1
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Uematsu M, Baskin JM. Chemical Approaches for Measuring and Manipulating Lipids at the Organelle Level. Cold Spring Harb Perspect Biol 2023; 15:a041407. [PMID: 37604586 PMCID: PMC10691496 DOI: 10.1101/cshperspect.a041407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
As the products of complex and often redundant metabolic pathways, lipids are challenging to measure and perturb using genetic tools. Yet by virtue of being the major constituents of cellular membranes, lipids are highly regulated in space and time. Chemists have stepped into this methodological void, developing an array of techniques for the precise quantification and manipulation of lipids at the subcellular, organelle level. Here, we survey the landscape of these methods. For measuring lipids, we summarize the use of metabolic labeling and click chemistry tagging, photoaffinity labeling, isotopic tagging for Raman microscopy, and chemoenzymatic labeling for tracking lipid production and interorganelle transport. For perturbing lipids, we describe synthetic photocaged lipids and membrane editing approaches using optogenetic enzymes for precise manipulation of lipid signaling. Collectively, these chemical and biochemical tools are revealing phenomena and mechanisms underlying lipid functions at the subcellular level.
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Affiliation(s)
- Masaaki Uematsu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Jeremy M Baskin
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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2
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Abstract
Lipids are key components of all organisms. We are well educated in their use as fuel and their essential role to form membranes. We also know much about their biosynthesis and metabolism. We are also aware that most lipids have signaling character meaning that a change in their concentration or location constitutes a signal that helps a living cell to respond to changes in the environment or to fulfill its specific function ranging from secretion to cell division. What is much less understood is how lipids change location in cells over time and what other biomolecules they interact with at each stage of their lifetime. Due to the large number of often quite similar lipid species and the sometimes very short lifetime of signaling lipids, we need highly specific tools to manipulate and visualize lipids and lipid-protein interactions. If successfully applied, these tools provide fabulous opportunities for discovery.In this Account, I summarize the development of synthetic tools from our lab that were designed to address crucial properties that allow them to function as tools in live cell experiments. Techniques to change the concentration of lipids by adding a small molecule or by light are described and complemented by examples of biological findings made when applying the tools. This ranges from chemical dimerizer-based systems to synthetic "caged" lipid derivatives. Furthermore, I discuss the problem of locating a lipid in an intact cell. Synthetic molecular probes are described that help to unravel the lipid location and to determine their binding proteins. These location studies require in-cell lipid tagging by click chemistry, photo-cross-linking to prevent further movement and the "caging" groups to avoid premature metabolism. The combination of these many technical features in a single tool allows for the analysis of not only lipid fluxes through metabolism but also lipid transport from one membrane to another as well as revealing the lipid interactome in a cell-dependent manner. This latter point is crucial because with these multifunctional tools in combination with lipidomics we can now address differences in healthy versus diseased cells and ultimately find the changes that are essential for disease development and new therapeutics that prevent these changes.
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Affiliation(s)
- Carsten Schultz
- Department of Chemical Physiology and
Biochemistry, Oregon Health & Science
University, Portland, Oregon 97239, United States
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3
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Schultz C, Farley SE, Tafesse FG. "Flash & Click": Multifunctionalized Lipid Derivatives as Tools To Study Viral Infections. J Am Chem Soc 2022; 144:13987-13995. [PMID: 35900117 PMCID: PMC9377334 DOI: 10.1021/jacs.2c02705] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this perspective article, we describe the current status of lipid tools for studying host lipid-virus interactions at the cellular level. We discuss the potential lipidomic changes that viral infections impose on host cells and then outline the tools available and the resulting options to investigate the host cell lipid interactome. The future outcome will reveal new targets for treating virus infections.
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Affiliation(s)
- Carsten Schultz
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University; 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
| | - Scotland E Farley
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University; 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239-3098, United States.,Department of Molecular Microbiology and Immunology, Oregon Health & Science University; 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
| | - Fikadu G Tafesse
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University; 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
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4
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Kneuttinger AC. A guide to designing photocontrol in proteins: methods, strategies and applications. Biol Chem 2022; 403:573-613. [PMID: 35355495 DOI: 10.1515/hsz-2021-0417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/08/2022] [Indexed: 12/20/2022]
Abstract
Light is essential for various biochemical processes in all domains of life. In its presence certain proteins inside a cell are excited, which either stimulates or inhibits subsequent cellular processes. The artificial photocontrol of specifically proteins is of growing interest for the investigation of scientific questions on the organismal, cellular and molecular level as well as for the development of medicinal drugs or biocatalytic tools. For the targeted design of photocontrol in proteins, three major methods have been developed over the last decades, which employ either chemical engineering of small-molecule photosensitive effectors (photopharmacology), incorporation of photoactive non-canonical amino acids by genetic code expansion (photoxenoprotein engineering), or fusion with photoreactive biological modules (hybrid protein optogenetics). This review compares the different methods as well as their strategies and current applications for the light-regulation of proteins and provides background information useful for the implementation of each technique.
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Affiliation(s)
- Andrea C Kneuttinger
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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5
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Gao F, Tom E, Skowronska-Krawczyk D. Dynamic Progress in Technological Advances to Study Lipids in Aging: Challenges and Future Directions. FRONTIERS IN AGING 2022; 3:851073. [PMID: 35821837 PMCID: PMC9261449 DOI: 10.3389/fragi.2022.851073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 02/23/2022] [Indexed: 11/29/2022]
Abstract
Lipids participate in all cellular processes. Diverse methods have been developed to investigate lipid composition and distribution in biological samples to understand the effect of lipids across an organism’s lifespan. Here, we summarize the advanced techniques for studying lipids, including mass spectrometry-based lipidomics, lipid imaging, chemical-based lipid analysis and lipid engineering and their advantages. We further discuss the limitation of the current methods to gain an in-depth knowledge of the role of lipids in aging, and the possibility of lipid-based therapy in aging-related diseases.
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Affiliation(s)
- Fangyuan Gao
- Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, United States
| | - Emily Tom
- Department of Physiology and Biophysics, Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, United States
| | - Dorota Skowronska-Krawczyk
- Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, United States
- Department of Physiology and Biophysics, Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, United States
- *Correspondence: Dorota Skowronska-Krawczyk,
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6
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Ryan A, Hammond GRV, Deiters A. Optical Control of Phosphoinositide Binding: Rapid Activation of Subcellular Protein Translocation and Cell Signaling. ACS Synth Biol 2021; 10:2886-2895. [PMID: 34748306 DOI: 10.1021/acssynbio.1c00328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cells utilize protein translocation to specific compartments for spatial and temporal regulation of protein activity, in particular in the context of signaling processes. Protein recognition and binding to various subcellular membranes is mediated by a network of phosphatidylinositol phosphate (PIP) species bearing one or multiple phosphate moieties on the polar inositol head. Here, we report a new, highly efficient method for optical control of protein localization through the site-specific incorporation of a photocaged amino acid for steric and electrostatic disruption of inositol phosphate recognition and binding. We demonstrate general applicability of the approach by photocaging two unrelated proteins, sorting nexin 3 (SNX3) and the pleckstrin homology (PH) domain of phospholipase C delta 1 (PLCδ1), with two distinct PIP binding domains and distinct subcellular localizations. We have established the applicability of this methodology through its application to Son of Sevenless 2 (SOS2), a signaling protein involved in the extracellular signal-regulated kinase/mitogen-activated protein kinase (ERK/MAPK) cascade. Upon fusing the photocaged plasma membrane-targeted construct PH-enhanced green fluorescent protein (EGFP), to the catalytic domain of SOS2, we demonstrated light-induced membrane localization of the construct resulting in fast and extensive activation of the ERK signaling pathway in NIH 3T3 cells. This approach can be readily extended to other proteins, with minimal protein engineering, and provides a method for acute optical control of protein translocation with rapid and complete activation.
