1
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Cao X, Huang S, Wagner MM, Cho YT, Chiu DC, Wartchow KM, Lazarian A, McIntire LB, Smolka MB, Baskin JM. A phosphorylation-controlled switch confers cell cycle-dependent protein relocalization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.05.597552. [PMID: 38895347 PMCID: PMC11185714 DOI: 10.1101/2024.06.05.597552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Tools for acute manipulation of protein localization enable elucidation of spatiotemporally defined functions, but their reliance on exogenous triggers can interfere with cell physiology. This limitation is particularly apparent for studying mitosis, whose highly choreographed events are sensitive to perturbations. Here we exploit the serendipitous discovery of a phosphorylation-controlled, cell cycle-dependent localization change of the adaptor protein PLEKHA5 to develop a system for mitosis-specific protein recruitment to the plasma membrane that requires no exogenous stimulus. Mitosis-enabled Anchor-away/Recruiter System (MARS) comprises an engineered, 15-kDa module derived from PLEKHA5 capable of recruiting functional protein cargoes to the plasma membrane during mitosis, either through direct fusion or via GFP-GFP nanobody interaction. Applications of MARS include both knock sideways to rapidly extract proteins from their native localizations during mitosis and conditional recruitment of lipid-metabolizing enzymes for mitosis-selective editing of plasma membrane lipid content, without the need for exogenous triggers or perturbative synchronization methods.
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Affiliation(s)
- Xiaofu Cao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States, 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
| | - Shiying Huang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States, 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
| | - Mateusz M. Wagner
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States, 14853
| | - Yuan-Ting Cho
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States, 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
| | - Din-Chi Chiu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States, 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
| | - Krista M. Wartchow
- Department of Radiology, Weill Cornell Medicine, New York, New York, United States, 10065
| | - Artur Lazarian
- Department of Radiology, Weill Cornell Medicine, New York, New York, United States, 10065
| | - Laura Beth McIntire
- Department of Radiology, Weill Cornell Medicine, New York, New York, United States, 10065
| | - Marcus B. Smolka
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States, 14853
| | - Jeremy M. Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States, 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
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2
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Li XL, Tei R, Uematsu M, Baskin JM. Ultralow Background Membrane Editors for Spatiotemporal Control of Phosphatidic Acid Metabolism and Signaling. ACS CENTRAL SCIENCE 2024; 10:543-554. [PMID: 38559292 PMCID: PMC10979500 DOI: 10.1021/acscentsci.3c01105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 04/04/2024]
Abstract
Phosphatidic acid (PA) is a multifunctional lipid with important metabolic and signaling functions, and efforts to dissect its pleiotropy demand strategies for perturbing its levels with spatiotemporal precision. Previous membrane editing approaches for generating local PA pools used light-mediated induced proximity to recruit a PA-synthesizing enzyme, phospholipase D (PLD), from the cytosol to the target organelle membrane. Whereas these optogenetic PLDs exhibited high activity, their residual activity in the dark led to undesired chronic lipid production. Here, we report ultralow background membrane editors for PA wherein light directly controls PLD catalytic activity, as opposed to localization and access to substrates, exploiting a light-oxygen-voltage (LOV) domain-based conformational photoswitch inserted into the PLD sequence and enabling their stable and nonperturbative targeting to multiple organelle membranes. By coupling organelle-targeted LOVPLD activation to lipidomics analysis, we discovered different rates of metabolism for PA and its downstream products depending on the subcellular location of PA production. We also elucidated signaling roles for PA pools on different membranes in conferring local activation of AMP-activated protein kinase signaling. This work illustrates how membrane editors featuring acute, optogenetic conformational switches can provide new insights into organelle-selective lipid metabolic and signaling pathways.
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Affiliation(s)
- Xiang-Ling Li
- Weill
Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Reika Tei
- Weill
Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Masaaki Uematsu
- Weill
Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Jeremy M. Baskin
- Weill
Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
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3
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Gabrielle M, Yudin Y, Wang Y, Su X, Rohacs T. Phosphatidic acid is an endogenous negative regulator of PIEZO2 channels and mechanical sensitivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582964. [PMID: 38464030 PMCID: PMC10925330 DOI: 10.1101/2024.03.01.582964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Mechanosensitive PIEZO2 ion channels play roles in touch, proprioception, and inflammatory pain. Currently, there are no small molecule inhibitors that selectively inhibit PIEZO2 over PIEZO1. The TMEM120A protein was shown to inhibit PIEZO2 while leaving PIEZO1 unaffected. Here we find that TMEM120A expression elevates cellular levels of phosphatidic acid and lysophosphatidic acid (LPA), aligning with its structural resemblance to lipid-modifying enzymes. Intracellular application of phosphatidic acid or LPA inhibited PIEZO2, but not PIEZO1 activity. Extended extracellular exposure to the non-hydrolyzable phosphatidic acid and LPA analogue carbocyclic phosphatidic acid (ccPA) also inhibited PIEZO2. Optogenetic activation of phospholipase D (PLD), a signaling enzyme that generates phosphatidic acid, inhibited PIEZO2, but not PIEZO1. Conversely, inhibiting PLD led to increased PIEZO2 activity and increased mechanical sensitivity in mice in behavioral experiments. These findings unveil lipid regulators that selectively target PIEZO2 over PIEZO1, and identify the PLD pathway as a regulator of PIEZO2 activity.
