1
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Simsek Papur O, Glatz JFC, Luiken JJFP. Protein kinase-D1 and downstream signaling mechanisms involved in GLUT4 translocation in cardiac muscle. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119748. [PMID: 38723678 DOI: 10.1016/j.bbamcr.2024.119748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 02/21/2024] [Accepted: 04/29/2024] [Indexed: 05/20/2024]
Abstract
The Ser/Thr kinase protein kinase-D1 (PKD1) is involved in induction of various cell physiological processes in the heart such as myocellular hypertrophy and inflammation, which may turn maladaptive during long-term stimulation. Of special interest is a key role of PKD1 in the regulation of cardiac substrate metabolism. Glucose and fatty acids are the most important substrates for cardiac energy provision, and the ratio at which they are utilized determines the health status of the heart. Cardiac glucose uptake is mainly regulated by translocation of the glucose transporter GLUT4 from intracellular stores (endosomes) to the sarcolemma, and fatty acid uptake via a parallel translocation of fatty acid transporter CD36 from endosomes to the sarcolemma. PKD1 is involved in the regulation of GLUT4 translocation, but not CD36 translocation, giving it the ability to modulate glucose uptake without affecting fatty acid uptake, thereby altering the cardiac substrate balance. PKD1 would therefore serve as an attractive target to combat cardiac metabolic diseases with a tilted substrate balance, such as diabetic cardiomyopathy. However, PKD1 activation also elicits cardiac hypertrophy and inflammation. Therefore, identification of the events upstream and downstream of PKD1 may provide superior therapeutic targets to alter the cardiac substrate balance. Recent studies have identified the lipid kinase phosphatidylinositol 4-kinase IIIβ (PI4KIIIβ) as signaling hub downstream of PKD1 to selectively stimulate GLUT4-mediated myocardial glucose uptake without inducing hypertrophy. Taken together, the PKD1 signaling pathway serves a pivotal role in cardiac glucose metabolism and is a promising target to selectively modulate glucose uptake in cardiac disease.
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Affiliation(s)
- Ozlenen Simsek Papur
- Department of Molecular Medicine, Institute of Health Science, Dokuz Eylül University, Izmir, Turkey
| | - Jan F C Glatz
- Department of Genetics & Cell Biology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center(+), Maastricht, the Netherlands
| | - Joost J F P Luiken
- Department of Genetics & Cell Biology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center(+), Maastricht, the Netherlands.
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2
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Hutchins CM, Gorfe AA. From disorder comes function: Regulation of small GTPase function by intrinsically disordered lipidated membrane anchor. Curr Opin Struct Biol 2024; 87:102869. [PMID: 38943706 DOI: 10.1016/j.sbi.2024.102869] [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: 04/15/2024] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 07/01/2024]
Abstract
The intrinsically disordered, lipid-modified membrane anchor of small GTPases is emerging as a critical modulator of function through its ability to sort lipids in a conformation-dependent manner. We reviewed recent computational and experimental studies that have begun to shed light on the sequence-ensemble-function relationship in this unique class of lipidated intrinsically disordered regions (LIDRs).
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Affiliation(s)
- Chase M Hutchins
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX 77030, USA; Biochemistry and Cell Biology Program & Therapeutics and Pharmacology Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 6431 Fannin St., Houston, TX 77030, USA. https://twitter.com/chasedsims
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX 77030, USA; Biochemistry and Cell Biology Program & Therapeutics and Pharmacology Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 6431 Fannin St., Houston, TX 77030, USA.
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3
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Amokrane L, Pokotylo I, Acket S, Ducloy A, Troncoso-Ponce A, Cacas JL, Ruelland E. Phospholipid Signaling in Crop Plants: A Field to Explore. PLANTS (BASEL, SWITZERLAND) 2024; 13:1532. [PMID: 38891340 PMCID: PMC11174929 DOI: 10.3390/plants13111532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024]
Abstract
In plant models such as Arabidopsis thaliana, phosphatidic acid (PA), a key molecule of lipid signaling, was shown not only to be involved in stress responses, but also in plant development and nutrition. In this article, we highlight lipid signaling existing in crop species. Based on open access databases, we update the list of sequences encoding phospholipases D, phosphoinositide-dependent phospholipases C, and diacylglycerol-kinases, enzymes that lead to the production of PA. We show that structural features of these enzymes from model plants are conserved in equivalent proteins from selected crop species. We then present an in-depth discussion of the structural characteristics of these proteins before focusing on PA binding proteins. For the purpose of this article, we consider RESPIRATORY BURST OXIDASE HOMOLOGUEs (RBOHs), the most documented PA target proteins. Finally, we present pioneering experiments that show, by different approaches such as monitoring of gene expression, use of pharmacological agents, ectopic over-expression of genes, and the creation of silenced mutants, that lipid signaling plays major roles in crop species. Finally, we present major open questions that require attention since we have only a perception of the peak of the iceberg when it comes to the exciting field of phospholipid signaling in plants.
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Affiliation(s)
- Lucas Amokrane
- Unité Génie Enzymatique & Cellulaire, Université de Technologie de Compiègne, UMR CNRS 7025, 60200 Compiègne, France; (L.A.); (I.P.); (S.A.); (A.T.-P.)
| | - Igor Pokotylo
- Unité Génie Enzymatique & Cellulaire, Université de Technologie de Compiègne, UMR CNRS 7025, 60200 Compiègne, France; (L.A.); (I.P.); (S.A.); (A.T.-P.)
- INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), University Paris-Saclay, 78000 Versailles, France (J.-L.C.)
| | - Sébastien Acket
- Unité Génie Enzymatique & Cellulaire, Université de Technologie de Compiègne, UMR CNRS 7025, 60200 Compiègne, France; (L.A.); (I.P.); (S.A.); (A.T.-P.)
| | - Amélie Ducloy
- INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), University Paris-Saclay, 78000 Versailles, France (J.-L.C.)
| | - Adrian Troncoso-Ponce
- Unité Génie Enzymatique & Cellulaire, Université de Technologie de Compiègne, UMR CNRS 7025, 60200 Compiègne, France; (L.A.); (I.P.); (S.A.); (A.T.-P.)
| | - Jean-Luc Cacas
- INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), University Paris-Saclay, 78000 Versailles, France (J.-L.C.)
| | - Eric Ruelland
- Unité Génie Enzymatique & Cellulaire, Université de Technologie de Compiègne, UMR CNRS 7025, 60200 Compiègne, France; (L.A.); (I.P.); (S.A.); (A.T.-P.)