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Affiliation(s)
- Amy Ryan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Gerald R. V. Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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7
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Citir M, Müller R, Hauke S, Traynor-Kaplan A, Schultz C. Monitoring the cellular metabolism of a membrane-permeant photo-caged phosphatidylinositol 3,4,5-trisphosphate derivative. Chem Phys Lipids 2021; 241:105124. [PMID: 34509466 PMCID: PMC11364432 DOI: 10.1016/j.chemphyslip.2021.105124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/22/2021] [Accepted: 08/13/2021] [Indexed: 01/07/2023]
Abstract
To deliver charged lipid derivatives to the cell interior, bioactivatable and photo-activatable protecting groups are frequently used. The intracellular metabolism of the protecting groups, as well as the lipid itself, are key factors that determine biological activity. Here we followed the cellular metabolism of cell-permeant photo-activatable ("caged") and non-caged membrane-permeant analogs of dioctanoyl phosphatidylinositol 3,4,5-trisphosphate (diC8PIP3) carrying biodegradable protecting groups by mass spectrometry. After successful cell entry, the photo-activatable group can be removed on demand by a light pulse. Hence, UV irradiation acts as a switch to expose the cellular metabolism to a bolus of active compound. To investigate lipid metabolites and to capture a more complete metabolome, we adapted standard extraction methods and employed multi-reaction monitoring mass spectrometry (MRM-MS). This required a previously developed permethylation method that stabilized metabolites and enhanced volatility of the phosphoinositide metabolites. The mass spectrometric analysis allowed for the monitoring of the intracellular removal of photo-activatable caging as well as biodegradable protecting groups from the membrane-permeant phosphoinositides along with cellular turnover, namely by dephosphorylation. We found that phosphate masking groups, namely acetoxymethyl esters, were rapidly removed by endogenous enzymes while butyrates masking hydroxy groups showed a longer lifetime, giving rise to trapped intermediates. We further identified key intermediate metabolites and demonstrated the beneficial effect of caging groups and their removal on the formation of favorable metabolites. Surprisingly, caging and protecting groups were found to influence each other's stability.
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Affiliation(s)
- Mevlut Citir
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany.
| | - Rainer Müller
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany.
| | - Sebastian Hauke
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany.
| | - Alexis Traynor-Kaplan
- ATK Innovation, Analytics and Discovery, North Bend, WA, 98045, USA; University of Washington, Department of Medicine, Seattle, WA, 98195, USA.
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany; Oregon Health & Science University (OHSU), Department of Chemical Physiology and Biochemistry, L334 3181 SW Sam Jackson Park Road, Portland, OR, 97239-3098, USA.
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8
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Müller R, Kojic A, Citir M, Schultz C. Synthesis and Cellular Labeling of Multifunctional Phosphatidylinositol Bis- and Trisphosphate Derivatives. Angew Chem Int Ed Engl 2021; 60:19759-19765. [PMID: 34075669 PMCID: PMC8390440 DOI: 10.1002/anie.202103599] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/07/2021] [Indexed: 12/15/2022]
Abstract
We synthesized the first multifunctionalized phosphoinositide polyphosphate derivatives featuring a photo-removable protecting group ("cage"), a photo-crosslinkable diazirine group, and a terminal alkyne group useful for click chemistry. We demonstrate that the lipid derivatives readily enter cells. After photo-crosslinking, cell fixation and fluorescent tagging via click chemistry, we determined the intracellular location of the lipid derivatives before and after uncaging of the lipids. We find that there is rapid trafficking of PI(3,4)P2 and PI(3,4,5)P3 derivatives to the plasma membrane, opening the intriguing possibility that there is active transport of these lipids involved. We employed the photo-crosslinking and click chemistry functions to analyze the proteome of PI(3,4,5)P3 -binding proteins. From the latter, we validated by RNAi that the putative lipid binding proteins ATP11A and MPP6 are involved in the transport of PI(3,4,5)P3 to the plasma membrane.
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Affiliation(s)
- Rainer Müller
- European Molecular Biology Laboratory (EMBL)Cell Biology & Biophysics UnitMeyerhofstr. 169117HeidelbergGermany
| | - Ana Kojic
- European Molecular Biology Laboratory (EMBL)Cell Biology & Biophysics UnitMeyerhofstr. 169117HeidelbergGermany
- Faculty of BiosciencesCollaboration for Joint Ph.D. Degree between EMBL and Heidelberg University69117HeidelbergGermany
- Oregon Health & Science UniversityDepartment of Chemical Physiology and Biochemistry3181 SW Sam Jackson Park RdPortlandOR97239-3098USA
| | - Mevlut Citir
- European Molecular Biology Laboratory (EMBL)Cell Biology & Biophysics UnitMeyerhofstr. 169117HeidelbergGermany
- Faculty of BiosciencesCollaboration for Joint Ph.D. Degree between EMBL and Heidelberg University69117HeidelbergGermany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL)Cell Biology & Biophysics UnitMeyerhofstr. 169117HeidelbergGermany
- Oregon Health & Science UniversityDepartment of Chemical Physiology and Biochemistry3181 SW Sam Jackson Park RdPortlandOR97239-3098USA
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9
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Müller R, Kojic A, Citir M, Schultz C. Synthesis and Cellular Labeling of Multifunctional Phosphatidylinositol Bis‐ and Trisphosphate Derivatives. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Rainer Müller
- European Molecular Biology Laboratory (EMBL) Cell Biology & Biophysics Unit Meyerhofstr. 1 69117 Heidelberg Germany
| | - Ana Kojic
- European Molecular Biology Laboratory (EMBL) Cell Biology & Biophysics Unit Meyerhofstr. 1 69117 Heidelberg Germany
- Faculty of Biosciences Collaboration for Joint Ph.D. Degree between EMBL and Heidelberg University 69117 Heidelberg Germany
- Oregon Health & Science University Department of Chemical Physiology and Biochemistry 3181 SW Sam Jackson Park Rd Portland OR 97239-3098 USA
| | - Mevlut Citir
- European Molecular Biology Laboratory (EMBL) Cell Biology & Biophysics Unit Meyerhofstr. 1 69117 Heidelberg Germany
- Faculty of Biosciences Collaboration for Joint Ph.D. Degree between EMBL and Heidelberg University 69117 Heidelberg Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL) Cell Biology & Biophysics Unit Meyerhofstr. 1 69117 Heidelberg Germany
- Oregon Health & Science University Department of Chemical Physiology and Biochemistry 3181 SW Sam Jackson Park Rd Portland OR 97239-3098 USA
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10
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Farley S, Laguerre A, Schultz C. Caged lipids for subcellular manipulation. Curr Opin Chem Biol 2021; 65:42-48. [PMID: 34119744 DOI: 10.1016/j.cbpa.2021.04.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/20/2022]
Abstract
We present recently developed strategies to manipulate lipid levels in live cells by light. We focus on photoremovable protecting groups that lead to subcellular restricted localization and activation and discuss alternative techniques. We emphasize the development of organelle targeting of caged lipids and discuss recent advances in chromatic orthogonality of caging groups for future applications.
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Affiliation(s)
- Scotland Farley
- Dept. Chemical Physiology & Biochemistry, Oregon Health and Science University (OHSU), Portland, OR, USA
| | - Aurélien Laguerre
- Dept. Chemical Physiology & Biochemistry, Oregon Health and Science University (OHSU), Portland, OR, USA
| | - Carsten Schultz
- Dept. Chemical Physiology & Biochemistry, Oregon Health and Science University (OHSU), Portland, OR, USA.
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11
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Yang L, Ozawa T, Dong H, Zhang X. Optogenetic Control of Phosphatidylinositol (3,4,5)‐Triphosphate Production by
Light‐Sensitive
Cryptochrome Proteins on the Plasma Membrane. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202000648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lingzhi Yang
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University Shenzhen Guangdong 518060 China
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo 7‐3‐1 Hongo, Bunkyo‐ku Tokyo 113‐0033 Japan
| | - Haifeng Dong
- School of Biomedical Engineering, Health Science Center, Shenzhen University Shenzhen Guangdong 518060 China
| | - Xueji Zhang
- School of Biomedical Engineering, Health Science Center, Shenzhen University Shenzhen Guangdong 518060 China
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12
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Abstract
The specific non-invasive control of intracellular signaling events requires advanced tools that enter cells by diffusion and are controllable by light. Here, we detail the synthesis and application of membrane-permeant caged inositol pyrophosphates with respect to cell entry and cell distribution. We recently published the synthesis of these tools as well as their effect on PH-domain localization in HeLa cells and oscillations of the intracellular calcium concentration in β-cells, which are known to drive insulin secretion. In this chapter, we discuss the possibilities and limitations when using cell-penetrating inositol pyrophosphates. We provide a detailed protocol for the application in live mouse β-cells and we discuss the image analysis needed for following effects on calcium signaling.
