1
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Montag K, Ivanov R, Bauer P. Role of SEC14-like phosphatidylinositol transfer proteins in membrane identity and dynamics. FRONTIERS IN PLANT SCIENCE 2023; 14:1181031. [PMID: 37255567 PMCID: PMC10225987 DOI: 10.3389/fpls.2023.1181031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/05/2023] [Indexed: 06/01/2023]
Abstract
Membrane identity and dynamic processes, that act at membrane sites, provide important cues for regulating transport, signal transduction and communication across membranes. There are still numerous open questions as to how membrane identity changes and the dynamic processes acting at the surface of membranes are regulated in diverse eukaryotes in particular plants and which roles are being played by protein interaction complexes composed of peripheral and integral membrane proteins. One class of peripheral membrane proteins conserved across eukaryotes comprises the SEC14-like phosphatidylinositol transfer proteins (SEC14L-PITPs). These proteins share a SEC14 domain that contributes to membrane identity and fulfills regulatory functions in membrane trafficking by its ability to sense, bind, transport and exchange lipophilic substances between membranes, such as phosphoinositides and diverse other lipophilic substances. SEC14L-PITPs can occur as single-domain SEC14-only proteins in all investigated organisms or with a modular domain structure as multi-domain proteins in animals and streptophytes (comprising charales and land plants). Here, we present an overview on the functional roles of SEC14L-PITPs, with a special focus on the multi-domain SEC14L-PITPs of the SEC14-nodulin and SEC14-GOLD group (PATELLINs, PATLs in plants). This indicates that SEC14L-PITPs play diverse roles from membrane trafficking to organism fitness in plants. We concentrate on the structure of SEC14L-PITPs, their ability to not only bind phospholipids but also other lipophilic ligands, and their ability to regulate complex cellular responses through interacting with proteins at membrane sites.
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Affiliation(s)
- Karolin Montag
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
| | - Rumen Ivanov
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
- Center of Excellence on Plant Sciences (CEPLAS), Germany
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2
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Hornbergs J, Montag K, Loschwitz J, Mohr I, Poschmann G, Schnake A, Gratz R, Brumbarova T, Eutebach M, Angrand K, Fink-Straube C, Stühler K, Zeier J, Hartmann L, Strodel B, Ivanov R, Bauer P. SEC14-GOLD protein PATELLIN2 binds IRON-REGULATED TRANSPORTER1 linking root iron uptake to vitamin E. PLANT PHYSIOLOGY 2023; 192:504-526. [PMID: 36493393 PMCID: PMC10152663 DOI: 10.1093/plphys/kiac563] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/23/2022] [Accepted: 12/07/2022] [Indexed: 05/03/2023]
Abstract
Organisms require micronutrients, and Arabidopsis (Arabidopsis thaliana) IRON-REGULATED TRANSPORTER1 (IRT1) is essential for iron (Fe2+) acquisition into root cells. Uptake of reactive Fe2+ exposes cells to the risk of membrane lipid peroxidation. Surprisingly little is known about how this is avoided. IRT1 activity is controlled by an intracellular variable region (IRT1vr) that acts as a regulatory protein interaction platform. Here, we describe that IRT1vr interacted with peripheral plasma membrane SEC14-Golgi dynamics (SEC14-GOLD) protein PATELLIN2 (PATL2). SEC14 proteins bind lipophilic substrates and transport or present them at the membrane. To date, no direct roles have been attributed to SEC14 proteins in Fe import. PATL2 affected root Fe acquisition responses, interacted with ROS response proteins in roots, and alleviated root lipid peroxidation. PATL2 had high affinity in vitro for the major lipophilic antioxidant vitamin E compound α-tocopherol. Molecular dynamics simulations provided insight into energetic constraints and the orientation and stability of the PATL2-ligand interaction in atomic detail. Hence, this work highlights a compelling mechanism connecting vitamin E with root metal ion transport at the plasma membrane with the participation of an IRT1-interacting and α-tocopherol-binding SEC14 protein.
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Affiliation(s)
- Jannik Hornbergs
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Karolin Montag
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Jennifer Loschwitz
- Institute of Theoretical Chemistry and Computer Chemistry, Heinrich Heine University, Düsseldorf 40225, Germany
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Inga Mohr
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Gereon Poschmann
- Institute of Molecular Medicine, Proteome Research, Medical Faculty and University Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Anika Schnake
- Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Regina Gratz
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | | | - Monique Eutebach
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Kalina Angrand
- Department of Biosciences-Plant Biology, Saarland University, Campus A2.4, D-66123 Saarbrücken, Germany
| | | | - Kai Stühler
- Institute of Molecular Medicine, Proteome Research, Medical Faculty and University Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Molecular Proteomics Laboratory, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Jürgen Zeier
- Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Düsseldorf 40225, Germany
- Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf 40225, Germany
| | - Laura Hartmann
- Institute of Macromolecular Chemistry, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Birgit Strodel
- Institute of Theoretical Chemistry and Computer Chemistry, Heinrich Heine University, Düsseldorf 40225, Germany
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rumen Ivanov
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
- Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf 40225, Germany
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3
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Chen XR, Poudel L, Hong Z, Johnen P, Katti S, Tripathi A, Nile AH, Green SM, Khan D, Schaaf G, Bono F, Bankaitis VA, Igumenova TI. Mechanisms by which small molecules of diverse chemotypes arrest Sec14 lipid transfer activity. J Biol Chem 2023; 299:102861. [PMID: 36603766 PMCID: PMC9898755 DOI: 10.1016/j.jbc.2022.102861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
Phosphatidylinositol (PtdIns) transfer proteins (PITPs) enhance the activities of PtdIns 4-OH kinases that generate signaling pools of PtdIns-4-phosphate. In that capacity, PITPs serve as key regulators of lipid signaling in eukaryotic cells. Although the PITP phospholipid exchange cycle is the engine that stimulates PtdIns 4-OH kinase activities, the underlying mechanism is not understood. Herein, we apply an integrative structural biology approach to investigate interactions of the yeast PITP Sec14 with small-molecule inhibitors (SMIs) of its phospholipid exchange cycle. Using a combination of X-ray crystallography, solution NMR spectroscopy, and atomistic MD simulations, we dissect how SMIs compete with native Sec14 phospholipid ligands and arrest phospholipid exchange. Moreover, as Sec14 PITPs represent new targets for the development of next-generation antifungal drugs, the structures of Sec14 bound to SMIs of diverse chemotypes reported in this study will provide critical information required for future structure-based design of next-generation lead compounds directed against Sec14 PITPs of virulent fungi.