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Affiliation(s)
- Matthew Gabrielle
- Department of Pharmacology, Physiology & Neuroscience, Rutgers University New Jersey Medical School, Newark NJ
| | - Yevgen Yudin
- Department of Pharmacology, Physiology & Neuroscience, Rutgers University New Jersey Medical School, Newark NJ
| | - Yujue Wang
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick NJ
- Present address: School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Xiaoyang Su
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick NJ
| | - Tibor Rohacs
- Department of Pharmacology, Physiology & Neuroscience, Rutgers University New Jersey Medical School, Newark NJ
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4
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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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5
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Su YA, Chiu HY, Chang YC, Sung CJ, Chen CW, Tei R, Huang XR, Hsu SC, Lin SS, Wang HC, Lin YC, Hsu JC, Bauer H, Feng Y, Baskin JM, Chang ZF, Liu YW. NME3 binds to phosphatidic acid and mediates PLD6-induced mitochondrial tethering. J Cell Biol 2023; 222:e202301091. [PMID: 37584589 PMCID: PMC10432850 DOI: 10.1083/jcb.202301091] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/10/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023] Open
Abstract
Mitochondria are dynamic organelles regulated by fission and fusion processes. The fusion of membranes requires elaborative coordination of proteins and lipids and is particularly crucial for the function and quality control of mitochondria. Phosphatidic acid (PA) on the mitochondrial outer membrane generated by PLD6 facilitates the fusion of mitochondria. However, how PA promotes mitochondrial fusion remains unclear. Here, we show that a mitochondrial outer membrane protein, NME3, is required for PLD6-induced mitochondrial tethering or clustering. NME3 is enriched at the contact interface of two closely positioned mitochondria depending on PLD6, and NME3 binds directly to PA-exposed lipid packing defects via its N-terminal amphipathic helix. The PA binding function and hexamerization confer NME3 mitochondrial tethering activity. Importantly, nutrient starvation enhances the enrichment efficiency of NME3 at the mitochondrial contact interface, and the tethering ability of NME3 contributes to fusion efficiency. Together, our findings demonstrate NME3 as a tethering protein promoting selective fusion between PLD6-remodeled mitochondria for quality control.
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Affiliation(s)
- You-An Su
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsin-Yi Chiu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Chen Chang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chieh-Ju Sung
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chih-Wei Chen
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Reika Tei
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Xuang-Rong Huang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shao-Chun Hsu
- Imaging Core, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shan-Shan Lin
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsien-Chu Wang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Yu-Chun Lin
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Jui-Cheng Hsu
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Hermann Bauer
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Yuxi Feng
- Department of Experimental Pharmacology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Jeremy M. Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Zee-Fen Chang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ya-Wen Liu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
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6
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Li XL, Tei R, Uematsu M, Baskin JM. Ultralow background membrane editors for spatiotemporal control of lipid metabolism and signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555787. [PMID: 37693485 PMCID: PMC10491157 DOI: 10.1101/2023.08.31.555787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Phosphatidic acid (PA) is a multifunctional lipid with important metabolic and signaling functions, and efforts to dissect its pleiotropy demand strategies for perturbing its levels with spatiotemporal precision. Previous membrane editing approaches for generating local PA pools used light-mediated induced proximity to recruit a PA-synthesizing enzyme, phospholipase D (PLD), from the cytosol to the target organelle membrane. Whereas these optogenetic PLDs exhibited high activity, their residual activity in the dark led to undesired chronic lipid production. Here, we report ultralow background membrane editors for PA wherein light directly controls PLD catalytic activity, as opposed to localization and access to substrates, exploiting a LOV domain-based conformational photoswitch inserted into the PLD sequence and enabling their stable and non-perturbative targeting to multiple organelle membranes. By coupling organelle-targeted LOVPLD activation to lipidomics analysis, we discovered different rates of metabolism for PA and its downstream products depending on the subcellular location of PA production. We also elucidated signaling roles for PA pools on different membranes in conferring local activation of AMP-activated protein kinase signaling. This work illustrates how membrane editors featuring acute, optogenetic conformational switches can provide new insights into organelle-selective lipid metabolic and signaling pathways.
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Affiliation(s)
- Xiang-Ling Li
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Reika Tei
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Masaaki Uematsu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jeremy M. Baskin
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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7
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Tei R, Bagde SR, Fromme JC, Baskin JM. Activity-based directed evolution of a membrane editor in mammalian cells. Nat Chem 2023; 15:1030-1039. [PMID: 37217787 PMCID: PMC10525039 DOI: 10.1038/s41557-023-01214-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023]
Abstract
Cellular membranes contain numerous lipid species, and efforts to understand the biological functions of individual lipids have been stymied by a lack of approaches for controlled modulation of membrane composition in situ. Here we present a strategy for editing phospholipids, the most abundant lipids in biological membranes. Our membrane editor is based on a bacterial phospholipase D (PLD), which exchanges phospholipid head groups through hydrolysis or transphosphatidylation of phosphatidylcholine with water or exogenous alcohols. Exploiting activity-dependent directed enzyme evolution in mammalian cells, we have developed and structurally characterized a family of 'superPLDs' with up to a 100-fold enhancement in intracellular activity. We demonstrate the utility of superPLDs for both optogenetics-enabled editing of phospholipids within specific organelle membranes in live cells and biocatalytic synthesis of natural and unnatural designer phospholipids in vitro. Beyond the superPLDs, activity-based directed enzyme evolution in mammalian cells is a generalizable approach to engineer additional chemoenzymatic biomolecule editors.