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13
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Müller R, Citir M, Hauke S, Schultz C. Synthesis and Cellular Labeling of Caged Phosphatidylinositol Derivatives. Chemistry 2019; 26:384-389. [PMID: 31550056 PMCID: PMC6973124 DOI: 10.1002/chem.201903704] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/22/2019] [Indexed: 01/25/2023]
Abstract
Phosphatidylinositol (PI) is the biosynthetic precursor for seven phosphoinositides, important signaling lipids in cells. A membrane‐permeant caged PI derivative featuring a photo‐removable coumarinyl group masking the negative charge of the phosphate, as well as two enzymatically removable butyrate esters for increased lipophilicity and for preventing phosphate migration, were synthesized. Rapid cell entry and cellular labeling in fixed cells was demonstrated by a photo‐cross‐linkable diazirine followed by attachment of a fluorophore through click chemistry. Using this technique, we found that the multifunctional caged PI derivative resided predominantly at internal membranes but rapidly changed to the plasma membrane after uncaging. Accordingly, a preliminary proteomic analysis of the lipid–protein conjugates revealed that the two major PI transport proteins PITPα and β were prime targets of the photo‐cross‐linked PI derivative.
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Affiliation(s)
- Rainer Müller
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Mevlut Citir
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Sebastian Hauke
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Carsten Schultz
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239-3098, USA
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14
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Hennig ALK, Deodato D, Asad N, Herbivo C, Dore TM. Two-Photon Excitable Photoremovable Protecting Groups Based on the Quinoline Scaffold for Use in Biology. J Org Chem 2019; 85:726-744. [DOI: 10.1021/acs.joc.9b02780] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Anna-Lisa K. Hennig
- New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Davide Deodato
- New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Naeem Asad
- New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Cyril Herbivo
- New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Timothy M. Dore
- New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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15
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Dore TM. Light-Activated Chemotaxis. Cell Chem Biol 2019; 23:531-532. [PMID: 27203370 DOI: 10.1016/j.chembiol.2016.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Using light to control cellular processes is one of the attractive areas of research. Here, availability of different, light-responsive caged compounds has played a critical role. In this issue of Cell Chemical Biology, Hövelmann et al. (2016) give us an example of how to design and use caged lipids to guide chemotaxis at the single cell level.
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Affiliation(s)
- Timothy M Dore
- New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates.
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16
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Light-triggered release of photocaged therapeutics - Where are we now? J Control Release 2019; 298:154-176. [PMID: 30742854 DOI: 10.1016/j.jconrel.2019.02.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 01/02/2023]
Abstract
The current available therapeutics face several challenges such as the development of ideal drug delivery systems towards the goal of personalized treatments for patients benefit. The application of light as an exogenous activation mechanism has shown promising outcomes, owning to the spatiotemporal confinement of the treatment in the vicinity of the diseased tissue, which offers many intriguing possibilities. Engineering therapeutics with light responsive moieties have been explored to enhance the bioavailability, and drug efficacy either in vitro or in vivo. The tailor-made character turns the so-called photocaged compounds highly desirable to reduce the side effects of drugs and, therefore, have received wide research attention. Herein, we seek to highlight the potential of photocaged compounds to obtain a clear understanding of the mechanisms behind its use in therapeutic delivery. A deep overview on the progress achieved in the design, fabrication as well as current and possible future applications in therapeutics of photocaged compounds is provided, so that novel formulations for biomedical field can be designed.
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17
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Hauke S, Dutta AK, Eisenbeis VB, Bezold D, Bittner T, Wittwer C, Thakor D, Pavlovic I, Schultz C, Jessen HJ. Photolysis of cell-permeant caged inositol pyrophosphates controls oscillations of cytosolic calcium in a β-cell line. Chem Sci 2019; 10:2687-2692. [PMID: 30996985 PMCID: PMC6419925 DOI: 10.1039/c8sc03479f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 01/09/2019] [Indexed: 12/16/2022] Open
Abstract
β-Cells respond directly to the intracellular photochemical release of caged inositol pyrophosphate isomers with modulations of oscillations in cytosolic Ca2+.
Among many cellular functions, inositol pyrophosphates (PP-InsPs) are metabolic messengers involved in the regulation of glucose uptake, insulin sensitivity, and weight gain. However, their mechanisms of action are still poorly understood. So far, the influence of PP-InsPs on cellular metabolism has been studied by overexpression or knockout/inhibition of relevant metabolizing kinases (IP6Ks, PPIP5Ks). These approaches are, inter alia, limited by time-resolution and potential compensation mechanisms. Here, we describe the synthesis of cell-permeant caged PP-InsPs as tools to rapidly modulate intracellular levels of defined isomers of PP-InsPs in a genetically non-perturbed cellular environment. We show that caged prometabolites readily enter live cells where they are enzymatically converted into still inactive, metabolically stable, photocaged PP-InsPs. Upon light-triggered release of 5-PP-InsP5, the major cellular inositol pyrophosphate, oscillations of intracellular Ca2+ levels in MIN6 cells were transiently reduced to spontaneously recover again. In contrast, uncaging of 1-PP-InsP5, a minor cellular isomer, was without effect. These results provide evidence that PP-InsPs play an active role in regulating [Ca2+]i oscillations, a key element in triggering exocytosis and secretion in β-cells.
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Affiliation(s)
- S Hauke
- EMBL, Heidelberg , 69117 Heidelberg , Germany .
| | - A K Dutta
- University of Freiburg , Institute of Organic Chemistry , 79104 Freiburg , Germany .
| | - V B Eisenbeis
- University of Freiburg , Institute of Organic Chemistry , 79104 Freiburg , Germany .
| | - D Bezold
- University of Freiburg , Institute of Organic Chemistry , 79104 Freiburg , Germany .
| | - T Bittner
- University of Freiburg , Institute of Organic Chemistry , 79104 Freiburg , Germany .
| | - C Wittwer
- University of Freiburg , Institute of Organic Chemistry , 79104 Freiburg , Germany .
| | - D Thakor
- University of Freiburg , Institute of Organic Chemistry , 79104 Freiburg , Germany .
| | - I Pavlovic
- University of Freiburg , Institute of Organic Chemistry , 79104 Freiburg , Germany .
| | - C Schultz
- EMBL, Heidelberg , 69117 Heidelberg , Germany . .,OHSU , Dept. Physiology & Pharmacology , Portland , OR , USA .
| | - H J Jessen
- University of Freiburg , Institute of Organic Chemistry , 79104 Freiburg , Germany .
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18
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Gaur P, Kucherak OA, Ermakova YG, Shvadchak VV, Yushchenko DA. Nitrobenzyl-based fluorescent photocages for spatial and temporal control of signalling lipids in cells. Chem Commun (Camb) 2019; 55:12288-12291. [DOI: 10.1039/c9cc05602e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Here we present a set of fluorescent cages prepared by tethering fluorescent dyes to a photolabile group.
