also detected by mass spectrometry. Dimerization was independent of actin cytoskeleton remodeling and was also observed using purified proteins. Mutagenesis studies of PIP5KIβ located the dimerization motif at the N terminus, in a region homologous to that implicated in PIP4KII dimerization. PIP5KIβ mutants whose dimerization was impaired showed a severe decrease in PI(4,5)P2 production and plasma membrane delocalization, although their association to lipid monolayers was unaltered. Our results identify dimerization as an integral feature of PIP5K proteins and a central determinant of their enzyme activity.
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Affiliation(s)
- Rosa Ana Lacalle
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Juan C de Karam
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Laura Martínez-Muñoz
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Ibai Artetxe
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Rosa M Peregil
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Jesús Sot
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Ana M Rojas
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Félix M Goñi
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Mario Mellado
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
| | - Santos Mañes
- *Department of Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, Madrid, Spain; Unidad de Biofísica Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Campus de Leioa, Barrio Sarriena s/n, Leioa, Bizkaia, Spain; and Computational Biology and Bioinformatics Group, Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío-Consejo Superior de Investigaciones Científicas, Manuel Siurot s/n, Seville, Spain
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Wright BD, Simpson C, Stashko M, Kireev D, Hull-Ryde EA, Zylka MJ, Janzen WP. Development of a High-Throughput Screening Assay to Identify Inhibitors of the Lipid Kinase PIP5K1C. ACTA ACUST UNITED AC 2014; 20:655-62. [PMID: 25534829 DOI: 10.1177/1087057114564057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [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: 08/20/2014] [Accepted: 11/23/2014] [Indexed: 11/16/2022]
Abstract
Phosphatidylinositol 4-phosphate 5-kinases (PIP5Ks) regulate a variety of cellular processes, including signaling through G protein-coupled receptors (GPCRs), endocytosis, exocytosis, and cell migration. These lipid kinases synthesize phosphatidylinositol 4,5-bisphosphate (PIP2) from phosphatidylinositol 4-phosphate [PI(4)P]. Because small-molecule inhibitors of these lipid kinases did not exist, molecular and genetic approaches were predominantly used to study PIP5K1 regulation of these cellular processes. Moreover, standard radioisotope-based lipid kinase assays cannot be easily adapted for high-throughput screening. Here, we report a novel, high-throughput, microfluidic mobility shift assay to identify inhibitors of PIP5K1C. This assay uses fluorescently labeled phosphatidylinositol 4-phosphate as the substrate and recombinant human PIP5K1C. Our assay exhibited high reproducibility, had a calculated adenosine triphosphate Michaelis constant (Km) of 15 µM, performed with z' values >0.7, and was used to screen a kinase-focused library of ~4700 compounds. From this screen, we identified several potent inhibitors of PIP5K1C, including UNC3230, a compound that we recently found can reduce nociceptive sensitization in animal models of chronic pain. This novel assay will allow continued drug discovery efforts for PIP5K1C and can be adapted easily to screen additional lipid kinases.
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Affiliation(s)
- Brittany D Wright
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA National Center for Advancing Translational Science, Rockville, MD 20850
| | - Catherine Simpson
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael Stashko
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dmitri Kireev
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily A Hull-Ryde
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark J Zylka
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Department of Cell Biology and Physiology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William P Janzen
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Baskaran S, Carlson LA, Stjepanovic G, Young LN, Kim DJ, Grob P, Stanley RE, Nogales E, Hurley JH. Architecture and dynamics of the autophagic phosphatidylinositol 3-kinase complex. eLife 2014; 3. [PMID: 25490155 PMCID: PMC4281882 DOI: 10.7554/elife.05115] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/08/2014] [Indexed: 12/31/2022] Open
Abstract