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4
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Narayan KB, Baeyens L, James HP, Swain A, Baumgart T. Fluorescence imaging of lamellipodin-mediated biomolecular condensates on solid supported lipid bilayer membranes. Methods Enzymol 2024; 700:33-48. [PMID: 38971606 DOI: 10.1016/bs.mie.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2024]
Abstract
Biomolecular condensates play a major role in numerous cellular processes, including several that occur on the surface of lipid bilayer membranes. There is increasing evidence that cellular membrane trafficking phenomena, including the internalization of the plasma membrane through endocytosis, are mediated by multivalent protein-protein interactions that can lead to phase separation. We have recently found that proteins involved in the clathrin-independent endocytic pathway named Fast Endophilin Mediated Endocytosis can undergo liquid-liquid phase separation (LLPS) in solution and on lipid bilayer membranes. Here, the protein solution concentrations required for phase separation to be observed are significantly smaller compared to those required for phase separation in solution. LLPS is challenging to systematically characterize in cellular systems in general, and on biological membranes in particular. Model membrane approaches are more suitable for this purpose as they allow for precise control over the nature and amount of the components present in a mixture. Here we describe a method that enables the imaging of LLPS domain formation on solid supported lipid bilayers. These allow for facile imaging, provide long-term stability, and avoid clustering of vesicles and vesicle-attached features (such as buds and tethers) in the presence of multi-valent membrane interacting proteins.
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Affiliation(s)
- Karthik B Narayan
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA
| | - Laura Baeyens
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA
| | - Honey Priya James
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA
| | - Aparna Swain
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA.
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5
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Houngue R, Sangaré LO, Alayi TD, Dieng A, Bitard-Feildel T, Boulogne C, Slomianny C, Atindehou CM, Fanou LA, Hathout Y, Callebaut I, Tomavo S. Toxoplasma membrane inositol phospholipid binding protein TgREMIND is essential for secretory organelle function and host infection. Cell Rep 2024; 43:113601. [PMID: 38157297 DOI: 10.1016/j.celrep.2023.113601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 10/25/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024] Open
Abstract
Apicomplexan parasites possess specialized secretory organelles called rhoptries, micronemes, and dense granules that play a vital role in host infection. In this study, we demonstrate that TgREMIND, a protein found in Toxoplasma gondii, is necessary for the biogenesis of rhoptries and dense granules. TgREMIND contains a Fes-CIP4 homology-Bin/Amphiphysin/Rvs (F-BAR) domain, which binds to membrane phospholipids, as well as a novel uncharacterized domain that we have named REMIND (regulator of membrane-interacting domain). Both the F-BAR domain and the REMIND are crucial for TgREMIND functions. When TgREMIND is depleted, there is a significant decrease in the abundance of dense granules and abnormal transparency of rhoptries, leading to a reduction in protein secretion from these organelles. The absence of TgREMIND inhibits host invasion and parasite dissemination, demonstrating that TgREMIND is essential for the proper function of critical secretory organelles required for successful infection by Toxoplasma.
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Affiliation(s)
- Rodrigue Houngue
- Université Paris Saclay, CNRS UMR 9198-CEA, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif sur Yvette, France
| | - Lamba Omar Sangaré
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Tchilabalo Dilezitoko Alayi
- Department of Pharmaceutical Science, School of Pharmacy and Pharmaceutical Sciences, Binghamton University-SUNY, Johnson City, NY 13790, USA
| | - Aissatou Dieng
- Université Paris Saclay, CNRS UMR 9198-CEA, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif sur Yvette, France
| | - Tristan Bitard-Feildel
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France
| | - Claire Boulogne
- Université Paris Saclay, CNRS UMR 9198-CEA, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif sur Yvette, France; Plateforme Imagerie-Gif, Institut de Biologie Intégrative de la Cellule (I2BC), 91190 Gif sur Yvette, France
| | - Christian Slomianny
- University of Lille, Laboratory of Cell Physiology, INSERM U 1003, 59655 Villeneuve d'Ascq, France
| | - Cynthia Menonve Atindehou
- Université d'Abomey Calavi, Laboratoire de Biochimie et de Biologie Moléculaire, Faculté des Sciences et Technologies, Cotonou, Bénin
| | - Lucie Ayi Fanou
- Université d'Abomey Calavi, Laboratoire de Biochimie et de Biologie Moléculaire, Faculté des Sciences et Technologies, Cotonou, Bénin
| | - Yetrib Hathout
- Department of Pharmaceutical Science, School of Pharmacy and Pharmaceutical Sciences, Binghamton University-SUNY, Johnson City, NY 13790, USA
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France
| | - Stanislas Tomavo
- Université Paris Saclay, CNRS UMR 9198-CEA, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif sur Yvette, France.
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6
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Yu J, Boehr DD. Regulatory mechanisms triggered by enzyme interactions with lipid membrane surfaces. Front Mol Biosci 2023; 10:1306483. [PMID: 38099197 PMCID: PMC10720463 DOI: 10.3389/fmolb.2023.1306483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Recruitment of enzymes to intracellular membranes often modulates their catalytic activity, which can be important in cell signaling and membrane trafficking. Thus, re-localization is not only important for these enzymes to gain access to their substrates, but membrane interactions often allosterically regulate enzyme function by inducing conformational changes across different time and amplitude scales. Recent structural, biophysical and computational studies have revealed how key enzymes interact with lipid membrane surfaces, and how this membrane binding regulates protein structure and function. This review summarizes the recent progress in understanding regulatory mechanisms involved in enzyme-membrane interactions.