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Affiliation(s)
- Xiao-Ru Chen
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA
| | - Lokendra Poudel
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA
| | - Zebin Hong
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Philipp Johnen
- Institute for Crop Science and Resource Conservation, Universität Bonn, Bonn, Germany
| | - Sachin Katti
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA
| | - Ashutosh Tripathi
- Department of Cell Biology & Genetics, Texas A&M University, College Station, Texas, USA
| | - Aaron H Nile
- Department of Cell Biology & Genetics, Texas A&M University, College Station, Texas, USA
| | - Savana M Green
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA; Department of Cell Biology & Genetics, Texas A&M University, College Station, Texas, USA
| | - Danish Khan
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA
| | - Gabriel Schaaf
- Institute for Crop Science and Resource Conservation, Universität Bonn, Bonn, Germany
| | - Fulvia Bono
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Vytas A Bankaitis
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA; Department of Cell Biology & Genetics, Texas A&M University, College Station, Texas, USA.
| | - Tatyana I Igumenova
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA.
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4
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Holič R, Šťastný D, Griač P. Sec14 family of lipid transfer proteins in yeasts. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158990. [PMID: 34118432 DOI: 10.1016/j.bbalip.2021.158990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022]
Abstract
The hydrophobicity of lipids prevents their free movement across the cytoplasm. To achieve highly heterogeneous and precisely regulated lipid distribution in different cellular membranes, lipids are transported by lipid transfer proteins (LTPs) in addition to their transport by vesicles. Sec14 family is one of the most extensively studied groups of LTPs. Here we provide an overview of Sec14 family of LTPs in the most studied yeast Saccharomyces cerevisiae as well as in other selected non-Saccharomyces yeasts-Schizosaccharomyces pombe, Kluyveromyces lactis, Candida albicans, Candida glabrata, Cryptococcus neoformans, and Yarrowia lipolytica. Discussed are specificities of Sec14-domain LTPs in various yeasts, their mode of action, subcellular localization, and physiological function. In addition, quite few Sec14 family LTPs are target of antifungal drugs, serve as modifiers of drug resistance or influence virulence of pathologic yeasts. Thus, they represent an important object of study from the perspective of human health.
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Affiliation(s)
- Roman Holič
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Dominik Šťastný
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Peter Griač
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava, Slovakia.
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5
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Lete MG, Tripathi A, Chandran V, Bankaitis VA, McDermott MI. Lipid transfer proteins and instructive regulation of lipid kinase activities: Implications for inositol lipid signaling and disease. Adv Biol Regul 2020; 78:100740. [PMID: 32992233 PMCID: PMC7986245 DOI: 10.1016/j.jbior.2020.100740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/16/2020] [Accepted: 06/24/2020] [Indexed: 05/17/2023]
Abstract
Cellular membranes are critical platforms for intracellular signaling that involve complex interfaces between lipids and proteins, and a web of interactions between a multitude of lipid metabolic pathways. Membrane lipids impart structural and functional information in this regulatory circuit that encompass biophysical parameters such as membrane thickness and fluidity, as well as chaperoning the interactions of protein binding partners. Phosphatidylinositol and its phosphorylated derivatives, the phosphoinositides, play key roles in intracellular membrane signaling, and these involvements are translated into an impressively diverse set of biological outcomes. The phosphatidylinositol transfer proteins (PITPs) are key regulators of phosphoinositide signaling. Found in a diverse array of organisms from plants, yeast and apicomplexan parasites to mammals, PITPs were initially proposed to be simple transporters of lipids between intracellular membranes. It now appears increasingly unlikely that the soluble versions of these proteins perform such functions within the cell. Rather, these serve to facilitate the activity of intrinsically biologically insufficient inositol lipid kinases and, in so doing, promote diversification of the biological outcomes of phosphoinositide signaling. The central engine for execution of such functions is the lipid exchange cycle that is a fundamental property of PITPs. How PITPs execute lipid exchange remains very poorly understood. Molecular dynamics simulation approaches are now providing the first atomistic insights into how PITPs, and potentially other lipid-exchange/transfer proteins, operate.
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Affiliation(s)
- Marta G Lete
- Department of Molecular and Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX, 77843-1114, USA; Institute Biofisika (UPV/EHU, CSIC) and University of the Basque Country, Leioa, Spain
| | - Ashutosh Tripathi
- Department of Molecular and Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX, 77843-1114, USA
| | - Vijay Chandran
- Department of Molecular and Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX, 77843-1114, USA
| | - Vytas A Bankaitis
- Department of Molecular and Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX, 77843-1114, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA; Department of Chemistry, Texas A&M University, College Station, TX, 77840, USA
| | - Mark I McDermott
- Department of Molecular and Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX, 77843-1114, USA.
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6
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Lipp NF, Ikhlef S, Milanini J, Drin G. Lipid Exchangers: Cellular Functions and Mechanistic Links With Phosphoinositide Metabolism. Front Cell Dev Biol 2020; 8:663. [PMID: 32793602 PMCID: PMC7385082 DOI: 10.3389/fcell.2020.00663] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/01/2020] [Indexed: 12/28/2022] Open
Abstract
Lipids are amphiphilic molecules that self-assemble to form biological membranes. Thousands of lipid species coexist in the cell and, once combined, define organelle identity. Due to recent progress in lipidomic analysis, we now know how lipid composition is finely tuned in different subcellular regions. Along with lipid synthesis, remodeling and flip-flop, lipid transfer is one of the active processes that regulates this intracellular lipid distribution. It is mediated by Lipid Transfer Proteins (LTPs) that precisely move certain lipid species across the cytosol and between the organelles. A particular subset of LTPs from three families (Sec14, PITP, OSBP/ORP/Osh) act as lipid exchangers. A striking feature of these exchangers is that they use phosphatidylinositol or phosphoinositides (PIPs) as a lipid ligand and thereby have specific links with PIP metabolism and are thus able to both control the lipid composition of cellular membranes and their signaling capacity. As a result, they play pivotal roles in cellular processes such as vesicular trafficking and signal transduction at the plasma membrane. Recent data have shown that some PIPs are used as energy by lipid exchangers to generate lipid gradients between organelles. Here we describe the importance of lipid counter-exchange in the cell, its structural basis, and presumed links with pathologies.