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Affiliation(s)
- Pankaj Gaur
- Laboratory of Chemical Biology
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 16610 Prague 6
- Czech Republic
| | - Oleksandr A. Kucherak
- Laboratory of Chemical Biology
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 16610 Prague 6
- Czech Republic
| | - Yulia G. Ermakova
- Cell Biology & Biophysics Unit
- European Molecular Biology Laboratory (EMBL)
- 69117 Heidelberg
- Germany
| | - Volodymyr V. Shvadchak
- Laboratory of Chemical Biology
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 16610 Prague 6
- Czech Republic
| | - Dmytro A. Yushchenko
- Laboratory of Chemical Biology
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 16610 Prague 6
- Czech Republic
- Group of Bioconjugation Chemistry
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19
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Heron PW, Abellán-Flos M, Salmon L, Sygusch J. Bisphosphonate Inhibitors of Mammalian Glycolytic Aldolase. J Med Chem 2018; 61:10558-10572. [PMID: 30418024 DOI: 10.1021/acs.jmedchem.8b01000] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The glycolytic enzyme aldolase is an emerging drug target in diseases such as cancer and protozoan infections which are dependent on a hyperglycolytic phenotype to synthesize adenosine 5'-triphosphate and metabolic precursors for biomass production. To date, structural information for the enzyme in complex with phosphate-derived inhibitors has been lacking. Thus, we determined the crystal structure of mammalian aldolase in complex with naphthalene 2,6-bisphosphate (1) that served as a template for the design of bisphosphonate-based inhibitors, namely, 2-phosphate-naphthalene 6-bisphosphonate (2), 2-naphthol 6-bisphosphonate (3), and 1-phosphate-benzene 4-bisphosphonate (4). All inhibitors targeted the active site, and the most promising lead, 2, exhibited slow-binding inhibition with an overall inhibition constant of ∼38 nM. Compound 2 inhibited proliferation of HeLa cancer cells, whereas HEK293 cells expressing a normal phenotype were not inhibited. The crystal structures delineated the essential features of high-affinity phosphate-derived inhibitors and provide a template for the development of inhibitors with prophylaxis potential.
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Affiliation(s)
- Paul W Heron
- Département de Biochimie et Médecine Moléculaire , Université de Montréal , CP 6128, Succursale Centre-Ville, Montréal , Québec H3C 3J7 , Canada
| | - Marta Abellán-Flos
- Equipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux D'Orsay (ICMMO) , Univ Paris-Saclay, Univ Paris-Sud, CNRS UMR8182, LabEx LERMIT , rue du doyen Georges Poitou , F-91405 Orsay , France
| | - Laurent Salmon
- Equipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux D'Orsay (ICMMO) , Univ Paris-Saclay, Univ Paris-Sud, CNRS UMR8182, LabEx LERMIT , rue du doyen Georges Poitou , F-91405 Orsay , France
| | - Jurgen Sygusch
- Département de Biochimie et Médecine Moléculaire , Université de Montréal , CP 6128, Succursale Centre-Ville, Montréal , Québec H3C 3J7 , Canada
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20
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Mohamed ZH, Rhein C, Saied EM, Kornhuber J, Arenz C. FRET probes for measuring sphingolipid metabolizing enzyme activity. Chem Phys Lipids 2018; 216:152-161. [DOI: 10.1016/j.chemphyslip.2018.09.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 09/21/2018] [Indexed: 12/31/2022]
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21
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Bumpus TW, Baskin JM. Greasing the Wheels of Lipid Biology with Chemical Tools. Trends Biochem Sci 2018; 43:970-983. [PMID: 30472989 DOI: 10.1016/j.tibs.2018.09.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/31/2018] [Accepted: 09/19/2018] [Indexed: 02/06/2023]
Abstract
Biological lipids are a structurally diverse and historically vexing group of hydrophobic metabolites. Here, we review recent advances in chemical imaging techniques that reveal changes in lipid biosynthesis, metabolism, dynamics, and interactions. We highlight tools for tagging many lipid classes via metabolic incorporation of bioorthogonally functionalized precursors, detectable via click chemistry, and photocaged, photoswitchable, and photocrosslinkable variants of different lipids. Certain lipid probes can supplant traditional protein-based markers of organelle membranes in super-resolution microscopy, and emerging vibrational imaging methods, such as stimulated Raman spectroscopy (SRS), enable simultaneous imaging of more than a dozen different types of target molecule, including lipids. Collectively, these chemical imaging techniques will illuminate, in living color, previously hidden aspects of lipid biology.
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Affiliation(s)
- Timothy W Bumpus
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
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22
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Huang W, Wang X, Endo-Streeter S, Barrett M, Waybright J, Wohlfeld C, Hajicek N, Harden TK, Sondek J, Zhang Q. A membrane-associated, fluorogenic reporter for mammalian phospholipase C isozymes. J Biol Chem 2017; 293:1728-1735. [PMID: 29263090 DOI: 10.1074/jbc.ra117.000926] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 12/05/2017] [Indexed: 11/06/2022] Open
Abstract
A diverse group of cell-surface receptors, including many G protein-coupled receptors and receptor tyrosine kinases, activate phospholipase C (PLC) isozymes to hydrolyze phosphatidylinositol 4,5-bisphosphate into the second messengers diacylglycerol and 1,4,5-inositol trisphosphate. Consequently, PLCs control various cellular processes, and their aberrant regulation contributes to many diseases, including cancer, atherosclerosis, and rheumatoid arthritis. Despite the widespread importance of PLCs in human biology and disease, it has been impossible to directly monitor the real-time activation of these enzymes at membranes. To overcome this limitation, here we describe XY-69, a fluorogenic reporter that preferentially partitions into membranes and provides a selective tool for measuring the real-time activity of PLCs as either purified enzymes or in cellular lysates. Indeed, XY-69 faithfully reported the membrane-dependent activation of PLC-β3 by Gαq Therefore, XY-69 can replace radioactive phosphatidylinositol 4,5-bisphosphate used in conventional PLC assays and will enable high-throughput screens to identify both orthosteric and allosteric PLC inhibitors. In the future, cell-permeable variants of XY-69 represent promising candidates for reporting the activation of PLCs in live cells with high spatiotemporal resolution.
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Affiliation(s)
- Weigang Huang
- From the Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy
| | - Xiaoyang Wang
- From the Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy
| | | | | | - Jarod Waybright
- From the Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy
| | - Christian Wohlfeld
- From the Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy
| | | | | | - John Sondek
- Departments of Pharmacology and.,Biochemistry and Biophysics, School of Medicine, and.,the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Qisheng Zhang
- From the Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, .,Departments of Pharmacology and.,the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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23
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Walter AM, Müller R, Tawfik B, Wierda KD, Pinheiro PS, Nadler A, McCarthy AW, Ziomkiewicz I, Kruse M, Reither G, Rettig J, Lehmann M, Haucke V, Hille B, Schultz C, Sørensen JB. Phosphatidylinositol 4,5-bisphosphate optical uncaging potentiates exocytosis. eLife 2017; 6:30203. [PMID: 29068313 PMCID: PMC5711374 DOI: 10.7554/elife.30203] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/24/2017] [Indexed: 12/14/2022] Open
Abstract
Phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2] is essential for exocytosis. Classical ways of manipulating PI(4,5)P2 levels are slower than its metabolism, making it difficult to distinguish effects of PI(4,5)P2 from those of its metabolites. We developed a membrane-permeant, photoactivatable PI(4,5)P2, which is loaded into cells in an inactive form and activated by light, allowing sub-second increases in PI(4,5)P2 levels. By combining this compound with electrophysiological measurements in mouse adrenal chromaffin cells, we show that PI(4,5)P2 uncaging potentiates exocytosis and identify synaptotagmin-1 (the Ca2+ sensor for exocytosis) and Munc13-2 (a vesicle priming protein) as the relevant effector proteins. PI(4,5)P2 activation of exocytosis did not depend on the PI(4,5)P2-binding CAPS-proteins, suggesting that PI(4,5)P2 uncaging may bypass CAPS-function. Finally, PI(4,5)P2 uncaging triggered the rapid fusion of a subset of readily-releasable vesicles, revealing a rapid role of PI(4,5)P2 in fusion triggering. Thus, optical uncaging of signaling lipids can uncover their rapid effects on cellular processes and identify lipid effectors. Cells in our body communicate by releasing compounds called transmitters that carry signals from one cell to the next. Packages called vesicles store transmitters within the signaling cell. When the cell needs to send a signal, the vesicles fuse with the cell's membrane and release their cargo. For many signaling processes, such as those used by neurons, this fusion is regulated, fast, and coupled to the signal that the cell receives to activate release. Specialized molecular machines made up of proteins and fatty acid molecules called signaling lipids enable this to happen. One signaling lipid called PI(4,5)P2 (short for phosphatidylinositol 4,5-bisphosphate) is essential for vesicle fusion as well as for other processes in cells. It interacts with several proteins that help it control fusion and the release of transmitter. While it is possible to study the role of these proteins using genetic tools to inactivate them, the signaling lipids are more difficult to manipulate. Existing methods result in slow changes in PI(4,5)P2 levels, making it hard to directly attribute later changes to PI(4,5)P2. Walter, Müller, Tawfik et al. developed a new method to measure how PI(4,5)P2 affects transmitter release in living mammalian cells, which causes a rapid increase in PI(4,5)P2 levels. The method uses a chemical compound called “caged PI(4,5)P2” that can be loaded into cells but remains undetected until ultraviolet light is shone on it. The ultraviolet light uncages the compound, generating active PI(4,5)P2 in less than one second. Walter et al. found that when they uncaged PI(4,5)P2 in this way, the amount of transmitter released by cells increased. Combining this with genetic tools, it was possible to investigate which proteins of the release machinery were required for this effect. The results suggest that two different types of proteins that interact with PI(4,5)P2 are needed: one must bind PI(4,5)P2 to carry out its role and the other helps PI(4,5)P2 accumulate at the site of vesicle fusion. The new method also allowed Walter et al. to show that a fast increase in PI(4,5)P2 triggers a subset of vesicles to fuse very rapidly. This shows that PI(4,5)P2 rapidly regulates the release of transmitter. Caged PI(4,5)P2 will be useful to study other processes in cells that need PI(4,5)P2, helping scientists understand more about how signaling lipids control many different events at cellular membranes.