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Affiliation(s)
| | - David D. Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
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7
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Llorente A, Loughran RM, Emerling BM. Targeting phosphoinositide signaling in cancer: relevant techniques to study lipids and novel avenues for therapeutic intervention. Front Cell Dev Biol 2023; 11:1297355. [PMID: 37954209 PMCID: PMC10634348 DOI: 10.3389/fcell.2023.1297355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/12/2023] [Indexed: 11/14/2023] Open
Abstract
Phosphoinositides serve as essential players in numerous biological activities and are critical for overall cellular function. Due to their complex chemical structures, localization, and low abundance, current challenges in the phosphoinositide field include the accurate measurement and identification of specific variants, particularly those with acyl chains. Researchers are intensively developing innovative techniques and approaches to address these challenges and advance our understanding of the impact of phosphoinositide signaling on cellular biology. This article provides an overview of recent advances in the study of phosphoinositides, including mass spectrometry, lipid biosensors, and real-time activity assays using fluorometric sensors. These methodologies have proven instrumental for a comprehensive exploration of the cellular distribution and dynamics of phosphoinositides and have shed light on the growing significance of these lipids in human health and various pathological processes, including cancer. To illustrate the importance of phosphoinositide signaling in disease, this perspective also highlights the role of a family of lipid kinases named phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks), which have recently emerged as exciting therapeutic targets for cancer treatment. The ongoing exploration of phosphoinositide signaling not only deepens our understanding of cellular biology but also holds promise for novel interventions in cancer therapy.
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Affiliation(s)
| | | | - Brooke M. Emerling
- Cancer Metabolism and Microenvironment Program, Sanford Burnham Prebys, La Jolla, CA, United States
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8
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Madsen RR, Toker A. PI3K signaling through a biochemical systems lens. J Biol Chem 2023; 299:105224. [PMID: 37673340 PMCID: PMC10570132 DOI: 10.1016/j.jbc.2023.105224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Following 3 decades of extensive research into PI3K signaling, it is now evidently clear that the underlying network does not equate to a simple ON/OFF switch. This is best illustrated by the multifaceted nature of the many diseases associated with aberrant PI3K signaling, including common cancers, metabolic disease, and rare developmental disorders. However, we are still far from a complete understanding of the fundamental control principles that govern the numerous phenotypic outputs that are elicited by activation of this well-characterized biochemical signaling network, downstream of an equally diverse set of extrinsic inputs. At its core, this is a question on the role of PI3K signaling in cellular information processing and decision making. Here, we review the determinants of accurate encoding and decoding of growth factor signals and discuss outstanding questions in the PI3K signal relay network. We emphasize the importance of quantitative biochemistry, in close integration with advances in single-cell time-resolved signaling measurements and mathematical modeling.
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Affiliation(s)
- Ralitsa R Madsen
- MRC-Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom.
| | - Alex Toker
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.
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9
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Ngubo M, Moradi F, Ito CY, Stanford WL. Tissue-Specific Tumour Suppressor and Oncogenic Activities of the Polycomb-like Protein MTF2. Genes (Basel) 2023; 14:1879. [PMID: 37895228 PMCID: PMC10606531 DOI: 10.3390/genes14101879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
The Polycomb repressive complex 2 (PRC2) is a conserved chromatin-remodelling complex that catalyses the trimethylation of histone H3 lysine 27 (H3K27me3), a mark associated with gene silencing. PRC2 regulates chromatin structure and gene expression during organismal and tissue development and tissue homeostasis in the adult. PRC2 core subunits are associated with various accessory proteins that modulate its function and recruitment to target genes. The multimeric composition of accessory proteins results in two distinct variant complexes of PRC2, PRC2.1 and PRC2.2. Metal response element-binding transcription factor 2 (MTF2) is one of the Polycomb-like proteins (PCLs) that forms the PRC2.1 complex. MTF2 is highly conserved, and as an accessory subunit of PRC2, it has important roles in embryonic stem cell self-renewal and differentiation, development, and cancer progression. Here, we review the impact of MTF2 in PRC2 complex assembly, catalytic activity, and spatiotemporal function. The emerging paradoxical evidence suggesting that MTF2 has divergent roles as either a tumour suppressor or an oncogene in different tissues merits further investigations. Altogether, our review illuminates the context-dependent roles of MTF2 in Polycomb group (PcG) protein-mediated epigenetic regulation. Its impact on disease paves the way for a deeper understanding of epigenetic regulation and novel therapeutic strategies.
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Affiliation(s)
- Mzwanele Ngubo
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
| | - Fereshteh Moradi
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Caryn Y. Ito
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - William L. Stanford
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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10
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Powis G, Meuillet EJ, Indarte M, Booher G, Kirkpatrick L. Pleckstrin Homology [PH] domain, structure, mechanism, and contribution to human disease. Biomed Pharmacother 2023; 165:115024. [PMID: 37399719 DOI: 10.1016/j.biopha.2023.115024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/14/2023] [Indexed: 07/05/2023] Open
Abstract
The pleckstrin homology [PH] domain is a structural fold found in more than 250 proteins making it the 11th most common domain in the human proteome. 25% of family members have more than one PH domain and some PH domains are split by one, or several other, protein domains although still folding to give functioning PH domains. We review mechanisms of PH domain activity, the role PH domain mutation plays in human disease including cancer, hyperproliferation, neurodegeneration, inflammation, and infection, and discuss pharmacotherapeutic approaches to regulate PH domain activity for the treatment of human disease. Almost half PH domain family members bind phosphatidylinositols [PIs] that attach the host protein to cell membranes where they interact with other membrane proteins to give signaling complexes or cytoskeleton scaffold platforms. A PH domain in its native state may fold over other protein domains thereby preventing substrate access to a catalytic site or binding with other proteins. The resulting autoinhibition can be released by PI binding to the PH domain, or by protein phosphorylation thus providing fine tuning of the cellular control of PH domain protein activity. For many years the PH domain was thought to be undruggable until high-resolution structures of human PH domains allowed structure-based design of novel inhibitors that selectively bind the PH domain. Allosteric inhibitors of the Akt1 PH domain have already been tested in cancer patients and for proteus syndrome, with several other PH domain inhibitors in preclinical development for treatment of other human diseases.