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Affiliation(s)
- Nicolas-Frédéric Lipp
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Valbonne, France
| | - Souade Ikhlef
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Valbonne, France
| | - Julie Milanini
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Valbonne, France
| | - Guillaume Drin
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Valbonne, France
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7
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Tripathi A, Martinez E, Obaidullah AJ, Lete MG, Lönnfors M, Khan D, Soni KG, Mousley CJ, Kellogg GE, Bankaitis VA. Functional diversification of the chemical landscapes of yeast Sec14-like phosphatidylinositol transfer protein lipid-binding cavities. J Biol Chem 2019; 294:19081-19098. [PMID: 31690622 DOI: 10.1074/jbc.ra119.011153] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/31/2019] [Indexed: 01/22/2023] Open
Abstract
Phosphatidylinositol-transfer proteins (PITPs) are key regulators of lipid signaling in eukaryotic cells. These proteins both potentiate the activities of phosphatidylinositol (PtdIns) 4-OH kinases and help channel production of specific pools of phosphatidylinositol 4-phosphate (PtdIns(4)P) dedicated to specific biological outcomes. In this manner, PITPs represent a major contributor to the mechanisms by which the biological outcomes of phosphoinositide are diversified. The two-ligand priming model proposes that the engine by which Sec14-like PITPs potentiate PtdIns kinase activities is a heterotypic lipid-exchange cycle where PtdIns is a common exchange substrate among the Sec14-like PITP family, but the second exchange ligand varies with the PITP. A major prediction of this model is that second-exchangeable ligand identity will vary from PITP to PITP. To address the heterogeneity in the second exchange ligand for Sec14-like PITPs, we used structural, computational, and biochemical approaches to probe the diversities of the lipid-binding cavity microenvironments of the yeast Sec14-like PITPs. The collective data report that yeast Sec14-like PITP lipid-binding pockets indeed define diverse chemical microenvironments that translate into differential ligand-binding specificities across this protein family.
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Affiliation(s)
- Ashutosh Tripathi
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, College Station, Texas 77843-1114
| | - Elliott Martinez
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
| | - Ahmad J Obaidullah
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0540
| | - Marta G Lete
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, College Station, Texas 77843-1114
| | - Max Lönnfors
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, College Station, Texas 77843-1114
| | - Danish Khan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
| | - Krishnakant G Soni
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, College Station, Texas 77843-1114
| | - Carl J Mousley
- School of Biomedical Sciences, Curtin Health Innovation Research Institute (CHIRI), Faculty of Health Sciences, Curtin University, Bentley, Western Australia 6102, Australia
| | - Glen E Kellogg
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0540
| | - Vytas A Bankaitis
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, College Station, Texas 77843-1114 .,Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128.,Department of Chemistry, Texas A&M University, College Station, Texas 77843-2128
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8
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Mizuike A, Kobayashi S, Rikukawa T, Ohta A, Horiuchi H, Fukuda R. Suppression of respiratory growth defect of mitochondrial phosphatidylserine decarboxylase deficient mutant by overproduction of Sfh1, a Sec14 homolog, in yeast. PLoS One 2019; 14:e0215009. [PMID: 30958856 PMCID: PMC6453485 DOI: 10.1371/journal.pone.0215009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 03/25/2019] [Indexed: 12/15/2022] Open
Abstract
Interorganelle phospholipid transfer is critical for eukaryotic membrane biogenesis. In the yeast Saccharomyces cerevisiae, phosphatidylserine (PS) synthesized by PS synthase, Pss1, in the endoplasmic reticulum (ER) is decarboxylated to phosphatidylethanolamine (PE) by PS decarboxylase, Psd1, in the ER and mitochondria or by Psd2 in the endosome, Golgi, and/or vacuole, but the mechanism of interorganelle PS transport remains to be elucidated. Here we report that Sfh1, a member of Sec14 family proteins of S. cerevisiae, possesses the ability to enhance PE production by Psd2. Overexpression of SFH1 in the strain defective in Psd1 restored its growth on non-fermentable carbon sources and increased the intracellular and mitochondrial PE levels. Sfh1 was found to bind various phospholipids, including PS, in vivo. Bacterially expressed and purified Sfh1 was suggested to have the ability to transport fluorescently labeled PS between liposomes by fluorescence dequenching assay in vitro. Biochemical subcellular fractionation suggested that a fraction of Sfh1 localizes to the endosome, Golgi, and/or vacuole. We propose a model that Sfh1 promotes PE production by Psd2 by transferring phospholipids between the ER and endosome.