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Affiliation(s)
- Reika Tei
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Saket R Bagde
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - J Christopher Fromme
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.
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8
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Gomez-Larrauri A, Gangoiti P, Camacho L, Presa N, Martin C, Gomez-Muñoz A. Phosphatidic Acid Stimulates Lung Cancer Cell Migration through Interaction with the LPA1 Receptor and Subsequent Activation of MAP Kinases and STAT3. Biomedicines 2023; 11:1804. [PMID: 37509443 PMCID: PMC10376810 DOI: 10.3390/biomedicines11071804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Phosphatidic acid (PA) is a key bioactive glycerophospholipid that is implicated in the regulation of vital cell functions such as cell growth, differentiation, and migration, and is involved in a variety of pathologic processes. However, the molecular mechanisms by which PA exerts its pathophysiological actions are incompletely understood. In the present work, we demonstrate that PA stimulates the migration of the human non-small cell lung cancer (NSCLC) A549 adenocarcinoma cells, as determined by the transwell migration assay. PA induced the rapid phosphorylation of mitogen-activated protein kinases (MAPKs) ERK1-2, p38, and JNK, and the pretreatment of cells with selective inhibitors of these kinases blocked the PA-stimulated migration of cancer cells. In addition, the chemotactic effect of PA was inhibited by preincubating the cells with pertussis toxin (PTX), a Gi protein inhibitor, suggesting the implication of a Gi protein-coupled receptor in this action. Noteworthy, a blockade of LPA receptor 1 (LPA1) with the specific LPA1 antagonist AM966, or with the selective LPA1 inhibitors Ki1645 or VPC32193, abolished PA-stimulated cell migration. Moreover, PA stimulated the phosphorylation of the transcription factor STAT3 downstream of JAK2, and inhibitors of either JAK2 or STAT3 blocked PA-stimulated cell migration. It can be concluded that PA stimulates lung adenocarcinoma cell migration through an interaction with the LPA1 receptor and subsequent activation of the MAPKs ERK1-2, p38, and JNK, and that the JAK2/STAT3 pathway is also important in this process. These findings suggest that targeting PA formation and/or the LPA1 receptor may provide new strategies to reduce malignancy in lung cancer.
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Affiliation(s)
- Ana Gomez-Larrauri
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48980 Bilbao, Bizkaia, Spain
- Respiratory Department, Cruces University Hospital, 48903 Barakaldo, Bizkaia, Spain
| | - Patricia Gangoiti
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48980 Bilbao, Bizkaia, Spain
| | - Laura Camacho
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48980 Bilbao, Bizkaia, Spain
| | - Natalia Presa
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48980 Bilbao, Bizkaia, Spain
| | - Cesar Martin
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48980 Bilbao, Bizkaia, Spain
- Department of Molecular Biophysics, Biofisika Institute, University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC), 48940 Leioa, Bizkaia, Spain
| | - Antonio Gomez-Muñoz
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48980 Bilbao, Bizkaia, Spain
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9
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Jin Z, Vighi A, Dong Y, Bureau JA, Ignea C. Engineering membrane architecture for biotechnological applications. Biotechnol Adv 2023; 64:108118. [PMID: 36773706 DOI: 10.1016/j.biotechadv.2023.108118] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
Cellular membranes, predominantly described as a dynamic bilayer, are composed of different lipids, transmembrane proteins, and carbohydrates. Most research on biological membranes focuses on the identification, characterization, and mechanistic aspects of their different components. These studies provide a fundamental understanding of membrane structure, function, and dynamics, establishing a basis for the development of membrane engineering strategies. To date, approaches in this field concentrate on membrane adaptation to harsh conditions during industrial fermentation, which can be caused by temperature, osmotic, or organic solvent stress. With advances in the field of metabolic engineering and synthetic biology, recent breakthroughs include proof of concept microbial production of essential medicines, such as cannabinoids and vinblastine. However, long pathways, low yields, and host adaptation continue to pose challenges to the efficient scale up production of many important compounds. The lipid bilayer is profoundly linked to the activity of heterologous membrane-bound enzymes and transport of metabolites. Therefore, strategies for improving enzyme performance, facilitating pathway reconstruction, and enabling storage of products to increase the yields directly involve cellular membranes. At the forefront of membrane engineering research are re-emerging approaches in lipid research and synthetic biology that manipulate membrane size and composition and target lipid profiles across species. This review summarizes engineering strategies applied to cellular membranes and discusses the challenges and future perspectives, particularly with regards to their applications in host engineering and bioproduction.
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Affiliation(s)
- Zimo Jin
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | - Asia Vighi
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | - Yueming Dong
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | | | - Codruta Ignea
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada.