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Affiliation(s)
- Garth Powis
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA.
| | | | - Martin Indarte
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
| | - Garrett Booher
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
| | - Lynn Kirkpatrick
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
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11
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Oh BC. Phosphoinositides and intracellular calcium signaling: novel insights into phosphoinositides and calcium coupling as negative regulators of cellular signaling. Exp Mol Med 2023; 55:1702-1712. [PMID: 37524877 PMCID: PMC10474053 DOI: 10.1038/s12276-023-01067-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 08/02/2023] Open
Abstract
Intracellular calcium (Ca2+) and phosphoinositides (PIPs) are crucial for regulating cellular activities such as metabolism and cell survival. Cells maintain precise intracellular Ca2+ and PIP levels via the actions of a complex system of Ca2+ channels, transporters, Ca2+ ATPases, and signaling effectors, including specific lipid kinases, phosphatases, and phospholipases. Recent research has shed light on the complex interplay between Ca2+ and PIP signaling, suggesting that elevated intracellular Ca2+ levels negatively regulate PIP signaling by inhibiting the membrane localization of PIP-binding proteins carrying specific domains, such as the pleckstrin homology (PH) and Ca2+-independent C2 domains. This dysregulation is often associated with cancer and metabolic diseases. PIPs recruit various proteins with PH domains to the plasma membrane in response to growth hormones, which activate signaling pathways regulating metabolism, cell survival, and growth. However, abnormal PIP signaling in cancer cells triggers consistent membrane localization and activation of PIP-binding proteins. In the context of obesity, an excessive intracellular Ca2+ level prevents the membrane localization of the PIP-binding proteins AKT, IRS1, and PLCδ via Ca2+-PIPs, contributing to insulin resistance and other metabolic diseases. Furthermore, an excessive intracellular Ca2+ level can cause functional defects in subcellular organelles such as the endoplasmic reticulum (ER), lysosomes, and mitochondria, causing metabolic diseases. This review explores how intracellular Ca2+ overload negatively regulates the membrane localization of PIP-binding proteins.
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Affiliation(s)
- Byung-Chul Oh
- Department of Physiology, Lee Gil Ya Cancer and Diabetes Institute, Gachon College of Medicine, Incheon, 21999, Republic of Korea.
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12
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Petsana M, Roumia AF, Bagos PG, Boleti H, Braliou GG. In Silico Identification and Analysis of Proteins Containing the Phox Homology Phosphoinositide-Binding Domain in Kinetoplastea Protists: Evolutionary Conservation and Uniqueness of Phox-Homology-Domain-Containing Protein Architectures. Int J Mol Sci 2023; 24:11521. [PMID: 37511280 PMCID: PMC10380299 DOI: 10.3390/ijms241411521] [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: 05/29/2023] [Revised: 06/27/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Kinetoplastea are free living and parasitic protists with unique features among Eukaryota. Pathogenic Kinetoplastea parasites (i.e., Trypanosoma and Leishmania spp.) undergo several developmental transitions essential for survival in their hosts. These transitions require membrane and cytoskeleton reorganizations that involve phosphoinositides (PIs). Phospholipids like PIs are key regulators of vital functions in all eukaryotes including signal transduction, protein transport and sorting, membrane trafficking, and cytoskeleton and membrane remodeling. A large repertoire of PI-metabolizing enzymes and PI-binding proteins/effectors carrying distinct PI-binding modules like the PX (phox homology) module could play significant roles in the life and virulence of pathogenic Kinetoplastea. The aim of this study was to retrieve the entire spectrum of Kinetoplastea protein sequences containing the PX module (PX-proteins), predict their structures, and identify in them evolutionary conserved and unique traits. Using a large array of bioinformatics tools, protein IDs from two searches (based on PFam's pHMM for PX domain (PF00787)) were combined, aligned, and utilized for the construction of a new Kinetoplastea_PX pHMM. This three-step search retrieved 170 PX-protein sequences. Structural domain configuration analysis identified PX, Pkinase, Lipocalin_5, and Vps5/BAR3-WASP domains and clustered them into five distinct subfamilies. Phylogenetic tree and domain architecture analysis showed that some domain architectures exist in proteomes of all Kinetoplastea spp., while others are genus-specific. Finally, amino acid conservation logos of the Kinetoplastea spp. and Homo sapiens PX domains revealed high evolutionary conservation in residues forming the critical structural motifs for PtdIns3P recognition. This study highlights the PX-Pkinase domain architecture as unique within Trypanosoma spp. and forms the basis for a targeted functional analysis of Kinetoplastea PX-proteins as putative targets for a rational design of anti-parasitic drugs.
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Affiliation(s)
- Marina Petsana
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2-4 Papasiopoulou Str., 35131 Lamia, Greece
- Intracellular Parasitism Laboratory, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Ahmed F Roumia
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2-4 Papasiopoulou Str., 35131 Lamia, Greece
- Department of Agricultural Biochemistry, Faculty of Agriculture, Menoufia University, Shibin El-Kom 32514, Egypt
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2-4 Papasiopoulou Str., 35131 Lamia, Greece
| | - Haralabia Boleti
- Intracellular Parasitism Laboratory, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Georgia G Braliou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2-4 Papasiopoulou Str., 35131 Lamia, Greece
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13
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Ru B, Hao X, Li W, Peng Q, Miao J, Liu X. A Novel FYVE Domain-Containing Protein Kinase, PsZFPK1, Plays a Critical Role in Vegetative Growth, Sporangium Formation, Oospore Production, and Virulence in Phytophthora sojae. J Fungi (Basel) 2023; 9:709. [PMID: 37504698 PMCID: PMC10381902 DOI: 10.3390/jof9070709] [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: 06/03/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
Proteins containing both FYVE and serine/threonine kinase catalytic (STKc) domains are exclusive to protists. However, the biological function of these proteins in oomycetes has rarely been reported. In the Phytophthora sojae genome database, we identified five proteins containing FYVE and STKc domains, which we named PsZFPK1, PsZFPK2, PsZFPK3, PsZFPK4, and PsZFPK5. In this study, we characterized the biological function of PsZFPK1 using a CRISPR/Cas9-mediated gene replacement system. Compared with the wild-type strain, P6497, the PsZFPK1-knockout mutants exhibited significantly reduced growth on a nutrient-rich V8 medium, while a more pronounced defect was observed on a nutrient-poor Plich medium. The PsZFPK1-knockout mutants also showed a significant increase in sporangium production. Furthermore, PsZFPK1 was found to be essential for oospore production and complete virulence but dispensable for the stress response in P. sojae. The N-terminal region, FYVE and STKc domains, and T602 phosphorylation site were found to be vital for the function of PsZFPK1. Conversely, these domains were not required for the localization of PsZFPK1 protein in the cytoplasm. Our results demonstrate that PsZFPK1 plays a critical role in vegetative growth, sporangium formation, oospore production, and virulence in P. sojae.