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Affiliation(s)
- Aya Mizuike
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shingo Kobayashi
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takashi Rikukawa
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Akinori Ohta
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Hiroyuki Horiuchi
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ryouichi Fukuda
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- * E-mail:
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9
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Guo Y, Guo C, Ha W, Ding Z. Carnosine improves diabetic retinopathy via the MAPK/ERK pathway. Exp Ther Med 2019; 17:2641-2647. [PMID: 30930967 PMCID: PMC6425270 DOI: 10.3892/etm.2019.7223] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 11/28/2018] [Indexed: 12/20/2022] Open
Abstract
Diabetic retinopathy (DR) is one of the most common causes of blindness in developed countries. Due to its asymptomatic onset and progressive disease course, DR is typically diagnosed at a late stage when treatment options are limited and therefore often results in irreversible blindness. Studies have demonstrated that carnosine may prevent and treat DR. In a previous study, the positive effect of carnosine on DR was determined and it was revealed that there may be an association between carnosine and the mitogen-activated protein kinase (MAPK)/extracellular signal related kinase (ERK) signaling pathway. To assess the interaction between carnosine and the MAPK/ERK signaling pathway, changes in PKC, ERK and p-ERK expression was assessed in diabetic rats following treatment with carnosine, PD98059 or U46619 via reverse transcription-quantitative polymerase chain reaction and western blotting. The results demonstrated that the expression of ERK and p-ERK were significantly suppressed following treatment with carnosine, but no significant effect on the expression of PKC was identified, which indicates that suppressing the activation of the MAPK/ERK signaling pathway may serve an important role in carnosine-induced DR prevention and treatment.
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Affiliation(s)
- Yong Guo
- Department of Ophthalmology, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Chenjun Guo
- Department of Ophthalmology, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Wenjing Ha
- Department of Ophthalmology, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Zhenhua Ding
- Department of Ophthalmology, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi 710038, P.R. China
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10
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Pemberton JG, Balla T. Polyphosphoinositide-Binding Domains: Insights from Peripheral Membrane and Lipid-Transfer Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1111:77-137. [PMID: 30483964 DOI: 10.1007/5584_2018_288] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Within eukaryotic cells, biochemical reactions need to be organized on the surface of membrane compartments that use distinct lipid constituents to dynamically modulate the functions of integral proteins or influence the selective recruitment of peripheral membrane effectors. As a result of these complex interactions, a variety of human pathologies can be traced back to improper communication between proteins and membrane surfaces; either due to mutations that directly alter protein structure or as a result of changes in membrane lipid composition. Among the known structural lipids found in cellular membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the membrane-anchored precursor of low-abundance regulatory lipids, the polyphosphoinositides (PPIn), which have restricted distributions within specific subcellular compartments. The ability of PPIn lipids to function as signaling platforms relies on both non-specific electrostatic interactions and the selective stereospecific recognition of PPIn headgroups by specialized protein folds. In this chapter, we will attempt to summarize the structural diversity of modular PPIn-interacting domains that facilitate the reversible recruitment and conformational regulation of peripheral membrane proteins. Outside of protein folds capable of capturing PPIn headgroups at the membrane interface, recent studies detailing the selective binding and bilayer extraction of PPIn species by unique functional domains within specific families of lipid-transfer proteins will also be highlighted. Overall, this overview will help to outline the fundamental physiochemical mechanisms that facilitate localized interactions between PPIn lipids and the wide-variety of PPIn-binding proteins that are essential for the coordinate regulation of cellular metabolism and membrane dynamics.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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11
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Grabon A, Bankaitis VA, McDermott MI. The interface between phosphatidylinositol transfer protein function and phosphoinositide signaling in higher eukaryotes. J Lipid Res 2018; 60:242-268. [PMID: 30504233 DOI: 10.1194/jlr.r089730] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/12/2018] [Indexed: 12/22/2022] Open
Abstract
Phosphoinositides are key regulators of a large number of diverse cellular processes that include membrane trafficking, plasma membrane receptor signaling, cell proliferation, and transcription. How a small number of chemically distinct phosphoinositide signals are functionally amplified to exert specific control over such a diverse set of biological outcomes remains incompletely understood. To this end, a novel mechanism is now taking shape, and it involves phosphatidylinositol (PtdIns) transfer proteins (PITPs). The concept that PITPs exert instructive regulation of PtdIns 4-OH kinase activities and thereby channel phosphoinositide production to specific biological outcomes, identifies PITPs as central factors in the diversification of phosphoinositide signaling. There are two evolutionarily distinct families of PITPs: the Sec14-like and the StAR-related lipid transfer domain (START)-like families. Of these two families, the START-like PITPs are the least understood. Herein, we review recent insights into the biochemical, cellular, and physiological function of both PITP families with greater emphasis on the START-like PITPs, and we discuss the underlying mechanisms through which these proteins regulate phosphoinositide signaling and how these actions translate to human health and disease.
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Affiliation(s)
- Aby Grabon
- E. L. Wehner-Welch Laboratory, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114
| | - Vytas A Bankaitis
- E. L. Wehner-Welch Laboratory, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114
| | - Mark I McDermott
- E. L. Wehner-Welch Laboratory, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114
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12
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Target Identification and Mechanism of Action of Picolinamide and Benzamide Chemotypes with Antifungal Properties. Cell Chem Biol 2018; 25:279-290.e7. [PMID: 29307839 DOI: 10.1016/j.chembiol.2017.12.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/18/2017] [Accepted: 12/06/2017] [Indexed: 11/20/2022]
Abstract
Invasive fungal infections are accompanied by high mortality rates that range up to 90%. At present, only three different compound classes are available for use in the clinic, and these often suffer from low bioavailability, toxicity, and drug resistance. These issues emphasize an urgent need for novel antifungal agents. Herein, we report the identification of chemically versatile benzamide and picolinamide scaffolds with antifungal properties. Chemogenomic profiling and biochemical assays with purified protein identified Sec14p, the major phosphatidylinositol/phosphatidylcholine transfer protein in Saccharomyces cerevisiae, as the sole essential target for these compounds. A functional variomics screen identified resistance-conferring residues that localized to the lipid-binding pocket of Sec14p. Determination of the X-ray co-crystal structure of a Sec14p-compound complex confirmed binding in this cavity and rationalized both the resistance-conferring residues and the observed structure-activity relationships. Taken together, these findings open new avenues for rational compound optimization and development of novel antifungal agents.