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10
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Lungu C, Meyer F, Hörning M, Steudle J, Braun A, Noll B, Benz D, Fränkle F, Schmid S, Eisler SA, Olayioye MA. Golgi screen identifies the RhoGEF Solo as a novel regulator of RhoB and endocytic transport. Traffic 2023; 24:162-176. [PMID: 36562184 DOI: 10.1111/tra.12880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
The control of intracellular membrane trafficking by Rho GTPases is central to cellular homeostasis. How specific guanine nucleotide exchange factors and GTPase-activating proteins locally balance GTPase activation in this process is nevertheless largely unclear. By performing a microscopy-based RNAi screen, we here identify the RhoGEF protein Solo as a functional counterplayer of DLC3, a RhoGAP protein with established roles in membrane trafficking. Biochemical, imaging and optogenetics assays further uncover Solo as a novel regulator of endosomal RhoB. Remarkably, we find that Solo and DLC3 control not only the activity, but also total protein levels of RhoB in an antagonistic manner. Together, the results of our study uncover the first functionally connected RhoGAP-RhoGEF pair at endomembranes, placing Solo and DLC3 at the core of endocytic trafficking.
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Affiliation(s)
- Cristiana Lungu
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany.,Stuttgart Research Center Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
| | - Florian Meyer
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Marcel Hörning
- Stuttgart Research Center Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany.,Institute of Biomaterials and Biomolecular Systems, Biobased Materials Group, University of Stuttgart, Stuttgart, Germany
| | - Jasmin Steudle
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Anja Braun
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Bettina Noll
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany.,Stuttgart Research Center Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
| | - David Benz
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Felix Fränkle
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Simone Schmid
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Stephan A Eisler
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany.,Stuttgart Research Center Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
| | - Monilola A Olayioye
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany.,Stuttgart Research Center Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
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11
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Wolf A, Tanguy E, Wang Q, Gasman S, Vitale N. Phospholipase D and cancer metastasis: A focus on exosomes. Adv Biol Regul 2023; 87:100924. [PMID: 36272918 DOI: 10.1016/j.jbior.2022.100924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 09/30/2022] [Accepted: 10/10/2022] [Indexed: 03/01/2023]
Abstract
In mammals, phospholipase D (PLD) enzymes involve 6 isoforms, of which only three have established lipase activity to produce the signaling lipid phosphatidic acid (PA). This phospholipase activity has been postulated to contribute to cancer progression for over three decades now, but the exact mechanisms involved have yet to be uncovered. Indeed, using various models, an altered PLD activity has been proposed altogether to increase cell survival rate, promote angiogenesis, boost rapamycin resistance, and favor metastasis. Although for some part, the molecular pathways by which this increase in PA is pro-oncogenic are partially known, the pleiotropic functions of PA make it quite difficult to distinguish which among these simple signaling pathways is responsible for each of these PLD facets. In this review, we will describe an additional potential contribution of PA generated by PLD1 and PLD2 in the biogenesis, secretion, and uptake of exosomes. Those extracellular vesicles are now viewed as membrane vehicles that carry informative molecules able to modify the fate of receiving cells at distance from the original tumor to favor homing of metastasis. The perspectives for a better understanding of these complex role of PLDs will be discussed.
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Affiliation(s)
- Alexander Wolf
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg, France
| | - Emeline Tanguy
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg, France
| | - Qili Wang
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg, France
| | - Stéphane Gasman
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg, France
| | - Nicolas Vitale
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg, France.
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12
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Zhang M, Xie D, Wang D, Xu W, Zhang C, Li P, Sun C. Lipidomic profile changes of yellow-feathered chicken meat during thermal processing based on UPLC-ESI-MS approach. Food Chem 2023; 399:133977. [DOI: 10.1016/j.foodchem.2022.133977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 08/15/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022]
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13
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Yu W, Lin Z, Woo CM, Baskin JM. A Chemoproteomics Approach to Profile Phospholipase D-Derived Phosphatidyl Alcohol Interactions. ACS Chem Biol 2022; 17:3276-3283. [PMID: 34908404 DOI: 10.1021/acschembio.1c00584] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Alcohol consumption leads to formation of phosphatidylethanol (PEth) via the transphosphatidylation activity of phospholipase D (PLD) enzymes. Though this non-natural phospholipid routinely serves as a biomarker of chronic alcoholism, its pathophysiological roles remain unknown. We use a minimalist diazirine alkyne alcohol as an ethanol surrogate to generate clickable, photoaffinity lipid reporters of PEth localization and lipid-protein interactions via PLD-mediated transphosphatidylation. We use these tools to visualize phosphatidyl alcohols in a manner compatible with standard permeabilization and immunofluorescence methods. We also use click chemistry tagging, enrichment, and proteomics analysis to define the phosphatidyl alcohol interactome. Our analysis reveals an enrichment of putative interactors at various membrane locations, and we validate one such interaction with the single-pass transmembrane protein basigin/CD147. This study provides a comprehensive view of the molecular interactions of phosphatidyl alcohols with the cellular proteome and points to future work to connect such interactions to potential pathophysiological roles of PEth.