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Affiliation(s)
- Alexander M Walter
- Neurosecretion group, Center for Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Rainer Müller
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Bassam Tawfik
- Neurosecretion group, Center for Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Keimpe Db Wierda
- Neurosecretion group, Center for Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Paulo S Pinheiro
- Neurosecretion group, Center for Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - André Nadler
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Anthony W McCarthy
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Iwona Ziomkiewicz
- Neurosecretion group, Center for Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Discovery Sciences, AstraZeneca, Cambridge, United Kingdom
| | - Martin Kruse
- Department of Physiology and Biophysics, School of Medicine, University of Washington, Seattle, United States
| | - Gregor Reither
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jens Rettig
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Bertil Hille
- Department of Physiology and Biophysics, School of Medicine, University of Washington, Seattle, United States
| | - Carsten Schultz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jakob Balslev Sørensen
- Neurosecretion group, Center for Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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24
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Li X, Che Z, Mazhar K, Price TJ, Qin Z. Ultrafast Near-Infrared Light-triggered Intracellular Uncaging to Probe Cell Signaling. ADVANCED FUNCTIONAL MATERIALS 2017; 27:1605778. [PMID: 29176940 PMCID: PMC5697715 DOI: 10.1002/adfm.201605778] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The possibility of regulating cell signaling with high spatial and temporal resolution within individual cells and complex cellular networks has important implications in biomedicine. In this report, we demonstrate a general strategy that uses near-infrared tissue-penetrating laser pulses to uncage biomolecules from plasmonic gold-coated liposomes, i.e. plasmonic liposomes, to activate cell signaling in a non-thermal, ultrafast and highly controllable fashion. Near-infrared picosecond laser pulse induces transient nanobubbles around plasmonic liposomes. The mechanical force generated from the collapse of nanobubbles rapidly ejects encapsulated compound within 0.1 ms. We showed that single pulse irradiation triggers the rapid intracellular uncaging of calcein from plasmonic liposomes inside endo-lysosomes. The uncaged calcein then evenly distributes over the entire cytosol and nucleus. Furthermore, we demonstrated the ability to trigger calcium signaling in both an immortalized cell line and primary dorsal root ganglion (DRG) neurons by intracellular uncaging of inositol triphosphate (IP3), an endogenous cell calcium signaling second messenger. Compared with other uncaging techniques, this ultrafast near-infrared light-driven molecular uncaging method is easily adaptable to deliver a wide range of bioactive molecules with an ultrafast optical switch, enabling new possibilities to investigate signaling pathways within individual cells and cellular networks.
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Affiliation(s)
- Xiuying Li
- Department of Mechanical Engineering, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Zifan Che
- Department of Materials Science and Engineering, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Khadijah Mazhar
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Theodore J Price
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Zhenpeng Qin
- Department of Mechanical Engineering, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Surgery, The University of Texas Southwestern Medical Center, 5323 Harry Lines Blvd, Dallas, Texas 75390
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25
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Trifunctional lipid probes for comprehensive studies of single lipid species in living cells. Proc Natl Acad Sci U S A 2017; 114:1566-1571. [PMID: 28154130 DOI: 10.1073/pnas.1611096114] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Lipid-mediated signaling events regulate many cellular processes. Investigations of the complex underlying mechanisms are difficult because several different methods need to be used under varying conditions. Here we introduce multifunctional lipid derivatives to study lipid metabolism, lipid-protein interactions, and intracellular lipid localization with a single tool per target lipid. The probes are equipped with two photoreactive groups to allow photoliberation (uncaging) and photo-cross-linking in a sequential manner, as well as a click-handle for subsequent functionalization. We demonstrate the versatility of the design for the signaling lipids sphingosine and diacylglycerol; uncaging of the probe for these two species triggered calcium signaling and intracellular protein translocation events, respectively. We performed proteomic screens to map the lipid-interacting proteome for both lipids. Finally, we visualized a sphingosine transport deficiency in patient-derived Niemann-Pick disease type C fibroblasts by fluorescence as well as correlative light and electron microscopy, pointing toward the diagnostic potential of such tools. We envision that this type of probe will become important for analyzing and ultimately understanding lipid signaling events in a comprehensive manner.
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26
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Papadopoulos T, Rhee HJ, Subramanian D, Paraskevopoulou F, Mueller R, Schultz C, Brose N, Rhee JS, Betz H. Endosomal Phosphatidylinositol 3-Phosphate Promotes Gephyrin Clustering and GABAergic Neurotransmission at Inhibitory Postsynapses. J Biol Chem 2016; 292:1160-1177. [PMID: 27941024 DOI: 10.1074/jbc.m116.771592] [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: 12/07/2016] [Indexed: 11/06/2022] Open
Abstract
The formation of neuronal synapses and the dynamic regulation of their efficacy depend on the proper assembly of the postsynaptic neurotransmitter receptor apparatus. Receptor recruitment to inhibitory GABAergic postsynapses requires the scaffold protein gephyrin and the guanine nucleotide exchange factor collybistin (Cb). In vitro, the pleckstrin homology domain of Cb binds phosphoinositides, specifically phosphatidylinositol 3-phosphate (PI3P). However, whether PI3P is required for inhibitory postsynapse formation is currently unknown. Here, we investigated the role of PI3P at developing GABAergic postsynapses by using a membrane-permeant PI3P derivative, time-lapse confocal imaging, electrophysiology, as well as knockdown and overexpression of PI3P-metabolizing enzymes. Our results provide the first in cellula evidence that PI3P located at early/sorting endosomes regulates the postsynaptic clustering of gephyrin and GABAA receptors and the strength of inhibitory, but not excitatory, postsynapses in cultured hippocampal neurons. In human embryonic kidney 293 cells, stimulation of gephyrin cluster formation by PI3P depends on Cb. We therefore conclude that the endosomal pool of PI3P, generated by the class III phosphatidylinositol 3-kinase, is important for the Cb-mediated recruitment of gephyrin and GABAA receptors to developing inhibitory postsynapses and thus the formation of postsynaptic membrane specializations.