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Affiliation(s)
- Binglu Ru
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang 712100, China
| | - Xinchang Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang 712100, China
| | - Wenhao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang 712100, China
| | - Qin Peng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang 712100, China
| | - Jianqiang Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang 712100, China
| | - Xili Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang 712100, China
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, 2 Yuanmingyuanxi Road, Beijing 100193, China
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14
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Vidalle MC, Sheth B, Fazio A, Marvi MV, Leto S, Koufi FD, Neri I, Casalin I, Ramazzotti G, Follo MY, Ratti S, Manzoli L, Gehlot S, Divecha N, Fiume R. Nuclear Phosphoinositides as Key Determinants of Nuclear Functions. Biomolecules 2023; 13:1049. [PMID: 37509085 PMCID: PMC10377365 DOI: 10.3390/biom13071049] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Polyphosphoinositides (PPIns) are signalling messengers representing less than five per cent of the total phospholipid concentration within the cell. Despite their low concentration, these lipids are critical regulators of various cellular processes, including cell cycle, differentiation, gene transcription, apoptosis and motility. PPIns are generated by the phosphorylation of the inositol head group of phosphatidylinositol (PtdIns). Different pools of PPIns are found at distinct subcellular compartments, which are regulated by an array of kinases, phosphatases and phospholipases. Six of the seven PPIns species have been found in the nucleus, including the nuclear envelope, the nucleoplasm and the nucleolus. The identification and characterisation of PPIns interactor and effector proteins in the nucleus have led to increasing interest in the role of PPIns in nuclear signalling. However, the regulation and functions of PPIns in the nucleus are complex and are still being elucidated. This review summarises our current understanding of the localisation, biogenesis and physiological functions of the different PPIns species in the nucleus.
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Affiliation(s)
- Magdalena C Vidalle
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Bhavwanti Sheth
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Antonietta Fazio
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Maria Vittoria Marvi
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Stefano Leto
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Foteini-Dionysia Koufi
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Irene Neri
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Irene Casalin
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Giulia Ramazzotti
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Matilde Y Follo
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Stefano Ratti
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Lucia Manzoli
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Sonakshi Gehlot
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Nullin Divecha
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Roberta Fiume
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
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15
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Tang T, Hasan M, Capelluto DGS. Phafins Are More Than Phosphoinositide-Binding Proteins. Int J Mol Sci 2023; 24:ijms24098096. [PMID: 37175801 PMCID: PMC10178739 DOI: 10.3390/ijms24098096] [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: 03/22/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Phafins are PH (Pleckstrin Homology) and FYVE (Fab1, YOTB, Vac1, and EEA1) domain-containing proteins. The Phafin protein family is classified into two groups based on their sequence homology and functional similarity: Phafin1 and Phafin2. This protein family is unique because both the PH and FYVE domains bind to phosphatidylinositol 3-phosphate [PtdIns(3)P], a phosphoinositide primarily found in endosomal and lysosomal membranes. Phafin proteins act as PtdIns(3)P effectors in apoptosis, endocytic cargo trafficking, and autophagy. Additionally, Phafin2 is recruited to macropinocytic compartments through coincidence detection of PtdIns(3)P and PtdIns(4)P. Membrane-associated Phafins serve as adaptor proteins that recruit other binding partners. In addition to the phosphoinositide-binding domains, Phafin proteins present a poly aspartic acid motif that regulates membrane binding specificity. In this review, we summarize the involvement of Phafins in several cellular pathways and their potential physiological functions while highlighting the similarities and differences between Phafin1 and Phafin2. Besides, we discuss research perspectives for Phafins.
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Affiliation(s)
- Tuoxian Tang
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mahmudul Hasan
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Fralin Life Sciences Institute and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Daniel G S Capelluto
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Fralin Life Sciences Institute and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
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16
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Mackrill JJ. Non-inositol 1,4,5-trisphosphate (IP3) receptor IP3-binding proteins. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - MOLECULAR CELL RESEARCH 2023; 1870:119470. [PMID: 37011730 DOI: 10.1016/j.bbamcr.2023.119470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023]
Abstract
Conventionally, myo-D-inositol 1, 4,5-trisphosphate (IP3) is thought to exert its second messenger effects through the gating of IP3R Ca2+ release channels, located in Ca2+-storage organelles like the endoplasmic reticulum. However, there is considerable indirect evidence to support the concept that IP3 might interact with other, non-IP3R proteins within cells. To explore this possibility further, the Protein Data Bank was searched using the term "IP3". This resulted in the retrieval of 203 protein structures, the majority of which were members of the IP3R/ryanodine receptor superfamily of channels. Only 49 of these structures were complexed with IP3. These were inspected for their ability to interact with the carbon-1 phosphate of IP3, since this is the least accessible phosphate group of its precursor, phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). This reduced the number of structures retrieved to 35, of which 9 were IP3Rs. The remaining 26 structures represent a diverse range of proteins, including inositol-lipid metabolizing enzymes, signal transducers, PH domain containing proteins, cytoskeletal anchor proteins, the TRPV4 ion channel, a retroviral Gag protein and fibroblast growth factor 2. Such proteins may impact on IP3 signalling and its effects on cell-biology. This represents an area open for exploration in the field of IP3 signalling.