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Affiliation(s)
- Weizhi Yu
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Zhi Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
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14
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Abstract
Membranes are multifunctional supramolecular assemblies that encapsulate our cells and the organelles within them. Glycerophospholipids are the most abundant component of membranes. They make up the majority of the lipid bilayer and play both structural and functional roles. Each organelle has a different phospholipid composition critical for its function that results from dynamic interplay and regulation of numerous lipid-metabolizing enzymes and lipid transporters. Because lipid structures and localizations are not directly genetically encoded, chemistry has much to offer to the world of lipid biology in the form of precision tools for visualizing lipid localization and abundance, manipulating lipid composition, and in general decoding the functions of lipids in cells.In this Account, we provide an overview of our recent efforts in this space focused on two overarching and complementary goals: imaging and editing the phospholipidome. On the imaging front, we have harnessed the power of bioorthogonal chemistry to develop fluorescent reporters of specific lipid pathways. Substantial efforts have centered on phospholipase D (PLD) signaling, which generates the humble lipid phosphatidic acid (PA) that acts variably as a biosynthetic intermediate and signaling agent. Though PLD is a hydrolase that generates PA from abundant phosphatidylcholine (PC) lipids, we have exploited its transphosphatidylation activity with exogenous clickable alcohols followed by bioorthogonal tagging to generate fluorescent lipid reporters of PLD signaling in a set of methods termed IMPACT.IMPACT and its variants have facilitated many biological discoveries. Using the rapid and fluorogenic tetrazine ligation, it has revealed the spatiotemporal dynamics of disease-relevant G protein-coupled receptor signaling and interorganelle lipid transport. IMPACT using diazirine photo-cross-linkers has enabled identification of lipid-protein interactions relevant to alcohol-related diseases. Varying the alcohol reporter can allow for organelle-selective labeling, and varying the bioorthogonal detection reagent can afford super-resolution lipid imaging via expansion microscopy. Combination of IMPACT with genome-wide CRISPR screening has revealed genes that regulate physiological PLD signaling.PLD enzymes themselves can also act as tools for precision editing of the phospholipid content of membranes. An optogenetic PLD for conditional blue-light-stimulated synthesis of PA on defined organelle compartments led to the discovery of the role of organelle-specific pools of PA in regulating oncogenic Hippo signaling. Directed enzyme evolution of PLD, enabled by IMPACT, has yielded highly active superPLDs with broad substrate tolerance and an ability to edit membrane phospholipid content and synthesize designer phospholipids in vitro. Finally, azobenzene-containing PA analogues represent an alternative, all-chemical strategy for light-mediated control of PA signaling.Collectively, the strategies described here summarize our progress to date in tackling the challenge of assigning precise functions to defined pools of phospholipids in cells. They also point to new challenges and directions for future study, including extension of imaging and membrane editing tools to other classes of lipids. We envision that continued application of bioorthogonal chemistry, optogenetics, and directed evolution will yield new tools and discoveries to interrogate the phospholipidome and reveal new mechanisms regulating phospholipid homeostasis and roles for phospholipids in cell signaling.
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Affiliation(s)
- Din-Chi Chiu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
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15
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Lazcano P, Schmidtke MW, Onu C, Greenberg ML. Phosphatidic acid inhibits inositol synthesis by inducing nuclear translocation of kinase IP6K1 and repression of myo-inositol-3-P synthase. J Biol Chem 2022; 298:102363. [PMID: 35963434 PMCID: PMC9478396 DOI: 10.1016/j.jbc.2022.102363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022] Open
Abstract
Inositol is an essential metabolite that serves as a precursor for structural and signaling molecules. Although perturbation of inositol homeostasis has been implicated in numerous human disorders, surprisingly little is known about how inositol levels are regulated in mammalian cells. A recent study in mouse embryonic fibroblasts demonstrated that nuclear translocation of inositol hexakisphosphate kinase 1 (IP6K1) mediates repression of myo-inositol-3-P synthase (MIPS), the rate-limiting inositol biosynthetic enzyme. Binding of IP6K1 to phosphatidic acid (PA) is required for this repression. Here, we elucidate the role of PA in IP6K1 repression. Our results indicate that increasing PA levels through pharmacological stimulation of phospholipase D (PLD) or direct supplementation of 18:1 PA induces nuclear translocation of IP6K1 and represses expression of the MIPS protein. We found that this effect was specific to PA synthesized in the plasma membrane, as endoplasmic reticulum–derived PA did not induce IP6K1 translocation. Furthermore, we determined that PLD-mediated PA synthesis can be stimulated by the master metabolic regulator 5′ AMP-activated protein kinase (AMPK). We show that activation of AMPK by glucose deprivation or by treatment with the mood-stabilizing drugs valproate or lithium recapitulated IP6K1 nuclear translocation and decreased MIPS expression. This study demonstrates for the first time that modulation of PA levels through the AMPK-PLD pathway regulates IP6K1-mediated repression of MIPS.
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Affiliation(s)
- Pablo Lazcano
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Michael W Schmidtke
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Chisom Onu
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States.