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13
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Grabon A, Orłowski A, Tripathi A, Vuorio J, Javanainen M, Róg T, Lönnfors M, McDermott MI, Siebert G, Somerharju P, Vattulainen I, Bankaitis VA. Dynamics and energetics of the mammalian phosphatidylinositol transfer protein phospholipid exchange cycle. J Biol Chem 2017; 292:14438-14455. [PMID: 28718450 DOI: 10.1074/jbc.m117.791467] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 07/14/2017] [Indexed: 11/06/2022] Open
Abstract
Phosphatidylinositol-transfer proteins (PITPs) regulate phosphoinositide signaling in eukaryotic cells. The defining feature of PITPs is their ability to exchange phosphatidylinositol (PtdIns) molecules between membranes, and this property is central to PITP-mediated regulation of lipid signaling. However, the details of the PITP-mediated lipid exchange cycle remain entirely obscure. Here, all-atom molecular dynamics simulations of the mammalian StART-like PtdIns/phosphatidylcholine (PtdCho) transfer protein PITPα, both on membrane bilayers and in solvated systems, informed downstream biochemical analyses that tested key aspects of the hypotheses generated by the molecular dynamics simulations. These studies provided five key insights into the PITPα lipid exchange cycle: (i) interaction of PITPα with the membrane is spontaneous and mediated by four specific protein substructures; (ii) the ability of PITPα to initiate closure around the PtdCho ligand is accompanied by loss of flexibility of two helix/loop regions, as well as of the C-terminal helix; (iii) the energy barrier of phospholipid extraction from the membrane is lowered by a network of hydrogen bonds between the lipid molecule and PITPα; (iv) the trajectory of PtdIns or PtdCho into and through the lipid-binding pocket is chaperoned by sets of PITPα residues conserved throughout the StART-like PITP family; and (v) conformational transitions in the C-terminal helix have specific functional involvements in PtdIns transfer activity. Taken together, these findings provide the first mechanistic description of key aspects of the PITPα PtdIns/PtdCho exchange cycle and offer a rationale for the high conservation of particular sets of residues across evolutionarily distant members of the metazoan StART-like PITP family.
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Affiliation(s)
- Aby Grabon
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843
| | - Adam Orłowski
- the Laboratory of Physics, Tampere University of Technology, FI-33720 Tampere, Finland.,the Department of Physics and Energy, University of Limerick, Limerick V94 T9PX, Ireland
| | - Ashutosh Tripathi
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843
| | - Joni Vuorio
- the Laboratory of Physics, Tampere University of Technology, FI-33720 Tampere, Finland.,the Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- the Laboratory of Physics, Tampere University of Technology, FI-33720 Tampere, Finland
| | - Tomasz Róg
- the Laboratory of Physics, Tampere University of Technology, FI-33720 Tampere, Finland.,the Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland
| | - Max Lönnfors
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843
| | - Mark I McDermott
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843
| | - Garland Siebert
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843
| | - Pentti Somerharju
- the Department of Biochemistry and Developmental Biology, University of Helsinki, P. O. Box 63, FI-00014 Helsinki, Finland
| | - Ilpo Vattulainen
- the Laboratory of Physics, Tampere University of Technology, FI-33720 Tampere, Finland, .,the Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland.,the Department of Physics and Chemistry, MEMPHYS, Center for Biomembrane Physics, University of Southern Denmark, DK-5230 Odense, Denmark, and
| | - Vytas A Bankaitis
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843, .,the Departments of Biochemistry and Biophysics and.,Chemistry, Texas A&M University, College Station, Texas 77843
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14
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Lipid transfer proteins and the tuning of compartmental identity in the Golgi apparatus. Chem Phys Lipids 2016; 200:42-61. [DOI: 10.1016/j.chemphyslip.2016.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 06/21/2016] [Accepted: 06/22/2016] [Indexed: 11/23/2022]
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15
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Huang J, Ghosh R, Bankaitis VA. Sec14-like phosphatidylinositol transfer proteins and the biological landscape of phosphoinositide signaling in plants. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:1352-1364. [PMID: 27038688 DOI: 10.1016/j.bbalip.2016.03.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 01/01/2023]
Abstract
Phosphoinositides and soluble inositol phosphates are essential components of a complex intracellular chemical code that regulates major aspects of lipid signaling in eukaryotes. These involvements span a broad array of biological outcomes and activities, and cells are faced with the problem of how to compartmentalize and organize these various signaling events into a coherent scheme. It is in the arena of how phosphoinositide signaling circuits are integrated and, and how phosphoinositide pools are functionally defined and channeled to privileged effectors, that phosphatidylinositol (PtdIns) transfer proteins (PITPs) are emerging as critical players. As plant systems offer some unique advantages and opportunities for study of these proteins, we discuss herein our perspectives regarding the progress made in plant systems regarding PITP function. We also suggest interesting prospects that plant systems hold for interrogating how PITPs work, particularly in multi-domain contexts, to diversify the biological outcomes for phosphoinositide signaling. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.
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Affiliation(s)
- Jin Huang
- Department of Molecular & Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX 77843-1114 USA.
| | - Ratna Ghosh
- Department of Molecular & Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX 77843-1114 USA
| | - Vytas A Bankaitis
- Department of Molecular & Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX 77843-1114 USA; Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843-1114 USA; Department of Chemistry, Texas A&M University, College Station, TX 77843-1114 USA.
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16
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Khan D, McGrath KR, Dorosheva O, Bankaitis VA, Tripathi A. Structural elements that govern Sec14-like PITP sensitivities to potent small molecule inhibitors. J Lipid Res 2016; 57:650-62. [PMID: 26921357 DOI: 10.1194/jlr.m066381] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Indexed: 12/15/2022] Open
Abstract
Sec14-like phosphatidylinositol transfer proteins (PITPs) play important biological functions in integrating multiple aspects of intracellular lipid metabolism with phosphatidylinositol-4-phosphate signaling. As such, these proteins offer new opportunities for highly selective chemical interference with specific phosphoinositide pathways in cells. The first and best characterized small molecule inhibitors of the yeast PITP, Sec14, are nitrophenyl(4-(2-methoxyphenyl)piperazin-1-yl)methanones (NPPMs), and a hallmark feature of NPPMs is their exquisite targeting specificities for Sec14 relative to other closely related Sec14-like PITPs. Our present understanding of Sec14::NPPM binding interactions is based on computational docking and rational loss-of-function approaches. While those approaches have been informative, we still lack an adequate understanding of the basis for the high selectivity of NPPMs among closely related Sec14-like PITPs. Herein, we describe a Sec14 motif, which we term the VV signature, that contributes significantly to the NPPM sensitivity/resistance of Sec14-like phosphatidylinositol (PtdIns)/phosphatidylcholine (PtdCho) transfer proteins. The data not only reveal previously unappreciated determinants that govern Sec14-like PITP sensitivities to NPPMs, but enable predictions of which Sec14-like PtdIns/PtdCho transfer proteins are likely to be NPPM resistant or sensitive based on primary sequence considerations. Finally, the data provide independent evidence in support of previous studies highlighting the importance of Sec14 residue Ser173 in the mechanism by which NPPMs engage and inhibit Sec14-like PITPs.