The class III phosphatidylinositol 3-kinase complex I (PI3KC3-C1) that functions in early autophagy consists of the lipid kinase VPS34, the scaffolding protein VPS15, the tumor suppressor BECN1, and the autophagy-specific subunit ATG14. The structure of the ATG14-containing PI3KC3-C1 was determined by single-particle EM, revealing a V-shaped architecture. All of the ordered domains of VPS34, VPS15, and BECN1 were mapped by MBP tagging. The dynamics of the complex were defined using hydrogen–deuterium exchange, revealing a novel 20-residue ordered region C-terminal to the VPS34 C2 domain. VPS15 organizes the complex and serves as a bridge between VPS34 and the ATG14:BECN1 subcomplex. Dynamic transitions occur in which the lipid kinase domain is ejected from the complex and VPS15 pivots at the base of the V. The N-terminus of BECN1, the target for signaling inputs, resides near the pivot point. These observations provide a framework for understanding the allosteric regulation of lipid kinase activity. DOI:http://dx.doi.org/10.7554/eLife.05115.001 To survive starvation and other hard times, cells have developed a unique recycling strategy: they can scavenge the resources they need from within the cell itself. To do this, the cell forms a double-layered envelope around particular sections of the cell to seal them off from the rest. Then, the contents of the envelope are taken apart and the resulting raw materials are sent elsewhere in the cell where they can be used as required. This process is called autophagy. In more complex organisms like humans, autophagy can have additional roles. One of the key proteins involved in autophagy—called BECN1—suppresses the growth of tumors, and the gene that makes BECN1 is missing in 40–70% of human breast, ovarian, and prostate cancers. Autophagy may also help to prevent Huntington's disease and other similar conditions by stopping disease-causing proteins or broken cell parts from building up inside brain cells. The BECN1 protein does not work alone. Instead, it becomes part of a group, or ‘complex’, of several proteins that are required to form the envelope made during autophagy. However, the three-dimensional structure of the protein complex is unclear. Baskaran et al. used electron microscopy and other techniques to investigate this structure and found that the complex forms a V shape with two arms, which is held together by its largest protein, VPS15. This protein also acts as a bridge between BECN1 and another protein that is a target for new cancer drugs, called VPS34. Next, Baskaran et al. used a different set of techniques to determine how the complex moves. This revealed that many of the connections between proteins in the complex are flexible. However, one of the arms is inflexible and this limits the ability of the VPS34 protein to move. Understanding this structural constraint may help us to design drugs that are able to target the protein complex more efficiently. DOI:http://dx.doi.org/10.7554/eLife.05115.002
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Affiliation(s)
- Sulochanadevi Baskaran
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Lars-Anders Carlson
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Goran Stjepanovic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Lindsey N Young
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Do Jin Kim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Patricia Grob
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Robin E Stanley
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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Wittinghofer A. Arf Proteins and Their Regulators: At the Interface Between Membrane Lipids and the Protein Trafficking Machinery. Ras Superfamily Small G Proteins: Biology and Mechanisms 2 2014. [PMCID: PMC7123483 DOI: 10.1007/978-3-319-07761-1_8] [Citation(s) in RCA: 5] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The Arf small GTP-binding (G) proteins regulate membrane traffic and organelle structure in eukaryotic cells through a regulated cycle of GTP binding and hydrolysis. The first function identified for Arf proteins was recruitment of cytosolic coat complexes to membranes to mediate vesicle formation. However, subsequent studies have uncovered additional functions, including roles in plasma membrane signalling pathways, cytoskeleton regulation, lipid droplet function, and non-vesicular lipid transport. In contrast to other families of G proteins, there are only a few Arf proteins in each organism, yet they function specifically at many different cellular locations. Part of this specificity is achieved by formation of complexes with their guanine nucleotide-exchange factors (GEFs) and GTPase activating proteins (GAPs) that catalyse GTP binding and hydrolysis, respectively. Because these regulators outnumber their Arf substrates by at least 3-to-1, an important aspect of understanding Arf function is elucidating the mechanisms by which a single Arf protein is incorporated into different GEF, GAP, and effector complexes. New insights into these mechanisms have come from recent studies showing GEF–effector interactions, Arf activation cascades, and positive feedback loops. A unifying theme in the function of Arf proteins, carried out in conjunction with their regulators and effectors, is sensing and modulating the properties of the lipids that make up cellular membranes.