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16
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Barriga HM, Pence IJ, Holme MN, Doutch JJ, Penders J, Nele V, Thomas MR, Carroni M, Stevens MM. Coupling Lipid Nanoparticle Structure and Automated Single-Particle Composition Analysis to Design Phospholipase-Responsive Nanocarriers. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2200839. [PMID: 35358374 PMCID: PMC7615489 DOI: 10.1002/adma.202200839] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Lipid nanoparticles (LNPs) are versatile structures with tunable physicochemical properties that are ideally suited as a platform for vaccine delivery and RNA therapeutics. A key barrier to LNP rational design is the inability to relate composition and structure to intracellular processing and function. Here Single Particle Automated Raman Trapping Analysis (SPARTA) is combined with small-angle X-ray and neutron scattering (SAXS/SANS) techniques to link LNP composition with internal structure and morphology and to monitor dynamic LNP-phospholipase D (PLD) interactions. This analysis demonstrates that PLD, a key intracellular trafficking mediator, can access the entire LNP lipid membrane to generate stable, anionic LNPs. PLD activity on vesicles with matched amounts of enzyme substrate is an order of magnitude lower, indicating that the LNP lipid membrane structure can be used to control enzyme interactions. This represents an opportunity to design enzyme-responsive LNP solutions for stimuli-responsive delivery and diseases where PLD is dysregulated.
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Affiliation(s)
- Hanna M.G. Barriga
- Department of Medical Biochemistry and Biophysics Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Isaac J. Pence
- Department of Materials, Department of Bioengineering,and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Margaret N. Holme
- Department of Medical Biochemistry and Biophysics Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - James J. Doutch
- ISIS Neutron and Muon Source, STFC, Rutherford Appleton Laboratory Didcot OX11 ODE, UK
| | - Jelle Penders
- Department of Materials, Department of Bioengineering,and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Valeria Nele
- Department of Materials, Department of Bioengineering,and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Michael R. Thomas
- Department of Materials, Department of Bioengineering,and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Science for Life Laboratory Stockholm University, Stockholm 171 65, Sweden
| | - Molly M. Stevens
- Department of Medical Biochemistry and Biophysics Karolinska Institutet, Stockholm SE-171 77, Sweden
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17
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Hammond GRV, Ricci MMC, Weckerly CC, Wills RC. An update on genetically encoded lipid biosensors. Mol Biol Cell 2022; 33:tp2. [PMID: 35420888 PMCID: PMC9282013 DOI: 10.1091/mbc.e21-07-0363] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 01/16/2023] Open
Abstract
Specific lipid species play central roles in cell biology. Their presence or enrichment in individual membranes can control properties or direct protein localization and/or activity. Therefore, probes to detect and observe these lipids in intact cells are essential tools in the cell biologist's freezer box. Herein, we discuss genetically encoded lipid biosensors, which can be expressed as fluorescent protein fusions to track lipids in living cells. We provide a state-of-the-art list of the most widely available and reliable biosensors and highlight new probes (circa 2018-2021). Notably, we focus on advances in biosensors for phosphatidylinositol, phosphatidic acid, and PI 3-kinase lipid products.
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Affiliation(s)
- Gerald R. V. Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Morgan M. C. Ricci
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Claire C. Weckerly
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Rachel C. Wills
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
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18
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Tei R, Baskin JM. Click chemistry and optogenetic approaches to visualize and manipulate phosphatidic acid signaling. J Biol Chem 2022; 298:101810. [PMID: 35276134 PMCID: PMC9006657 DOI: 10.1016/j.jbc.2022.101810] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/12/2022] [Accepted: 02/19/2022] [Indexed: 12/28/2022] Open
Abstract
The simple structure of phosphatidic acid (PA) belies its complex biological functions as both a key phospholipid biosynthetic intermediate and a potent signaling molecule. In the latter role, PA controls processes including vesicle trafficking, actin dynamics, cell growth, and migration. However, experimental methods to decode the pleiotropy of PA are sorely lacking. Because PA metabolism and trafficking are rapid, approaches to accurately visualize and manipulate its levels require high spatiotemporal precision. Here, we describe recent efforts to create a suite of chemical tools that enable imaging and perturbation of PA signaling. First, we describe techniques to visualize PA production by phospholipase D (PLD) enzymes, which are major producers of PA, called Imaging Phospholipase D Activity with Clickable Alcohols via Transphosphatidylation (IMPACT). IMPACT harnesses the ability of endogenous PLD enzymes to accept bioorthogonally tagged alcohols in transphosphatidylation reactions to generate functionalized reporter lipids that are subsequently fluorescently tagged via click chemistry. Second, we describe two light-controlled approaches for precisely manipulating PA signaling. Optogenetic PLDs use light-mediated heterodimerization to recruit a bacterial PLD to desired organelle membranes, and photoswitchable PA analogs contain azobenzene photoswitches in their acyl tails, enabling molecular shape and bioactivity to be controlled by light. We highlight select applications of these tools for studying GPCR–Gq signaling, discovering regulators of PLD signaling, tracking intracellular lipid transport pathways, and elucidating new oncogenic signaling roles for PA. We envision that these chemical tools hold promise for revealing many new insights into lipid signaling pathways.
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Affiliation(s)
- Reika Tei
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA 14853
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA 14853.