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Affiliation(s)
- Danish Khan
- Departments of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128
| | - Kaitlyn R McGrath
- Departments of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128
| | - Oleksandra Dorosheva
- Departments of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128
| | - Vytas A Bankaitis
- Departments of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128 Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, College Station, TX 77843-1114 Chemistry, Texas A&M University, College Station, TX 77843-2128
| | - Ashutosh Tripathi
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, College Station, TX 77843-1114
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17
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Sec14-like phosphatidylinositol-transfer proteins and diversification of phosphoinositide signalling outcomes. Biochem Soc Trans 2015; 42:1383-8. [PMID: 25233419 DOI: 10.1042/bst20140187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The physiological functions of phosphatidylinositol (PtdIns)-transfer proteins (PITPs)/phosphatidylcholine (PtdCho)-transfer proteins are poorly characterized, even though these proteins are conserved throughout the eukaryotic kingdom. Much of the progress in elucidating PITP functions has come from exploitation of genetically tractable model organisms, but the mechanisms for how PITPs execute their biological activities remain unclear. Structural and molecular dynamics approaches are filling in the details for how these proteins actually work as molecules. In the present paper, we discuss our recent work with Sec14-like PITPs and describe how PITPs integrate diverse territories of the lipid metabolome with phosphoinositide signalling.
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18
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Grabon A, Khan D, Bankaitis VA. Phosphatidylinositol transfer proteins and instructive regulation of lipid kinase biology. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1851:724-35. [PMID: 25592381 PMCID: PMC5221696 DOI: 10.1016/j.bbalip.2014.12.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 11/21/2014] [Accepted: 12/16/2014] [Indexed: 11/25/2022]
Abstract
Phosphatidylinositol is a metabolic precursor of phosphoinositides and soluble inositol phosphates. Both sets of molecules represent versatile intracellular chemical signals in eukaryotes. While much effort has been invested in understanding the enzymes that produce and consume these molecules, central aspects for how phosphoinositide production is controlled and functionally partitioned remain unresolved and largely unappreciated. It is in this regard that phosphatidylinositol (PtdIns) transfer proteins (PITPs) are emerging as central regulators of the functional channeling of phosphoinositide pools produced on demand for specific signaling purposes. The physiological significance of these proteins is amply demonstrated by the consequences that accompany deficits in individual PITPs. Although the biological problem is fascinating, and of direct relevance to disease, PITPs remain largely uncharacterized. Herein, we discuss our perspectives regarding what is known about how PITPs work as molecules, and highlight progress in our understanding of how PITPs are integrated into cellular physiology. This article is part of a Special Issue entitled Phosphoinositides.
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Affiliation(s)
- Aby Grabon
- Department of Molecular & Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114, USA
| | - Danish Khan
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| | - Vytas A Bankaitis
- Department of Molecular & Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114, USA; Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
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19
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Ghosh R, de Campos MKF, Huang J, Huh SK, Orlowski A, Yang Y, Tripathi A, Nile A, Lee HC, Dynowski M, Schäfer H, Róg T, Lete MG, Ahyayauch H, Alonso A, Vattulainen I, Igumenova TI, Schaaf G, Bankaitis VA. Sec14-nodulin proteins and the patterning of phosphoinositide landmarks for developmental control of membrane morphogenesis. Mol Biol Cell 2015; 26:1764-81. [PMID: 25739452 PMCID: PMC4436786 DOI: 10.1091/mbc.e14-10-1475] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/26/2015] [Indexed: 12/12/2022] Open
Abstract
A Sec14-nodulin protein model is used to identify the nodulin domain as a novel phosphoinositide effector module with a role in controlling lateral organization of phosphoinositide. The domain organization of Sec14-nodulin proteins suggests a versatile principle for the bit mapping of membrane surfaces into high-definition lipid-signaling screens. Polarized membrane morphogenesis is a fundamental activity of eukaryotic cells. This process is essential for the biology of cells and tissues, and its execution demands exquisite temporal coordination of functionally diverse membrane signaling reactions with high spatial resolution. Moreover, mechanisms must exist to establish and preserve such organization in the face of randomizing forces that would diffuse it. Here we identify the conserved AtSfh1 Sec14-nodulin protein as a novel effector of phosphoinositide signaling in the extreme polarized membrane growth program exhibited by growing Arabidopsis root hairs. The data are consistent with Sec14-nodulin proteins controlling the lateral organization of phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) landmarks for polarized membrane morphogenesis in plants. This patterning activity requires both the PtdIns(4,5)P2 binding and homo-oligomerization activities of the AtSfh1 nodulin domain and is an essential aspect of the polarity signaling program in root hairs. Finally, the data suggest a general principle for how the phosphoinositide signaling landscape is physically bit mapped so that eukaryotic cells are able to convert a membrane surface into a high-definition lipid-signaling screen.