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Affiliation(s)
- John James Mackrill
- Department of Physiology, University College Cork, Western Gateway Building, Western Road, Cork T12 XF62, Ireland.
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17
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He R, Liu F, Wang H, Huang S, Xu K, Zhang C, Liu Y, Yu H. ORP9 and ORP10 form a heterocomplex to transfer phosphatidylinositol 4-phosphate at ER-TGN contact sites. Cell Mol Life Sci 2023; 80:77. [PMID: 36853333 PMCID: PMC11072704 DOI: 10.1007/s00018-023-04728-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 03/01/2023]
Abstract
Oxysterol-binding protein (OSBP) and its related proteins (ORPs) are a family of lipid transfer proteins (LTPs) that mediate non-vesicular lipid transport. ORP9 and ORP10, members of the OSBP/ORPs family, are located at the endoplasmic reticulum (ER)-trans-Golgi network (TGN) membrane contact sites (MCSs). It remained unclear how they mediate lipid transport. In this work, we discovered that ORP9 and ORP10 form a binary complex through intermolecular coiled-coil (CC) domain-CC domain interaction. The PH domains of ORP9 and ORP10 specially interact with phosphatidylinositol 4-phosphate (PI4P), mediating the TGN targeting. The ORP9-ORP10 complex plays a critical role in regulating PI4P levels at the TGN. Using in vitro reconstitution assays, we observed that while full-length ORP9 efficiently transferred PI4P between two apposed membranes, the lipid transfer kinetics was further accelerated by ORP10. Interestingly, our data showed that the PH domains of ORP9 and ORP10 participate in membrane tethering simultaneously, whereas ORDs of both ORP9 and ORP10 are required for lipid transport. Furthermore, our data showed that the depletion of ORP9 and ORP10 led to increased vesicle transport to the plasma membrane (PM). These findings demonstrate that ORP9 and ORP10 form a binary complex through the CC domains, maintaining PI4P homeostasis at ER-TGN MCSs and regulating vesicle trafficking.
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Affiliation(s)
- Ruyue He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Furong Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Hui Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shuai Huang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Kai Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Conggang Zhang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Yinghui Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Haijia Yu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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18
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Balaban C, Sztacho M, Antiga L, Miladinović A, Harata M, Hozák P. PIP2-Effector Protein MPRIP Regulates RNA Polymerase II Condensation and Transcription. Biomolecules 2023; 13:biom13030426. [PMID: 36979361 PMCID: PMC10046169 DOI: 10.3390/biom13030426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
The specific post-translational modifications of the C-terminal domain (CTD) of the Rpb1 subunit of RNA polymerase II (RNAPII) correlate with different stages of transcription. The phosphorylation of the Ser5 residues of this domain associates with the initiation condensates, which are formed through liquid-liquid phase separation (LLPS). The subsequent Tyr1 phosphorylation of the CTD peaks at the promoter-proximal region and is involved in the pause-release of RNAPII. By implementing super-resolution microscopy techniques, we previously reported that the nuclear Phosphatidylinositol 4,5-bisphosphate (PIP2) associates with the Ser5-phosphorylated-RNAPII complex and facilitates the RNAPII transcription. In this study, we identified Myosin Phosphatase Rho-Interacting Protein (MPRIP) as a novel regulator of the RNAPII transcription that recruits Tyr1-phosphorylated CTD (Tyr1P-CTD) to nuclear PIP2-containing structures. The depletion of MPRIP increases the number of the initiation condensates, indicating a defect in the transcription. We hypothesize that MPRIP regulates the condensation and transcription through affecting the association of the RNAPII complex with nuclear PIP2-rich structures. The identification of Tyr1P-CTD as an interactor of PIP2 and MPRIP further points to a regulatory role in RNAPII pause-release, where the susceptibility of the transcriptional complex to leave the initiation condensate depends on its association with nuclear PIP2-rich structures. Moreover, the N-terminal domain of MPRIP, which is responsible for the interaction with the Tyr1P-CTD, contains an F-actin binding region that offers an explanation of how nuclear F-actin formations can affect the RNAPII transcription and condensation. Overall, our findings shed light on the role of PIP2 in RNAPII transcription through identifying the F-actin binding protein MPRIP as a transcription regulator and a determinant of the condensation of RNAPII.
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Affiliation(s)
- Can Balaban
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Martin Sztacho
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
- Correspondence: (M.S.); (P.H.)
| | - Ludovica Antiga
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Ana Miladinović
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Masahiko Harata
- Laboratory of Molecular Biochemistry, Division of Life Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
- Correspondence: (M.S.); (P.H.)
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19
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Structural Insights Uncover the Specific Phosphoinositide Recognition by the PH1 Domain of Arap3. Int J Mol Sci 2023; 24:ijms24021125. [PMID: 36674645 PMCID: PMC9865853 DOI: 10.3390/ijms24021125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Arap3, a dual GTPase-activating protein (GAP) for the small GTPases Arf6 and RhoA, plays key roles in regulating a wide range of biological processes, including cancer cell invasion and metastasis. It is known that Arap3 is a PI3K effector that can bind directly to PI(3,4,5)P3, and the PI(3,4,5)P3-mediated plasma membrane recruitment is crucial for its function. However, the molecular mechanism of how the protein recognizes PI(3,4,5)P3 remains unclear. Here, using liposome pull-down and surface plasmon resonance (SPR) analysis, we found that the N-terminal first pleckstrin homology (PH) domain (Arap3-PH1) can interact with PI(3,4,5)P3 and, with lower affinity, with PI(4,5)P2. To understand how Arap3-PH1 and phosphoinositide (PIP) lipids interact, we solved the crystal structure of the Arap3-PH1 in the apo form and complex with diC4-PI(3,4,5)P3. We also characterized the interactions of Arap3-PH1 with diC4-PI(3,4,5)P3 and diC4-PI(4,5)P2 in solution by nuclear magnetic resonance (NMR) spectroscopy. Furthermore, we found overexpression of Arap3 could inhibit breast cancer cell invasion in vitro, and the PIPs-binding ability of the PH1 domain is essential for this function.