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19
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Tei R, Morstein J, Shemet A, Trauner D, Baskin JM. Optical Control of Phosphatidic Acid Signaling. ACS CENTRAL SCIENCE 2021; 7:1205-1215. [PMID: 34345670 PMCID: PMC8323247 DOI: 10.1021/acscentsci.1c00444] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Indexed: 05/31/2023]
Abstract
Phosphatidic acids (PAs) are glycerophospholipids that regulate key cell signaling pathways governing cell growth and proliferation, including the mTOR and Hippo pathways. Their acyl chains vary in tail length and degree of saturation, leading to marked differences in the signaling functions of different PA species. For example, in mTOR signaling, saturated forms of PA are inhibitory, whereas unsaturated forms are activating. To enable rapid control over PA signaling, we describe here the development of photoswitchable analogues of PA, termed AzoPA and dAzoPA, that contain azobenzene groups in one or both lipid tails, respectively. These photolipids enable optical control of their tail structure and can be reversibly switched between a straight trans form and a relatively bent cis form. We found that cis-dAzoPA selectively activates mTOR signaling, mimicking the bioactivity of unsaturated forms of PA. Further, in the context of Hippo signaling, whose growth-suppressing activity is blocked by PA, we found that the cis forms of both AzoPA and dAzoPA selectively inhibit this pathway. Collectively, these photoswitchable PA analogues enable optical control of mTOR and Hippo signaling, and we envision future applications of these probes to dissect the pleiotropic effects of physiological and pathological PA signaling.
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Affiliation(s)
- Reika Tei
- Department
of Chemistry and Chemical Biology and Weill Institute for Cell and
Molecular Biology, Cornell University, Ithaca, New York 14850, United States
| | - Johannes Morstein
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Andrej Shemet
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Dirk Trauner
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Jeremy M. Baskin
- Department
of Chemistry and Chemical Biology and Weill Institute for Cell and
Molecular Biology, Cornell University, Ithaca, New York 14850, United States
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20
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Tei R, Baskin JM. Induced proximity tools for precise manipulation of lipid signaling. Curr Opin Chem Biol 2021; 65:93-100. [PMID: 34304140 DOI: 10.1016/j.cbpa.2021.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/03/2021] [Accepted: 06/18/2021] [Indexed: 01/07/2023]
Abstract
Lipids are highly dynamic molecules that, due to their hydrophobicity, are spatially confined to membrane environments. From these locations, certain privileged lipids serve as signaling molecules. For understanding the biological functions of subcellular pools of signaling lipids, induced proximity tools have been invaluable. These methods involve controlled heterodimerization, by either small-molecule or light triggers, of functional proteins. In the arena of lipid signaling, induced proximity tools can recruit lipid-metabolizing enzymes to manipulate lipid signaling and create artificial tethers between organelle membranes to control lipid trafficking pathways at membrane contact sites. Here, we review recent advances in methodology development and biological application of chemical-induced and light-induced proximity tools for manipulating lipid metabolism, trafficking, and signaling.
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Affiliation(s)
- Reika Tei
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, 14853, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, 14853, USA.
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21
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Oh TJ, Fan H, Skeeters SS, Zhang K. Steering Molecular Activity with Optogenetics: Recent Advances and Perspectives. Adv Biol (Weinh) 2021; 5:e2000180. [PMID: 34028216 PMCID: PMC8218620 DOI: 10.1002/adbi.202000180] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/14/2020] [Indexed: 12/24/2022]
Abstract
Optogenetics utilizes photosensitive proteins to manipulate the localization and interaction of molecules in living cells. Because light can be rapidly switched and conveniently confined to the sub-micrometer scale, optogenetics allows for controlling cellular events with an unprecedented resolution in time and space. The past decade has witnessed an enormous progress in the field of optogenetics within the biological sciences. The ever-increasing amount of optogenetic tools, however, can overwhelm the selection of appropriate optogenetic strategies. Considering that each optogenetic tool may have a distinct mode of action, a comparative analysis of the current optogenetic toolbox can promote the further use of optogenetics, especially by researchers new to this field. This review provides such a compilation that highlights the spatiotemporal accuracy of current optogenetic systems. Recent advances of optogenetics in live cells and animal models are summarized, the emerging work that interlinks optogenetics with other research fields is presented, and exciting clinical and industrial efforts to employ optogenetic strategy toward disease intervention are reported.
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Affiliation(s)
- Teak-Jung Oh
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
| | - Huaxun Fan
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
| | - Savanna S Skeeters
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
| | - Kai Zhang
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
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22
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Thaller DJ, Tong D, Marklew CJ, Ader NR, Mannino PJ, Borah S, King MC, Ciani B, Lusk CP. Direct binding of ESCRT protein Chm7 to phosphatidic acid-rich membranes at nuclear envelope herniations. J Cell Biol 2021; 220:e202004222. [PMID: 33464310 PMCID: PMC7816628 DOI: 10.1083/jcb.202004222] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 11/04/2020] [Accepted: 12/11/2020] [Indexed: 12/03/2022] Open
Abstract
Mechanisms that control nuclear membrane remodeling are essential to maintain the integrity of the nucleus but remain to be fully defined. Here, we identify a phosphatidic acid (PA)-binding capacity in the nuclear envelope (NE)-specific ESCRT, Chm7, in budding yeast. Chm7's interaction with PA-rich membranes is mediated through a conserved hydrophobic stretch of amino acids, which confers recruitment to the NE in a manner that is independent of but required for Chm7's interaction with the LAP2-emerin-MAN1 (LEM) domain protein Heh1 (LEM2). Consistent with the functional importance of PA binding, mutation of this region abrogates recruitment of Chm7 to membranes and abolishes Chm7 function in the context of NE herniations that form during defective nuclear pore complex (NPC) biogenesis. In fact, we show that a PA sensor specifically accumulates within these NE herniations. We suggest that local control of PA metabolism is important for ensuring productive NE remodeling and that its dysregulation may contribute to pathologies associated with defective NPC assembly.