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Affiliation(s)
- Theofilos Papadopoulos
- From the Department of Molecular Biology, Center of Biochemistry and Molecular Cell Biology, Universitätsmedizin Göttingen, Humboldtallee 23, 37073 Göttingen, Germany,
| | - Hong Jun Rhee
- the Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Devaraj Subramanian
- the European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Foteini Paraskevopoulou
- From the Department of Molecular Biology, Center of Biochemistry and Molecular Cell Biology, Universitätsmedizin Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Rainer Mueller
- the European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Carsten Schultz
- the European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.,the Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, Oregon 97239-3098
| | - Nils Brose
- the Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Jeong-Seop Rhee
- the Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Heinrich Betz
- the Department of Neurochemistry, Max Planck Institute for Brain Research, Deutschordenstrasse 46, 60528 Frankfurt am Main, Germany, and.,the Max Planck Institute of Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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27
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Optopharmacological control of TRPC channels by coumarin-caged lipids is associated with a phototoxic membrane effect. SCIENCE CHINA-LIFE SCIENCES 2016; 59:802-10. [DOI: 10.1007/s11427-016-5095-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/06/2016] [Indexed: 10/21/2022]
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28
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Hövelmann F, Kedziora KM, Nadler A, Müller R, Jalink K, Schultz C. Optotaxis: Caged Lysophosphatidic Acid Enables Optical Control of a Chemotactic Gradient. Cell Chem Biol 2016; 23:629-634. [PMID: 27161483 DOI: 10.1016/j.chembiol.2015.11.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/10/2015] [Accepted: 11/18/2015] [Indexed: 11/28/2022]
Abstract
Lysophosphatidic acid (LPA) is a serum-borne lipid mediator that binds to a variety of different G protein-coupled receptors to trigger an exceptionally wide range of biological effects, including cell survival and differentiation, cancer cell migration, and embryonic development. Here we synthesized caged LPA (cgLPA), a "photolysable" coumarin-masked derivative of LPA. We demonstrate that illumination of cgLPA with 405 nm light liberates bioactive LPA on a subsecond scale to evoke Ca(2+) signaling, Rho activation, and cytoskeletal contraction. In addition, we developed an "optotaxis" assay to attract melanoma cells through a stable chemotactic gradient by repeated liberation of LPA through local photolysis of extracellular cgLPA. We expect that this method of light-controlled chemotaxis will be generally applicable to a large variety of small molecules that drive cellular migration or other responses.
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Affiliation(s)
- Felix Hövelmann
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Katarzyna M Kedziora
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - André Nadler
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Rainer Müller
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Kees Jalink
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Carsten Schultz
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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29
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Marat AL, Haucke V. Phosphatidylinositol 3-phosphates-at the interface between cell signalling and membrane traffic. EMBO J 2016; 35:561-79. [PMID: 26888746 DOI: 10.15252/embj.201593564] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 01/26/2016] [Indexed: 12/31/2022] Open
Abstract
Phosphoinositides (PIs) form a minor class of phospholipids with crucial functions in cell physiology, ranging from cell signalling and motility to a role as signposts of compartmental membrane identity. Phosphatidylinositol 3-phosphates are present at the plasma membrane and within the endolysosomal system, where they serve as key regulators of both cell signalling and of intracellular membrane traffic. Here, we provide an overview of the metabolic pathways that regulate cellular synthesis of PI 3-phosphates at distinct intracellular sites and discuss the mechanisms by which these lipids regulate cell signalling and membrane traffic. Finally, we provide a framework for how PI 3-phosphate metabolism is integrated into the cellular network.
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Affiliation(s)
- Andrea L Marat
- Leibniz Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Volker Haucke
- Leibniz Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
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30
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Pavlovic I, Thakor DT, Vargas JR, McKinlay CJ, Hauke S, Anstaett P, Camuña RC, Bigler L, Gasser G, Schultz C, Wender PA, Jessen HJ. Cellular delivery and photochemical release of a caged inositol-pyrophosphate induces PH-domain translocation in cellulo. Nat Commun 2016; 7:10622. [PMID: 26842801 PMCID: PMC4743007 DOI: 10.1038/ncomms10622] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/05/2016] [Indexed: 02/07/2023] Open
Abstract
Inositol pyrophosphates, such as diphospho-myo-inositol pentakisphosphates (InsP7), are an important family of signalling molecules, implicated in many cellular processes and therapeutic indications including insulin secretion, glucose homeostasis and weight gain. To understand their cellular functions, chemical tools such as photocaged analogues for their real-time modulation in cells are required. Here we describe a concise, modular synthesis of InsP7 and caged InsP7. The caged molecule is stable and releases InsP7 only on irradiation. While photocaged InsP7 does not enter cells, its cellular uptake is achieved using nanoparticles formed by association with a guanidinium-rich molecular transporter. This novel synthesis and unprecedented polyphosphate delivery strategy enable the first studies required to understand InsP7 signalling in cells with controlled spatiotemporal resolution. It is shown herein that cytoplasmic photouncaging of InsP7 leads to translocation of the PH-domain of Akt, an important signalling-node kinase involved in glucose homeostasis, from the membrane into the cytoplasm. Photocaged inositol-pyrophosphates offer a tool to study cellular signalling, but their challenging synthesis has precluded any biological studies so far. Here, the authors report the synthesis and cellular delivery of a photocaged analogue, and show that it mediates protein translocation in cellulo.
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Affiliation(s)
- Igor Pavlovic
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Divyeshsinh T Thakor
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Jessica R Vargas
- Departments of Chemistry and Chemical and Systems Biology, Stanford University, Stanford, California 94305, USA
| | - Colin J McKinlay
- Departments of Chemistry and Chemical and Systems Biology, Stanford University, Stanford, California 94305, USA
| | - Sebastian Hauke
- European Molecular Biology Laboratory (EMBL), Cell Biology &Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Philipp Anstaett
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Rafael C Camuña
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Málaga, Malaga 29071, Spain
| | - Laurent Bigler
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Gilles Gasser
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL), Cell Biology &Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Paul A Wender
- Departments of Chemistry and Chemical and Systems Biology, Stanford University, Stanford, California 94305, USA
| | - Henning J Jessen
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
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31
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Thomas MP, Mills SJ, Potter BVL. The "Other" Inositols and Their Phosphates: Synthesis, Biology, and Medicine (with Recent Advances in myo-Inositol Chemistry). Angew Chem Int Ed Engl 2016; 55:1614-50. [PMID: 26694856 PMCID: PMC5156312 DOI: 10.1002/anie.201502227] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Indexed: 12/24/2022]
Abstract
Cell signaling via inositol phosphates, in particular via the second messenger myo-inositol 1,4,5-trisphosphate, and phosphoinositides comprises a huge field of biology. Of the nine 1,2,3,4,5,6-cyclohexanehexol isomers, myo-inositol is pre-eminent, with "other" inositols (cis-, epi-, allo-, muco-, neo-, L-chiro-, D-chiro-, and scyllo-) and derivatives rarer or thought not to exist in nature. However, neo- and d-chiro-inositol hexakisphosphates were recently revealed in both terrestrial and aquatic ecosystems, thus highlighting the paucity of knowledge of the origins and potential biological functions of such stereoisomers, a prevalent group of environmental organic phosphates, and their parent inositols. Some "other" inositols are medically relevant, for example, scyllo-inositol (neurodegenerative diseases) and d-chiro-inositol (diabetes). It is timely to consider exploration of the roles and applications of the "other" isomers and their derivatives, likely by exploiting techniques now well developed for the myo series.
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Affiliation(s)
- Mark P Thomas
- Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Stephen J Mills
- Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Barry V L Potter
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.
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32
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Aiba T, Sato M, Umegaki D, Iwasaki T, Kambe N, Fukase K, Fujimoto Y. Regioselective phosphorylation of myo-inositol with BINOL-derived phosphoramidites and its application for protozoan lysophosphatidylinositol. Org Biomol Chem 2016; 14:6672-5. [DOI: 10.1039/c6ob01062h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
BINOL-derived phosphoramidites enabled a regioselective phosphorylation of myo-inositol. The method was applied for the first total synthesis of a protozoan lysophosphatidylinositol, EhPIa.