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Affiliation(s)
- Alfred Wittinghofer
- Max-Planck-Institute of Molecular Physiology, Dortmund, Nordrhein-Westfalen Germany
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Shah ZH, Jones DR, Sommer L, Foulger R, Bultsma Y, D'Santos C, Divecha N. Nuclear phosphoinositides and their impact on nuclear functions. FEBS J 2013; 280:6295-310. [PMID: 24112514 DOI: 10.1111/febs.12543] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [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: 07/22/2013] [Revised: 09/11/2013] [Accepted: 09/16/2013] [Indexed: 12/23/2022]
Abstract
Polyphosphoinositides (PPIn) are important lipid molecules whose levels are de-regulated in human diseases such as cancer, neurodegenerative disorders and metabolic syndromes. PPIn are synthesized and degraded by an array of kinases, phosphatases and lipases which are localized to various subcellular compartments and are subject to regulation in response to both extra- and intracellular cues. Changes in the activities of enzymes that metabolize PPIn lead to changes in the profiles of PPIn in various subcellular compartments. Understanding how subcellular PPIn are regulated and how they affect downstream signaling is critical to understanding their roles in human diseases. PPIn are present in the nucleus, and their levels are changed in response to various stimuli, suggesting that they may serve to regulate specific nuclear functions. However, the lack of nuclear downstream targets has hindered the definition of which pathways nuclear PPIn affect. Over recent years, targeted and global proteomic studies have identified a plethora of potential PPIn-interacting proteins involved in many aspects of transcription, chromatin remodelling and mRNA maturation, suggesting that PPIn signalling within the nucleus represents a largely unexplored novel layer of complexity in the regulation of nuclear functions.
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Affiliation(s)
- Zahid H Shah
- Cancer Research UK Inositide Laboratory, Paterson Institute for Cancer Research, Manchester, UK
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38
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Dbouk HA, Backer JM. A beta version of life: p110β takes center stage. Oncotarget 2010; 1:729-33. [PMID: 21321382 DOI: 10.18632/oncotarget.101205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The PI3K pathway is frequently activated in tumors, most commonly through p110α mutation or PTEN deletion. In contrast to p110α, p110β is oncogenic when over-expressed in the wild-type state, suggesting that its regulation by p85 is different than that of p110α. In this perspective, we summarize recent data concerning the regulation of p110β, which shows that wild-type p110β acts like an oncogenic mutant of p110α. We also discuss the significance of this altered regulation in tumor models of PTEN deletion, as well as the potential implications of the unique p110β regulation on GPCR-driven tumorigenesis.
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Abstract
Phosphatidylinositol 4,5-bisphosphate (PIP2) is a minority phospholipid of the inner leaflet of plasma membranes. Many plasma membrane ion channels and ion transporters require PIP2 to function and can be turned off by signaling pathways that deplete PIP2. This review discusses the dependence of ion channels on phosphoinositides and considers possible mechanisms by which PIP2 and analogues regulate ion channel activity.
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Affiliation(s)
- Byung-Chang Suh
- Department of Physiology and Biophysics University of Washington School of Medicine, Seattle, Washington 98195
| | - Bertil Hille
- Department of Physiology and Biophysics University of Washington School of Medicine, Seattle, Washington 98195
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Geering B, Cutillas PR, Nock G, Gharbi SI, Vanhaesebroeck B. Class IA phosphoinositide 3-kinases are obligate p85-p110 heterodimers. Proc Natl Acad Sci U S A 2007; 104:7809-14. [PMID: 17470792 PMCID: PMC1876529 DOI: 10.1073/pnas.0700373104] [Citation(s) in RCA: 172] [Impact Index Per Article: 10.1] [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: 01/18/2007] [Indexed: 12/31/2022] Open
Abstract
Class IA phosphoinositide 3-kinases (PI3Ks) signal downstream of tyrosine kinases and Ras and control a wide variety of biological responses. In mammals, these heterodimeric PI3Ks consist of a p110 catalytic subunit (p110alpha, p110beta, or p110delta) bound to any of five distinct regulatory subunits (p85alpha, p85beta, p55gamma, p55alpha, and p50alpha, collectively referred to as "p85s"). The relative expression levels of p85 and p110 have been invoked to explain key features of PI3K signaling. For example, free (i.e., non-p110-bound) p85alpha has been proposed to negatively regulate PI3K signaling by competition with p85/p110 for recruitment to phosphotyrosine docking sites. Using affinity and ion exchange chromatography and quantitative mass spectrometry, we demonstrate that the p85 and p110 subunits are present in equimolar amounts in mammalian cell lines and tissues. No evidence for free p85 or p110 subunits could be obtained. Cell lines contain 10,000-15,000 p85/p110 complexes per cell, with p110beta and p110delta being the most prevalent catalytic subunits in nonleukocytes and leukocytes, respectively. These results argue against a role of free p85 in PI3K signaling and provide insights into the nonredundant functions of the different class IA PI3K isoforms.