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Affiliation(s)
- Ratna Ghosh
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843
| | - Marília K F de Campos
- Center for Plant Molecular Biology, Plant Physiology, Universität Tübingen, 72076 Tübingen, Germany
| | - Jin Huang
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843
| | - Seong K Huh
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843
| | - Adam Orlowski
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
| | - Yuan Yang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Ashutosh Tripathi
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843
| | - Aaron Nile
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843
| | - Hsin-Chieh Lee
- Center for Plant Molecular Biology, Plant Physiology, Universität Tübingen, 72076 Tübingen, Germany
| | - Marek Dynowski
- Zentrum für Datenverarbeitung, Universität Tübingen, 72074 Tübingen, Germany
| | - Helen Schäfer
- Center for Plant Molecular Biology, Plant Physiology, Universität Tübingen, 72076 Tübingen, Germany
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
| | - Marta G Lete
- Unidad de Biofísica (CSIC, UPV/EHU), Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain
| | - Hasna Ahyayauch
- Unidad de Biofísica (CSIC, UPV/EHU), Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain Institut de Formation aux Carrieres de Sante de Rabat, 10000 Rabat, Morocco
| | - Alicia Alonso
- Unidad de Biofísica (CSIC, UPV/EHU), Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Gabriel Schaaf
- Center for Plant Molecular Biology, Plant Physiology, Universität Tübingen, 72076 Tübingen, Germany
| | - Vytas A Bankaitis
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843 Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843 Department of Chemistry, Texas A&M University, College Station, TX 77843
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20
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Lee AY, St Onge RP, Proctor MJ, Wallace IM, Nile AH, Spagnuolo PA, Jitkova Y, Gronda M, Wu Y, Kim MK, Cheung-Ong K, Torres NP, Spear ED, Han MKL, Schlecht U, Suresh S, Duby G, Heisler LE, Surendra A, Fung E, Urbanus ML, Gebbia M, Lissina E, Miranda M, Chiang JH, Aparicio AM, Zeghouf M, Davis RW, Cherfils J, Boutry M, Kaiser CA, Cummins CL, Trimble WS, Brown GW, Schimmer AD, Bankaitis VA, Nislow C, Bader GD, Giaever G. Mapping the cellular response to small molecules using chemogenomic fitness signatures. Science 2014; 344:208-11. [PMID: 24723613 DOI: 10.1126/science.1250217] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genome-wide characterization of the in vivo cellular response to perturbation is fundamental to understanding how cells survive stress. Identifying the proteins and pathways perturbed by small molecules affects biology and medicine by revealing the mechanisms of drug action. We used a yeast chemogenomics platform that quantifies the requirement for each gene for resistance to a compound in vivo to profile 3250 small molecules in a systematic and unbiased manner. We identified 317 compounds that specifically perturb the function of 121 genes and characterized the mechanism of specific compounds. Global analysis revealed that the cellular response to small molecules is limited and described by a network of 45 major chemogenomic signatures. Our results provide a resource for the discovery of functional interactions among genes, chemicals, and biological processes.
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Affiliation(s)
- Anna Y Lee
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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21
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Nile AH, Tripathi A, Yuan P, Mousley CJ, Suresh S, Wallace IM, Shah SD, Pohlhaus DT, Temple B, Nislow C, Giaever G, Tropsha A, Davis RW, St Onge RP, Bankaitis VA. PITPs as targets for selectively interfering with phosphoinositide signaling in cells. Nat Chem Biol 2014; 10:76-84. [PMID: 24292071 PMCID: PMC4059020 DOI: 10.1038/nchembio.1389] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 10/02/2013] [Indexed: 01/26/2023]
Abstract
Sec14-like phosphatidylinositol transfer proteins (PITPs) integrate diverse territories of intracellular lipid metabolism with stimulated phosphatidylinositol-4-phosphate production and are discriminating portals for interrogating phosphoinositide signaling. Yet, neither Sec14-like PITPs nor PITPs in general have been exploited as targets for chemical inhibition for such purposes. Herein, we validate what is to our knowledge the first small-molecule inhibitors (SMIs) of the yeast PITP Sec14. These SMIs are nitrophenyl(4-(2-methoxyphenyl)piperazin-1-yl)methanones (NPPMs) and are effective inhibitors in vitro and in vivo. We further establish that Sec14 is the sole essential NPPM target in yeast and that NPPMs exhibit exquisite targeting specificities for Sec14 (relative to related Sec14-like PITPs), propose a mechanism for how NPPMs exert their inhibitory effects and demonstrate that NPPMs exhibit exquisite pathway selectivity in inhibiting phosphoinositide signaling in cells. These data deliver proof of concept that PITP-directed SMIs offer new and generally applicable avenues for intervening with phosphoinositide signaling pathways with selectivities superior to those afforded by contemporary lipid kinase-directed strategies.
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Affiliation(s)
- Aaron H. Nile
- Department of Molecular & Cellular Medicine, Department of Biochemistry & Biophysics, Department of Chemistry, Texas A&M University, College Station, Texas 77843-1114 USA
- Department of Cell & Developmental Biology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7090 USA
| | - Ashutosh Tripathi
- Department of Molecular & Cellular Medicine, Department of Biochemistry & Biophysics, Department of Chemistry, Texas A&M University, College Station, Texas 77843-1114 USA
- Laboratory for Molecular Modeling, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7355 USA
| | - Peihua Yuan
- Department of Molecular & Cellular Medicine, Department of Biochemistry & Biophysics, Department of Chemistry, Texas A&M University, College Station, Texas 77843-1114 USA
| | - Carl J. Mousley
- Department of Molecular & Cellular Medicine, Department of Biochemistry & Biophysics, Department of Chemistry, Texas A&M University, College Station, Texas 77843-1114 USA
| | - Sundari Suresh
- Department of Biochemistry, Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
| | - Iain Michael Wallace
- Department of Biochemistry, Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
| | - Sweety D. Shah
- Department of Cell & Developmental Biology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7090 USA
| | - Denise Teotico Pohlhaus
- Laboratory for Molecular Modeling, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7355 USA
| | - Brenda Temple
- R. L. Juliano Structural Bioinformatics Core, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260 USA
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences,, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Guri Giaever
- Faculty of Pharmaceutical Sciences,, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7355 USA
| | - Ronald W. Davis
- Department of Biochemistry, Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
| | - Robert P. St Onge
- Department of Biochemistry, Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
| | - Vytas A. Bankaitis
- Department of Molecular & Cellular Medicine, Department of Biochemistry & Biophysics, Department of Chemistry, Texas A&M University, College Station, Texas 77843-1114 USA
- Department of Cell & Developmental Biology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7090 USA
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22
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Bromley D, Anderson PC, Daggett V. Structural consequences of mutations to the α-tocopherol transfer protein associated with the neurodegenerative disease ataxia with vitamin E deficiency. Biochemistry 2013; 52:4264-73. [PMID: 23713716 DOI: 10.1021/bi4001084] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The α-tocopherol transfer protein (α-TTP) is a liver protein that transfers α-tocopherol (vitamin E) to very-low-density lipoproteins (VLDLs). These VLDLs are then circulated throughout the body to maintain blood α-tocopherol levels. Mutations to the α-TTP gene are associated with ataxia with vitamin E deficiency, a disease characterized by peripheral nerve degeneration. In this study, molecular dynamics simulations of the E141K and R59W disease-associated mutants were performed. The mutants displayed disruptions in and around the ligand-binding pocket. Structural analysis and ligand docking to the mutant structures predicted a decreased affinity for α-tocopherol. To determine the detailed mechanism of the mutation-related changes, we developed a new tool called ContactWalker that analyzes contact differences between mutant and wild-type proteins and highlights pathways of altered contacts within the mutant proteins. Taken together, our findings are in agreement with experiment and suggest structural explanations for the weakened ability of the mutants to bind and carry α-tocopherol.