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20
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Fission Yeast Rho1p-GEFs: From Polarity and Cell Wall Synthesis to Genome Stability. Int J Mol Sci 2022; 23:ijms232213888. [PMID: 36430366 PMCID: PMC9697909 DOI: 10.3390/ijms232213888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Rho1p is a membrane-associated protein that belongs to the Rho family of small GTPases. These proteins coordinate processes such as actin remodelling and polarised secretion to maintain the shape and homeostasis of yeast cells. In response to extracellular stimuli, Rho1p undergoes conformational switching between a guanosine triphosphate (GTP)-bound active state and a guanosine diphosphate (GDP)-bound inactive state. Cycling is improved with guanine nucleotide exchange factor (GEF) activity necessary to activate signalling and GTPase activating protein (GAP) activity required for subsequent signal depletion. This review focuses on fission yeast Rho1p GEFs, Rgf1p, Rgf2p, and Rgf3p that belong to the family of DH-PH domain-containing Dbl-related GEFs. They are multi-domain proteins that detect biological signals that induce or inhibit their catalytic activity over Rho1p. Each of them activates Rho1p in different places and times. Rgf1p acts preferentially during polarised growth. Rgf2p is required for sporulation, and Rgf3p plays an essential function in septum synthesis. In addition, we outline the noncanonical roles of Rho1p-GEFs in genomic instability.
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21
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PRMT4-mediated arginine methylation promotes tyrosine phosphorylation of VEGFR-2 and regulates filopodia protrusions. iScience 2022; 25:104736. [PMID: 35942094 PMCID: PMC9356023 DOI: 10.1016/j.isci.2022.104736] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/09/2022] [Accepted: 07/07/2022] [Indexed: 11/24/2022] Open
Abstract
Through tightly controlled multilayer mechanisms, vascular endothelial growth factor receptor-2 (VEGFR-2) activation and its downstream signal transduction govern vasculogenesis and pathological angiogenesis, such as tumor angiogenesis. Therefore, it is critical to understand the molecular mechanisms governing VEGFR-2 signal transduction. We report that protein arginine methyltransferase 4 (PRMT4) via its highly conserved EVH1 and PH domain-like N-terminal domain binds to VEGFR-2 and mediates methylation of the juxtamembrane arginine 817 (R817) on VEGFR-2. Methylation of R817 selectively increases phosphorylation of tyrosine 820 (Y820). Phosphorylation of Y820 facilitates the c-Src binding with VEGFR-2 via Src homology domain 2 (SH2). Interfering with the methylation of R817 or phosphorylation of Y820 inhibits VEGFR-2-induced filopodia protrusions, a process that is critical for the core angiogenic responses of VEGFR-2. Methylation of R817 is an important previously unrecognized mechanism of the angiogenic signaling of VEGFR-2, with implications for the development of novel-targeted VEGFR-2 inhibitors. Arginine 817 methylation regulates phosphorylation of Y820 on VEGFR-2 Phosphorylation of Y820 recruits c-Src kinase to VEGFR-2, leading to its activation VEGFR-2/c-Src axis mediates filopodia protrusions in endothelial cells
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22
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Le Huray KIP, Wang H, Sobott F, Kalli AC. Systematic simulation of the interactions of pleckstrin homology domains with membranes. SCIENCE ADVANCES 2022; 8:eabn6992. [PMID: 35857458 PMCID: PMC9258823 DOI: 10.1126/sciadv.abn6992] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Pleckstrin homology (PH) domains can recruit proteins to membranes by recognition of phosphatidylinositol phosphate (PIP) lipids. Several family members are linked to diseases including cancer. We report the systematic simulation of the interactions of 100 mammalian PH domains with PIP-containing membranes. The observed PIP interaction hotspots recapitulate crystallographic binding sites and reveal a number of insights: (i) The β1 and β2 strands and their connecting loop constitute the primary PIP interaction site but are typically supplemented by interactions at the β3-β4 and β5-β6 loops; (ii) we reveal exceptional cases such as the Exoc8 PH domain; (iii) PH domains adopt different membrane-bound orientations and induce clustering of anionic lipids; and (iv) beyond family-level insights, our dataset sheds new light on individual PH domains, e.g., by providing molecular detail of secondary PIP binding sites. This work provides a global view of PH domain/membrane association involving multivalent association with anionic lipids.
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Affiliation(s)
- Kyle I. P. Le Huray
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Astbury Centre for Structural and Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - He Wang
- School of Computing, University of Leeds, Leeds, UK
| | - Frank Sobott
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Astbury Centre for Structural and Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Antreas C. Kalli
- Astbury Centre for Structural and Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
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23
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The PH Domain and C-Terminal polyD Motif of Phafin2 Exhibit a Unique Concurrence in Animals. MEMBRANES 2022; 12:membranes12070696. [PMID: 35877899 PMCID: PMC9324892 DOI: 10.3390/membranes12070696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 01/27/2023]
Abstract
Phafin2, a member of the Phafin family of proteins, contributes to a plethora of cellular activities including autophagy, endosomal cargo transportation, and macropinocytosis. The PH and FYVE domains of Phafin2 play key roles in membrane binding, whereas the C-terminal poly aspartic acid (polyD) motif specifically autoinhibits the PH domain binding to the membrane phosphatidylinositol 3-phosphate (PtdIns3P). Since the Phafin2 FYVE domain also binds PtdIns3P, the role of the polyD motif remains unclear. In this study, bioinformatics tools and resources were employed to determine the concurrence of the PH-FYVE module with the polyD motif among Phafin2 and PH-, FYVE-, or polyD-containing proteins from bacteria to humans. FYVE was found to be an ancient domain of Phafin2 and is related to proteins that are present in both prokaryotes and eukaryotes. Interestingly, the polyD motif only evolved in Phafin2 and PH- or both PH-FYVE-containing proteins in animals. PolyD motifs are absent in PH domain-free FYVE-containing proteins, which usually display cellular trafficking or autophagic functions. Moreover, the prediction of the Phafin2-interacting network indicates that Phafin2 primarily cross-talks with proteins involved in autophagy, protein trafficking, and neuronal function. Taken together, the concurrence of the polyD motif with the PH domain may be associated with complex cellular functions that evolved specifically in animals.