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Affiliation(s)
- David J. Thaller
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - Danqing Tong
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - Christopher J. Marklew
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Brook Hill, Sheffield, UK
| | - Nicholas R. Ader
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | | | - Sapan Borah
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - Megan C. King
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - Barbara Ciani
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Brook Hill, Sheffield, UK
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
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23
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Flores J, White BM, Brea RJ, Baskin JM, Devaraj NK. Lipids: chemical tools for their synthesis, modification, and analysis. Chem Soc Rev 2020; 49:4602-4614. [PMID: 32691785 PMCID: PMC7380508 DOI: 10.1039/d0cs00154f] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Lipids remain one of the most enigmatic classes of biological molecules. Whereas lipids are well known to form basic units of membrane structure and energy storage, deciphering the exact roles and biological interactions of distinct lipid species has proven elusive. How these building blocks are synthesized, trafficked, and stored are also questions that require closer inspection. This tutorial review covers recent advances on the preparation, derivatization, and analysis of lipids. In particular, we describe several chemical approaches that form part of a powerful toolbox for controlling and characterizing lipid structure. We believe these tools will be helpful in numerous applications, including the study of lipid-protein interactions and the development of novel drug delivery systems.
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Affiliation(s)
- Judith Flores
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Brittany M White
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Roberto J Brea
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
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24
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Block MR, Brunner M, Ziegelmeyer T, Lallemand D, Pezet M, Chevalier G, Rondé P, Gauthier-Rouviere C, Wehrle-Haller B, Bouvard D. The mechano-sensitive response of β1 integrin promotes SRC-positive late endosome recycling and activation of Yes-associated protein. J Biol Chem 2020; 295:13474-13487. [PMID: 32690605 DOI: 10.1074/jbc.ra120.013503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/02/2020] [Indexed: 11/06/2022] Open
Abstract
Yes-associated protein (YAP) signaling has emerged as a crucial pathway in several normal and pathological processes. Although the main upstream effectors that regulate its activity have been extensively studied, the role of the endosomal system has been far less characterized. Here, we identified the late endosomal/lysosomal adaptor MAPK and mTOR activator (LAMTOR) complex as an important regulator of YAP signaling in a preosteoblast cell line. We found that p18/LAMTOR1-mediated peripheral positioning of late endosomes allows delivery of SRC proto-oncogene, nonreceptor tyrosine kinase (SRC) to the plasma membrane and promotes activation of an SRC-dependent signaling cascade that controls YAP nuclear shuttling. Moreover, β1 integrin engagement and mechano-sensitive cues, such as external stiffness and related cell contractility, controlled LAMTOR targeting to the cell periphery and thereby late endosome recycling and had a major impact on YAP signaling. Our findings identify the late endosome recycling pathway as a key mechanism that controls YAP activity and explains YAP mechano-sensitivity.
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Affiliation(s)
- Marc R Block
- Institute for Advanced Bioscience, Université Grenoble Alpes, La Tronche, France; Institut National de la Santé et la Recherche Médicale-INSERM U1209, La Tronche, France; CNRS UMR 5309, La Tronche, France
| | - Molly Brunner
- Institute for Advanced Bioscience, Université Grenoble Alpes, La Tronche, France; Institut National de la Santé et la Recherche Médicale-INSERM U1209, La Tronche, France; CNRS UMR 5309, La Tronche, France
| | - Théo Ziegelmeyer
- Institute for Advanced Bioscience, Université Grenoble Alpes, La Tronche, France; Institut National de la Santé et la Recherche Médicale-INSERM U1209, La Tronche, France; CNRS UMR 5309, La Tronche, France
| | | | - Mylène Pezet
- Institute for Advanced Bioscience, Université Grenoble Alpes, La Tronche, France; Institut National de la Santé et la Recherche Médicale-INSERM U1209, La Tronche, France; CNRS UMR 5309, La Tronche, France
| | - Genevieve Chevalier
- Institute for Advanced Bioscience, Université Grenoble Alpes, La Tronche, France; Institut National de la Santé et la Recherche Médicale-INSERM U1209, La Tronche, France; CNRS UMR 5309, La Tronche, France
| | - Philippe Rondé
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Université de Strasbourg, Strasbourg, France
| | - Cécile Gauthier-Rouviere
- Montpellier Cell Biology Research Center (CRBM), University of Montpellier, CNRS, Montpellier, France
| | - Bernhard Wehrle-Haller
- Department of Cell Physiology and Metabolism, Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
| | - Daniel Bouvard
- Institute for Advanced Bioscience, Université Grenoble Alpes, La Tronche, France; Institut National de la Santé et la Recherche Médicale-INSERM U1209, La Tronche, France; CNRS UMR 5309, La Tronche, France.
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