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Affiliation(s)
- Barbara Geering
- *Ludwig Institute for Cancer Research, 91 Riding House Street, London W1W 7BS, United Kingdom; and
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Pedro R. Cutillas
- *Ludwig Institute for Cancer Research, 91 Riding House Street, London W1W 7BS, United Kingdom; and
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Gemma Nock
- *Ludwig Institute for Cancer Research, 91 Riding House Street, London W1W 7BS, United Kingdom; and
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Severine I. Gharbi
- *Ludwig Institute for Cancer Research, 91 Riding House Street, London W1W 7BS, United Kingdom; and
| | - Bart Vanhaesebroeck
- *Ludwig Institute for Cancer Research, 91 Riding House Street, London W1W 7BS, United Kingdom; and
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
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41
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Ford CP, Stemkowski PL, Light PE, Smith PA. Experiments to test the role of phosphatidylinositol 4,5-bisphosphate in neurotransmitter-induced M-channel closure in bullfrog sympathetic neurons. J Neurosci 2003; 23:4931-41. [PMID: 12832515 PMCID: PMC6741177] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Various neurotransmitters excite neurons by suppressing a ubiquitous, voltage-dependent, noninactivating K+ conductance called the M-conductance (gM). In bullfrog sympathetic ganglion neurons the suppression of gM by the P2Y agonist ATP involves phospholipase C (PLC). The present results are consistent with the involvement of the lipid and inositol phosphate cycles in the effects of both P2Y and muscarinic cholinergic agonists on gM. Impairment of resynthesis of phosphatidylinositol 4,5-bisphosphate (PIP2) with the phosphatidylinositol 4-kinase inhibitor wortmannin (10 microm) slowed or blocked the recovery of agonist-induced gM suppression. This effect could not be attributed to an action of wortmannin on myosin light chain kinase or on phosphatidylinositol 3-kinase. Inhibition of PIP2 synthesis at an earlier point in the lipid cycle by the use of R59022 (40 microm) to inhibit diacylglycerol kinase also slowed the rate of recovery of successive ATP responses. This effect required several applications of agonist to deplete levels of various phospholipid intermediates in the lipid cycle. PIP2 antibodies attenuated the suppression of gM by agonists. Intracellular application of 20 microm PIP2 slowed the rundown of KCNQ2/3 currents expressed in COS-1 or tsA-201 cells, and 100 microm PIP2 produced a small potentiation of native M-current bullfrog sympathetic neurons. These are the results that might be expected if agonist-induced activation of PLC and the concomitant depletion of PIP2 contribute to the excitatory action of neurotransmitters that suppress gM.
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Affiliation(s)
- Christopher P Ford
- Centre for Neuroscience, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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Abstract
The trans-Golgi network (TGN) is a major secretory pathway sorting station that directs newly synthesized proteins to different subcellular destinations. The TGN also receives extracellular materials and recycled molecules from endocytic compartments. In this review, we summarize recent progress on understanding TGN structure and the dynamics of trafficking to and from this compartment. Protein sorting into different transport vesicles requires specific interactions between sorting motifs on the cargo molecules and vesicle coat components that recognize these motifs. Current understanding of the various targeting signals and vesicle coat components that are involved in TGN sorting are discussed, as well as the molecules that participate in retrieval to this compartment in both yeast and mammalian cells. Besides proteins, lipids and lipid-modifying enzymes also participate actively in the formation of secretory vesicles. The possible mechanisms of action of these lipid hydrolases and lipid kinases are discussed. Finally, we summarize the fundamentally different apical and basolateral cell surface delivery mechanisms and the current facts and hypotheses on protein sorting from the TGN into the regulated secretory pathway in neuroendocrine cells.