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Affiliation(s)
- Toshihiko Aiba
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Masaki Sato
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Daichi Umegaki
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Takanori Iwasaki
- Department of Applied Chemistry
- Graduate School of Engineering
- Osaka University
- Suita
- Japan
| | - Nobuaki Kambe
- Department of Applied Chemistry
- Graduate School of Engineering
- Osaka University
- Suita
- Japan
| | - Koichi Fukase
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Yukari Fujimoto
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
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33
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Thomas MP, Mills SJ, Potter BVL. Die “anderen” Inositole und ihre Phosphate: Synthese, Biologie und Medizin (sowie jüngste Fortschritte in dermyo-Inositolchemie). Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mark P. Thomas
- Department of Pharmacy & Pharmacology; University of Bath; Claverton Down Bath BA2 7AY Vereinigtes Königreich
| | - Stephen J. Mills
- Department of Pharmacy & Pharmacology; University of Bath; Claverton Down Bath BA2 7AY Vereinigtes Königreich
| | - Barry V. L. Potter
- Department of Pharmacology; University of Oxford; Mansfield Road Oxford OX1 3QT Vereinigtes Königreich
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34
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Bliman D, Nilsson JR, Kettunen P, Andréasson J, Grøtli M. A Caged Ret Kinase Inhibitor and its Effect on Motoneuron Development in Zebrafish Embryos. Sci Rep 2015; 5:13109. [PMID: 26300345 PMCID: PMC4547397 DOI: 10.1038/srep13109] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 07/14/2015] [Indexed: 02/02/2023] Open
Abstract
Proto-oncogene tyrosine-protein kinase receptor RET is implicated in the development and maintenance of neurons of the central and peripheral nervous systems. Attaching activity-compromising photocleavable groups (caging) to inhibitors could allow for external spatiotemporally controlled inhibition using light, potentially providing novel information on how these kinase receptors are involved in cellular processes. Here, caged RET inhibitors were obtained from 3-substituted pyrazolopyrimidine-based compounds by attaching photolabile groups to the exocyclic amino function. The most promising compound displayed excellent inhibitory effect in cell-free, as well as live-cell assays upon decaging. Furthermore, inhibition could be efficiently activated with light in vivo in zebrafish embryos and was shown to effect motoneuron development.
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Affiliation(s)
- David Bliman
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Jesper R. Nilsson
- Department of Chemistry and Chemical Engineering, Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Petronella Kettunen
- Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, SE-413 45 Gothenburg, Sweden
| | - Joakim Andréasson
- Department of Chemistry and Chemical Engineering, Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
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35
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Fouda AE, Pflum MKH. A Cell-Permeable ATP Analogue for Kinase-Catalyzed Biotinylation. Angew Chem Int Ed Engl 2015; 54:9618-21. [PMID: 26119262 PMCID: PMC4551444 DOI: 10.1002/anie.201503041] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/07/2015] [Indexed: 01/20/2023]
Abstract
ATP analogues have been powerful compounds for the study of kinase-catalyzed phosphorylation. However, the cell impermeability of ATP analogues has largely limited their use to in vitro lysate-based experiments. Herein, we report the first cell-permeable ATP analogue, ATP-polyamine-biotin (APB). APB is shown to promote biotin labeling of kinase substrates in live cells and has future applications in phosphoprotein purification and analysis. More generally, these studies provide a foundation for the development of additional cell-permeable ATP analogues for cell-signaling research.
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Affiliation(s)
- Ahmed E Fouda
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202 (USA) http://chem.wayne.edu/pflumgroup/
| | - Mary Kay H Pflum
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202 (USA) http://chem.wayne.edu/pflumgroup/.
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36
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Fouda AE, Pflum MKH. A Cell-Permeable ATP Analogue for Kinase-Catalyzed Biotinylation. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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37
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Pavlovic I, Thakor DT, Bigler L, Wilson MSC, Laha D, Schaaf G, Saiardi A, Jessen HJ. Prometabolites of 5-Diphospho-myo-inositol Pentakisphosphate. Angew Chem Int Ed Engl 2015; 54:9622-6. [PMID: 26014370 DOI: 10.1002/anie.201503094] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Indexed: 11/10/2022]
Abstract
Diphospho-myo-inositol phosphates (PP-InsP(y)) are an important class of cellular messengers. Thus far, no method for the transport of PP-InsP(y) into living cells is available. Owing to their high negative charge density, PP-InsP(y) will not cross the cell membrane. A strategy to circumvent this issue involves the generation of precursors in which the negative charges are masked with biolabile groups. A PP-InsP(y) prometabolite would require twelve to thirteen biolabile groups, which need to be cleaved by cellular enzymes to release the parent molecules. Such densely modified prometabolites of phosphate esters and anhydrides have never been reported to date. This study discloses the synthesis of such agents and an analysis of their metabolism in tissue homogenates by gel electrophoresis. The acetoxybenzyl-protected system is capable of releasing 5-PP-InsP5 in mammalian cell/tissue homogenates within a few minutes and can be used to release 5-PP-InsP5 inside cells. These molecules will serve as a platform for the development of fundamental tools required to study PP-InsP(y) physiology.
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Affiliation(s)
- Igor Pavlovic
- Department of Chemistry, University of Zürich (UZH), Winterthurerstrasse 190, 8057 Zürich (Switzerland)
| | - Divyeshsinh T Thakor
- Department of Chemistry, University of Zürich (UZH), Winterthurerstrasse 190, 8057 Zürich (Switzerland)
| | - Laurent Bigler
- Department of Chemistry, University of Zürich (UZH), Winterthurerstrasse 190, 8057 Zürich (Switzerland)
| | | | - Debabrata Laha
- Center for Plant Molecular Biology, University of Tübingen (Germany)
| | - Gabriel Schaaf
- Center for Plant Molecular Biology, University of Tübingen (Germany)
| | | | - Henning J Jessen
- Department of Chemistry, University of Zürich (UZH), Winterthurerstrasse 190, 8057 Zürich (Switzerland).
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38
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Pavlovic I, Thakor DT, Bigler L, Wilson MSC, Laha D, Schaaf G, Saiardi A, Jessen HJ. Prometabolites of 5-Diphospho-myo-inositol Pentakisphosphate. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503094] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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39
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Schifferer M, Feng S, Stein F, Tischer C, Schultz C. Reversible chemical dimerizer-induced recovery of PIP2 levels moves clathrin to the plasma membrane. Bioorg Med Chem 2015; 23:2862-7. [PMID: 25840797 DOI: 10.1016/j.bmc.2015.03.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/16/2015] [Accepted: 03/18/2015] [Indexed: 12/24/2022]
Abstract
Chemical dimerizers are powerful non-invasive tools for bringing molecules together inside intact cells. We recently introduced a rapidly reversible chemical dimerizer system which enables transient translocation of enzymes to and from the plasma membrane (PM). Here we have applied this system to transiently activate phosphatidylinositol 4,5-bisphosphate (PIP2) breakdown at the PM via translocation of phosphoinositide 5-phosphatase (5Ptase). We found that the PIP2 sensor phospholipase C-δ PH domain (PLCδ-PH) is released from the PM upon addition of the reversible chemical dimerizer rCD1. By outcompeting rCD1, rapid release of the 5Ptase from the PM is followed by PIP2 recovery. This permits the observation of the PIP2-dependent clathrin assembly at the PM.
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Affiliation(s)
- Martina Schifferer
- European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Suihan Feng
- European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Christian Tischer
- European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany.
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40
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Muro E, Atilla-Gokcumen GE, Eggert US. Lipids in cell biology: how can we understand them better? Mol Biol Cell 2015; 25:1819-23. [PMID: 24925915 PMCID: PMC4055261 DOI: 10.1091/mbc.e13-09-0516] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Lipids are a major class of biological molecules and play many key roles in different processes. The diversity of lipids is on the same order of magnitude as that of proteins: cells express tens of thousands of different lipids and hundreds of proteins to regulate their metabolism and transport. Despite their clear importance and essential functions, lipids have not been as well studied as proteins. We discuss here some of the reasons why it has been challenging to study lipids and outline technological developments that are allowing us to begin lifting lipids out of their “Cinderella” status. We focus on recent advances in lipid identification, visualization, and investigation of their biophysics and perturbations and suggest that the field has sufficiently advanced to encourage broader investigation into these intriguing molecules.
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Affiliation(s)
- Eleonora Muro
- Department of Chemistry and Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom
| | - G Ekin Atilla-Gokcumen
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY 14260
| | - Ulrike S Eggert
- Department of Chemistry and Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom
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41
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Idevall-Hagren O, De Camilli P. Detection and manipulation of phosphoinositides. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1851:736-45. [PMID: 25514766 DOI: 10.1016/j.bbalip.2014.12.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/27/2014] [Accepted: 12/09/2014] [Indexed: 12/23/2022]
Abstract
Phosphoinositides (PIs) are minor components of cell membranes, but play key roles in cell function. Recent refinements in techniques for their detection, together with imaging methods to study their distribution and changes, have greatly facilitated the study of these lipids. Such methods have been complemented by the parallel development of techniques for the acute manipulation of their levels, which in turn allow bypassing the long-term adaptive changes implicit in genetic perturbations. Collectively, these advancements have helped elucidate the role of PIs in physiology and the impact of the dysfunction of their metabolism in disease. Combining methods for detection and manipulation enables the identification of specific roles played by each of the PIs and may eventually lead to the complete deconstruction of the PI signaling network. Here, we review current techniques used for the study and manipulation of cellular PIs and also discuss advantages and disadvantages associated with the various methods. This article is part of a Special Issue entitled Phosphoinositides.