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Affiliation(s)
- Dennis Bromley
- Division of Biomedical and Health Informatics, Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington 98195, USA
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23
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Yang H, Tong J, Leonard TA, Im YJ. Structural determinants for phosphatidylinositol recognition by Sfh3 and substrate-induced dimer-monomer transition during lipid transfer cycles. FEBS Lett 2013; 587:1610-6. [DOI: 10.1016/j.febslet.2013.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 03/13/2013] [Accepted: 04/05/2013] [Indexed: 10/26/2022]
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24
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Yuan Y, Zhao W, Wang X, Gao Y, Niu L, Teng M. Dimeric Sfh3 has structural changes in its binding pocket that are associated with a dimer–monomer state transformation induced by substrate binding. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:313-23. [DOI: 10.1107/s0907444912046161] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 11/08/2012] [Indexed: 12/31/2022]
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Winklbauer EM, de Campos MKF, Dynowski M, Schaaf G. A blueprint for functional engineering: Single point mutations reconstitute phosphatidylinositol presentation in a pseudo-Sec14 protein. Commun Integr Biol 2012; 4:674-8. [PMID: 22446525 DOI: 10.4161/cib.17064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Phosphoinositides, phosphorylated species of phosphatidylinositol (PtdIns), are critical regulatory lipids in all eukaryotic cells. The molecular mechanisms that lead to the phosphorylation of an individual PtdIns- or phosphoinositide molecule remain largely unkown even though lipid kinases and phosphatases involved in these processes have been studied in detail. The observation by us and others that liposomal PtdIns (and phosphoinositide) molecules are poor in vitro substrates for kinases and phosphatases raises the question of how these enzymes execute their function in living cells. Recent work indicates that Sec14, the founding member of a large superfamily of eukaryotic proteins, is crucial for the process of PtdIns phosphorylation. The collective data suggest that Sec14 mediates a heterotypic phospholipid exchange reaction of PtdIns with phosphatidylcholine (PtdCho) during which PtdIns becomes vulnerable for kinase attack and thereby promotes the generation of phosphoinositides.1,2 In a recent paper we address the molecular mechanism of this phospholipid (PL) exchange reaction in a pseudo-Sec14 protein (Sfh1) that we rendered functional by a directed evolution approach. We find that enhanced PL-cycling into and out of the hydrophobic pocket of these activated Sfh1 mutants depends on the reconfiguration of interactions between a C-terminal string motif and the floor of the hydrophobic pocket that results in increased oscillations in a helical gate that controls pocket access. Here we further discuss our findings and propose molecular dynamics simulations as a tool to approach energetically unfavorable transition states and to identify novel protein-ligand interactions invisible to X-ray crystallography.
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Bankaitis VA, Ile KE, Nile AH, Ren J, Ghosh R, Schaaf G. Thoughts on Sec14-like nanoreactors and phosphoinositide signaling. Adv Biol Regul 2012; 52:115-21. [PMID: 22776890 DOI: 10.1016/j.jbior.2011.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 11/11/2011] [Indexed: 10/28/2022]
Affiliation(s)
- Vytas A Bankaitis
- Department of Cell & Developmental Biology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7090, USA.
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Devising Powerful Genetics, Biochemical and Structural Tools in the Functional Analysis of Phosphatidylinositol Transfer Proteins (PITPs) Across Diverse Species. Methods Cell Biol 2012; 108:249-302. [DOI: 10.1016/b978-0-12-386487-1.00013-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Mousley CJ, Davison JM, Bankaitis VA. Sec14 like PITPs couple lipid metabolism with phosphoinositide synthesis to regulate Golgi functionality. Subcell Biochem 2012; 59:271-87. [PMID: 22374094 DOI: 10.1007/978-94-007-3015-1_9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An interface coordinating lipid metabolism with proteins that regulate membrane trafficking is necessary to regulate Golgi morphology and dynamics. Such an interface facilitates the membrane deformations required for vesicularization, forms platforms for protein recruitment and assembly on appropriate sites on a membrane surface and provides lipid co-factors for optimal protein activity in the proper spatio-temporally regulated manner. Importantly, Sec14 and Sec14-like proteins are a unique superfamily of proteins that sense specific aspects of lipid metabolism, employing this information to potentiate phosphoinositide production. Therefore, Sec14 and Sec14 like proteins form central conduits to integrate multiple aspects of lipid metabolism with productive phosphoinositide signaling.
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Affiliation(s)
- Carl J Mousley
- Department of Cell & Developmental Biology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, 27599-7090, Chapel Hill, NC, USA,
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