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24
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Larsen A, John L, Sansom M, Corey R. Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us? Biosci Rep 2022; 42:BSR20211406. [PMID: 35297484 PMCID: PMC9008707 DOI: 10.1042/bsr20211406] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 12/04/2022] Open
Abstract
Peripheral membrane proteins (PMPs) can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding domains are typically solved in a soluble form, sometimes with a lipid or lipid headgroup at the binding site. To provide a detailed molecular view of PMP interactions with the membrane, computational methods such as molecular dynamics (MD) simulations can be applied. Here, we outline recent attempts to characterise these binding interactions, focusing on both intracellular proteins, such as phosphatidylinositol phosphate (PIP)-binding domains, and extracellular proteins such as glycolipid-binding bacterial exotoxins. We compare methods used to identify and analyse lipid-binding sites from simulation data and highlight recent work characterising the energetics of these interactions using free energy calculations. We describe how improvements in methodologies and computing power will help MD simulations to continue to contribute to this field in the future.
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Affiliation(s)
| | - Laura H. John
- Department of Biochemistry, University of Oxford, Oxford, U.K
| | | | - Robin A. Corey
- Department of Biochemistry, University of Oxford, Oxford, U.K
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Khaliq SA, Umair Z, Yoon MS. Role of ARHGEF3 as a GEF and mTORC2 Regulator. Front Cell Dev Biol 2022; 9:806258. [PMID: 35174167 PMCID: PMC8841341 DOI: 10.3389/fcell.2021.806258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/24/2021] [Indexed: 11/26/2022] Open
Abstract
Guanine nucleotide exchange factors (GEFs) activate GTPases by stimulating the release of guanosine diphosphate to permit the binding of guanosine triphosphate. ARHGEF3 or XPLN (exchange factor found in platelets, leukemic, and neuronal tissues) is a selective guanine nucleotide exchange factor for Rho GTPases (RhoGEFs) that activates RhoA and RhoB but not RhoC, RhoG, Rac1, or Cdc42. ARHGEF3 contains the diffuse B-cell lymphoma homology and pleckstrin homology domains but lacks similarity with other known functional domains. ARHGEF3 also binds the mammalian target of rapamycin complex 2 (mTORC2) and subsequently inhibits mTORC2 and Akt. In vivo investigation has also indicated the communication between ARHGEF3 and autophagy-related muscle pathologies. Moreover, studies on genetic variation in ARHGEF3 and genome-wide association studies have predicted exciting novel roles of ARHGEF3 in controlling bone mineral density, platelet formation and differentiation, and Hirschsprung disease. In conclusion, we hypothesized that additional biochemical and functional studies are required to elucidate the detailed mechanism of ARHGEF3-related pathologies and therapeutics.
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Affiliation(s)
- Sana Abdul Khaliq
- Department of Molecular Medicine, Gachon University College of Medicine, Incheon, South Korea
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, South Korea
| | - Zobia Umair
- Department of Molecular Medicine, Gachon University College of Medicine, Incheon, South Korea
- *Correspondence: Zobia Umair, ; Mee-Sup Yoon,
| | - Mee-Sup Yoon
- Department of Molecular Medicine, Gachon University College of Medicine, Incheon, South Korea
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, South Korea
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, South Korea
- *Correspondence: Zobia Umair, ; Mee-Sup Yoon,
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26
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He J, Zeng Z, Wang Y, Deng J, Tang X, Liu F, Huang J, Chen H, Liang R, Zan X, Liu Z, Tong A, Guo G, Xu J, Zhu X, Zhou L, Peng Y. Characterization of novel CTNNB1 mutation in Craniopharyngioma by whole-genome sequencing. Mol Cancer 2021; 20:168. [PMID: 34922552 PMCID: PMC8684236 DOI: 10.1186/s12943-021-01468-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 11/22/2021] [Indexed: 02/08/2023] Open
Abstract
Background Craniopharyngioma (CP) is rare histologically benign but clinically challenging tumor because of its intimate relationship with the critical structure in the central brain. CP can be divided into two major histologic subtypes: adamantinomatous-type CP (ACP) and papillary-type CP (PCP). Although some genetic aberrations for both categories have been revealed in previous studies, the complete spectrum of genetic changes of this tumor remains unknown. Methods In this study, we conducted whole genome sequencing (WGS) on twenty-six CPs including 16 ACPs and 10 PCPs together with their matched blood samples. Somatic variants (SNVs, InDels, SVs and CNVs) were identified and mutational signatures were characterized for each patient. We investigated the impact of a novel CTNNB1 mutant on its protein stability, ubiquitination and Wnt pathway activity. Cell proliferation ability of the CTNNB1 mutant in ACP primary cells was additionally analyzed by CCK8 and colony formation assays. Results We found that CPs had showed less complexity with fewer somatic mutations compared with malignant tumors. Moreover, mutations in CTNNB1 (68.75% of ACP) and BRAF V600E (70.00% of PCP) are mutually exclusive in ACP and PCP, consolidating that the driving roles of these two genes in ACP and PCP, respectively. A novel mutation in the exon 3 of CTNNB1 which compromised both a transversion and in-frame deletion was identified in ACP. This mutation was experimentally validated to confer β-catenin increased stability by inhibiting its ubiquitination, thus activating Wnt-signaling pathway and promoting cell proliferation. Conclusions Whole genome landscape for CP was revealed by WGS analysis, and a novel mutation in the exon 3 of CTNNB1 was identified. This novel mutation activates Wnt-signaling pathway through increasing the stability of β-catenin. Our findings provided us with more comprehensive insight into the spectrum of genetic alterations in CP. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-021-01468-7.
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Affiliation(s)
- Juan He
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhen Zeng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Yuelong Wang
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.,Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jiaojiao Deng
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 20040, China
| | - Xin Tang
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Fujun Liu
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jianhan Huang
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.,Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hongxu Chen
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ruichao Liang
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xin Zan
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhiyong Liu
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Aiping Tong
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Gang Guo
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jianguo Xu
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaofeng Zhu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China.
| | - Liangxue Zhou
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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27
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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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