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Affiliation(s)
- Olof Idevall-Hagren
- Department of Medical Cell Biology, Uppsala University, BMC Box 571, 75123 Uppsala, Sweden.
| | - Pietro De Camilli
- Department of Cell Biology, Howard Hughes Medical Institute and Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510, USA.
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42
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Abstract
Proteins synthesised at the endoplasmic reticulum (ER) have to undergo a number of consecutive and coordinated steps to reach the Golgi complex. To understand the dynamic complexity of ER-to-Golgi transport at the structural and molecular level, light microscopy approaches are fundamental tools that allow in vivo observations of protein dynamics and interactions of fluorescent proteins in living cells. Imaging protein and organelle dynamics close to the ultra-structural level became possible by combining light microscopy with electron microscopy analyses or super-resolution light microscopy methods. Besides, increasing evidence suggests that the early secretory pathway is tightly connected to other cellular processes, such as signal transduction, and quantitative information at the systems level is fundamental to achieve a comprehensive molecular understanding of these connections. High-throughput microscopy in fixed and living cells in combination with systematic perturbation of gene expression by, e.g. RNA interference, will open new avenues to gain such an understanding of the early secretory pathway at the systems level. In this Commentary, we first outline examples that revealed the dynamic organisation of ER-to-Golgi transport in living cells. Next, we discuss the use of advanced imaging methods in studying ER-to-Golgi transport and, finally, delineate the efforts in understanding ER-to-Golgi transport at the systems level.
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Affiliation(s)
- Fatima Verissimo
- European Molecular Biology Laboratory, Cell Biology and Cell Biophysics Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
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43
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Wu M, Chong LS, Capolicchio S, Jessen HJ, Resnick AC, Fiedler D. Elucidating diphosphoinositol polyphosphate function with nonhydrolyzable analogues. Angew Chem Int Ed Engl 2014; 53:7192-7. [PMID: 24888434 DOI: 10.1002/anie.201402905] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/25/2014] [Indexed: 11/11/2022]
Abstract
The diphosphoinositol polyphosphates (PP-IPs) represent a novel class of high-energy phosphate-containing messengers which control a wide variety of cellular processes. It is thought that PP-IPs exert their pleiotropic effects as allosteric regulators and through pyrophosphorylation of protein substrates. However, most details of PP-IP signaling have remained elusive because of a paucity of suitable tools. We describe the synthesis of PP-IP bisphosphonate analogues (PCP-IPs), which are resistant to chemical and biochemical degradation. While the two regioisomers 1PCP-IP5 and 5PCP-IP5 inhibited Akt phosphorylation with similar potencies, 1PCP-IP5 was much more effective at inhibiting its cognate phosphatase hDIPP1. Furthermore, the PCP analogues inhibit protein pyrophosphorylation because of their inability to transfer the β-phosphoryl group, and thus enable the distinction between PP-IP signaling mechanisms. As such, the PCP analogues will find widespread applications for the structural and biochemical characterization of PP-IP signaling properties.
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Affiliation(s)
- Mingxuan Wu
- Department of Chemistry, Princeton University, Washington Rd, Princeton, NJ 08544 (USA)
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44
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Wu M, Chong LS, Capolicchio S, Jessen HJ, Resnick AC, Fiedler D. Elucidating Diphosphoinositol Polyphosphate Function with Nonhydrolyzable Analogues. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402905] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mingxuan Wu
- Department of Chemistry, Princeton University, Washington Rd, Princeton, NJ 08544 (USA)
| | - Lucy S. Chong
- Colket Translational Research Bldg, The Children's Hospital of Philadelphia, 3501 Civic Center Blvd, Philadelphia, PA 19104 (USA)
| | - Samanta Capolicchio
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich (Switzerland)
| | - Henning J. Jessen
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich (Switzerland)
| | - Adam C. Resnick
- Colket Translational Research Bldg, The Children's Hospital of Philadelphia, 3501 Civic Center Blvd, Philadelphia, PA 19104 (USA)
| | - Dorothea Fiedler
- Department of Chemistry, Princeton University, Washington Rd, Princeton, NJ 08544 (USA)
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45
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Feng S, Laketa V, Stein F, Rutkowska A, MacNamara A, Depner S, Klingmüller U, Saez-Rodriguez J, Schultz C. A rapidly reversible chemical dimerizer system to study lipid signaling in living cells. Angew Chem Int Ed Engl 2014; 53:6720-3. [PMID: 24841150 DOI: 10.1002/anie.201402294] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Indexed: 01/11/2023]
Abstract
Chemical dimerizers are powerful tools for non-invasive manipulation of enzyme activities in intact cells. Here we introduce the first rapidly reversible small-molecule-based dimerization system and demonstrate a sufficiently fast switch-off to determine kinetics of lipid metabolizing enzymes in living cells. We applied this new method to induce and stop phosphatidylinositol 3-kinase (PI3K) activity, allowing us to quantitatively measure the turnover of phosphatidylinositol 3,4,5-trisphosphate (PIP3) and its downstream effectors by confocal fluorescence microscopy as well as standard biochemical methods.
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Affiliation(s)
- Suihan Feng
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany)
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46
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Feng S, Laketa V, Stein F, Rutkowska A, MacNamara A, Depner S, Klingmüller U, Saez-Rodriguez J, Schultz C. A Rapidly Reversible Chemical Dimerizer System to Study Lipid Signaling in Living Cells. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402294] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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47
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Wakelam MJO. The uses and limitations of the analysis of cellular phosphoinositides by lipidomic and imaging methodologies. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:1102-7. [PMID: 24769341 DOI: 10.1016/j.bbalip.2014.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/14/2014] [Accepted: 04/17/2014] [Indexed: 01/24/2023]
Abstract
The advent of mass spectrometric methods has facilitated the determination of multiple molecular species of cellular lipid classes including the polyphosphoinositides, though to date methods to analyse and quantify each of the individual three PtdInsP and three PtdInsP2 species are lacking. The use of imaging methods has allowed intracellular localization of the phosphoinositide classes but this methodology does not determine the acyl structures. The range of molecular species suggests a greater complexity in polyphosphoinositide signaling than yet defined but elucidating this will require further method development to be achieved. This article is part of a Special Issue entitled Tools to study lipid functions.
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48
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Höglinger D, Nadler A, Schultz C. Caged lipids as tools for investigating cellular signaling. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:1085-96. [PMID: 24713581 DOI: 10.1016/j.bbalip.2014.03.012] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 03/27/2014] [Accepted: 03/27/2014] [Indexed: 12/21/2022]
Abstract
Lipid derivatives that can be activated by light, often referred to as 'caged' lipids, are useful tools to manipulate intact cells non-invasively. Here we focus on experimental approaches that have made use of caged lipids. Apart from summarizing the recent advances and available tools in the field, we strive to highlight the experimental challenges that arise from lipid-specific biophysical properties and the abundance of an enormous diversity of distinct molecular lipid species in cells. This article is part of a Special Issue entitled Tools to study lipid functions.
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Affiliation(s)
- Doris Höglinger
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - André Nadler
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.
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49
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Bayer AM, Alam S, Mattern-Schain SI, Best MD. Triggered Liposomal Release through a Synthetic Phosphatidylcholine Analogue Bearing a Photocleavable Moiety Embedded within thesn-2 Acyl Chain. Chemistry 2014; 20:3350-7. [DOI: 10.1002/chem.201304094] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Indexed: 01/31/2023]
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50
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Laketa V, Zarbakhsh S, Traynor-Kaplan A, MacNamara A, Subramanian D, Putyrski M, Mueller R, Nadler A, Mentel M, Saez-Rodriguez J, Pepperkok R, Schultz C. PIP3 Induces the Recycling of Receptor Tyrosine Kinases. Sci Signal 2014; 7:ra5. [DOI: 10.1126/scisignal.2004532] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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