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Affiliation(s)
- F Gu
- Vollum Institute, Oregon Health Science University, Portland 97201, USA
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Gary JD, Wurmser AE, Bonangelino CJ, Weisman LS, Emr SD. Fab1p is essential for PtdIns(3)P 5-kinase activity and the maintenance of vacuolar size and membrane homeostasis. J Cell Biol 1998; 143:65-79. [PMID: 9763421 PMCID: PMC2132800 DOI: 10.1083/jcb.143.1.65] [Citation(s) in RCA: 339] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/1998] [Revised: 09/03/1998] [Indexed: 11/22/2022] Open
Abstract
The Saccharomyces cerevisiae FAB1 gene encodes a 257-kD protein that contains a cysteine-rich RING-FYVE domain at its NH2-terminus and a kinase domain at its COOH terminus. Based on its sequence, Fab1p was initially proposed to function as a phosphatidylinositol 4-phosphate (PtdIns(4)P) 5-kinase (). Additional sequence analysis of the Fab1p kinase domain, reveals that Fab1p defines a subfamily of putative PtdInsP kinases that is distinct from the kinases that synthesize PtdIns(4,5)P2. Consistent with this, we find that unlike wild-type cells, fab1Delta, fab1(tsf), and fab1 kinase domain point mutants lack detectable levels of PtdIns(3,5)P2, a phosphoinositide recently identified both in yeast and mammalian cells. PtdIns(4,5)P2 synthesis, on the other hand, is only moderately affected even in fab1Delta mutants. The presence of PtdIns(3)P in fab1 mutants, combined with previous data, indicate that PtdIns(3,5)P2 synthesis is a two step process, requiring the production of PtdIns(3)P by the Vps34p PtdIns 3-kinase and the subsequent Fab1p- dependent phosphorylation of PtdIns(3)P yielding PtdIns(3,5)P2. Although Vps34p-mediated synthesis of PtdIns(3)P is required for the proper sorting of hydrolases from the Golgi to the vacuole, the production of PtdIns(3,5)P2 by Fab1p does not directly affect Golgi to vacuole trafficking, suggesting that PtdIns(3,5)P2 has a distinct function. The major phenotypes resulting from Fab1p kinase inactivation include temperature-sensitive growth, vacuolar acidification defects, and dramatic increases in vacuolar size. Based on our studies, we hypothesize that whereas Vps34p is essential for anterograde trafficking of membrane and protein cargoes to the vacuole, Fab1p may play an important compensatory role in the recycling/turnover of membranes deposited at the vacuole. Interestingly, deletion of VAC7 also results in an enlarged vacuole morphology and has no detectable PtdIns(3,5)P2, suggesting that Vac7p functions as an upstream regulator, perhaps in a complex with Fab1p. We propose that Fab1p and Vac7p are components of a signal transduction pathway which functions to regulate the efflux or turnover of vacuolar membranes through the regulated production of PtdIns(3,5)P2.
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Affiliation(s)
- J D Gary
- Division of Cellular and Molecular Medicine and Howard Hughes Medical Institute, University of California at San Diego, School of Medicine, La Jolla, California 92093-0668, USA
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Wiedemann C, Schäfer T, Burger MM, Sihra TS. An essential role for a small synaptic vesicle-associated phosphatidylinositol 4-kinase in neurotransmitter release. J Neurosci 1998; 18:5594-602. [PMID: 9671651 PMCID: PMC6793044] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Glutamate release from nerve terminals is the consequence of Ca2+-triggered fusion of small synaptic vesicles with the presynaptic plasma membrane. ATP dependence of neurotransmitter release has been suggested to be founded, in part, on phosphorylation steps preceding membrane fusion. Here we present evidence for an essential role of phosphatidylinositol phosphorylation in stimulated release of neurotransmitter glutamate from isolated nerve terminals (synaptosomes). Specifically, we show that a phosphatidylinositol 4-kinase (PtdIns 4-kinase) activity resides on nerve terminal-derived small synaptic vesicles (SSVs) and that inhibition of the PtdIns 4-kinase activity in intact synaptosomes leads to attenuation of the evoked release of glutamate. The attenuation of transmitter release is reversible and correlates with respective changes in intrasynaptosomal PtdIns 4-kinase activity. Because only the Ca2+-dependent release of glutamate is affected, regulation appears to be at the level of exocytosis. Taken together, our data imply a mandatory role for PtdIns 4-kinase and phosphoinositide products in the regulated exocytosis of SSV in mammalian nerve terminals.
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Affiliation(s)
- C Wiedemann
- Friedrich Miescher-Institute, 4002 Basel, Switzerland
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