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Escudeiro-Lopes S, Filimonenko VV, Jarolimová L, Hozák P. Lamin A/C and PI(4,5)P2-A Novel Complex in the Cell Nucleus. Cells 2024; 13:399. [PMID: 38474363 DOI: 10.3390/cells13050399] [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: 10/06/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 03/14/2024] Open
Abstract
Lamins, the nuclear intermediate filaments, are important regulators of nuclear structural integrity as well as nuclear functional processes such as DNA transcription, replication and repair, and epigenetic regulations. A portion of phosphorylated lamin A/C localizes to the nuclear interior in interphase, forming a lamin A/C pool with specific properties and distinct functions. Nucleoplasmic lamin A/C molecular functions are mainly dependent on its binding partners; therefore, revealing new interactions could give us new clues on the lamin A/C mechanism of action. In the present study, we show that lamin A/C interacts with nuclear phosphoinositides (PIPs), and with nuclear myosin I (NM1). Both NM1 and nuclear PIPs have been previously reported as important regulators of gene expression and DNA damage/repair. Furthermore, phosphorylated lamin A/C forms a complex with NM1 in a phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2)-dependent manner in the nuclear interior. Taken together, our study reveals a previously unidentified interaction between phosphorylated lamin A/C, NM1, and PI(4,5)P2 and suggests new possible ways of nucleoplasmic lamin A/C regulation, function, and importance for the formation of functional nuclear microdomains.
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Affiliation(s)
- Sara Escudeiro-Lopes
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Vlada V Filimonenko
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
- Electron Microscopy Core Facility, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Lenka Jarolimová
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
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Johansen KH, Golec DP, Okkenhaug K, Schwartzberg PL. Mind the GAP: RASA2 and RASA3 GTPase-activating proteins as gatekeepers of T cell activation and adhesion. Trends Immunol 2023; 44:917-931. [PMID: 37858490 PMCID: PMC10621891 DOI: 10.1016/j.it.2023.09.002] [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: 08/26/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023]
Abstract
Following stimulation, the T cell receptor (TCR) and its coreceptors integrate multiple intracellular signals to initiate T cell proliferation, migration, gene expression, and metabolism. Among these signaling molecules are the small GTPases RAS and RAP1, which induce MAPK pathways and cellular adhesion to activate downstream effector functions. Although many studies have helped to elucidate the signaling intermediates that mediate T cell activation, the molecules and pathways that keep naive T cells in check are less understood. Several recent studies provide evidence that RASA2 and RASA3, which are GAP1-family GTPase-activating proteins (GAPs) that inactivate RAS and RAP1, respectively, are crucial molecules that limit T cell activation and adhesion. In this review we describe recent data on the roles of RASA2 and RASA3 as gatekeepers of T cell activation and migration.
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Affiliation(s)
- Kristoffer H Johansen
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK; Section of Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Dominic P Golec
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Klaus Okkenhaug
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Pamela L Schwartzberg
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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3
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Trudeau SJ, Hwang H, Mathur D, Begum K, Petrey D, Murray D, Honig B. PrePCI: A structure- and chemical similarity-informed database of predicted protein compound interactions. Protein Sci 2023; 32:e4594. [PMID: 36776141 PMCID: PMC10019447 DOI: 10.1002/pro.4594] [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: 09/13/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
We describe the Predicting Protein-Compound Interactions (PrePCI) database which comprises over 5 billion predicted interactions between 6.8 million chemical compounds and 19,797 human proteins. PrePCI relies on a proteome-wide database of structural models based on both traditional modeling techniques and the AlphaFold Protein Structure Database. Sequence- and structural similarity-based metrics are established between template proteins, T, in the Protein Data Bank that bind compounds, C, and query proteins in the model database, Q. When the metrics exceed threshold values, it is assumed that C also binds to Q with a likelihood ratio (LR) derived from machine learning. If the relationship is based on structural similarity, the LR is based on a scoring function that measures the extent to which C is compatible with the binding site of Q as described in the LT-scanner algorithm. For every predicted complex derived in this way, chemical similarity based on the Tanimoto coefficient identifies other small molecules that may bind to Q. An overall LR for the binding of C to Q is obtained from Naive Bayesian statistics. The PrePCI database can be queried by entering a UniProt ID or gene name for a protein to obtain a list of compounds predicted to bind to it along with associated LRs. Alternatively, entering an identifier for the compound outputs a list of proteins it is predicted to bind. Specific applications of the database to lead discovery, elucidation of drug mechanism of action, and biological function annotation are described.
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Affiliation(s)
- Stephen J. Trudeau
- Department of Systems BiologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
- Integrated Graduate Program in Cellular, Molecular and Biomedical Studies (CMBS), Columbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Howook Hwang
- Department of Systems BiologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
- Schrodinger, Inc.New YorkNew YorkUSA
| | - Deepika Mathur
- Department of Systems BiologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of PsychiatryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Kamrun Begum
- Department of Systems BiologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Donald Petrey
- Department of Systems BiologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Diana Murray
- Department of Systems BiologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Barry Honig
- Department of Systems BiologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
- Department of Biochemistry and Molecular BiophysicsColumbia University Irving Medical CenterNew YorkNew YorkUSA
- Department of MedicineColumbia UniversityNew YorkNew YorkUSA
- Zuckerman Mind Brain and Behavior InstituteColumbia UniversityNew YorkNew YorkUSA
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4
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Palmieri M, Catimel B, Mouradov D, Sakthianandeswaren A, Kapp E, Ang CS, Williamson NA, Nowell CJ, Christie M, Desai J, Gibbs P, Burgess AW, Sieber OM. PI3K-alpha translocation mediates nuclear PtdIns(3,4,5)P 3 effector signaling in colorectal cancer. Mol Cell Proteomics 2023; 22:100529. [PMID: 36931626 PMCID: PMC10130476 DOI: 10.1016/j.mcpro.2023.100529] [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: 05/12/2022] [Revised: 03/05/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The canonical view of phosphatidylinositol 3-kinase alpha (PI3Kα) signaling describes PtdIns(3,4,5)P3 generation and activation of downstream effectors at the plasma membrane or at microtubule-bound endosomes. Here, we show that colorectal cancer (CRC) cell lines exhibit a diverse plasma membrane-nuclear distribution of PI3Kα, controlling corresponding levels of subcellular PtdIns(3,4,5)P3 pools. PI3Kα nuclear translocation was mediated by the importin β-dependent nuclear import pathway. By PtdIns(3,4,5)P3 affinity capture mass spectrometry done in the presence of SDS on CRC cell lines with PI3Kα nuclear localization, we identified 867 potential nuclear PtdIns(3,4,5)P3 effector proteins. Nuclear PtdIns(3,4,5)P3 interactome proteins were characterized by non-canonical PtdIns(3,4,5)P3 binding domains and showed overrepresentation for nuclear membrane, nucleolus and nuclear speckles. The nuclear PtdIns(3,4,5)P3 interactome was enriched for proteins related to RNA metabolism, with splicing reporter assays and SC-35 foci staining suggesting a role of EGF-stimulated nuclear PI3Kα signaling in modulating pre-mRNA splicing. In patient tumors, nuclear p110α staining was associated with lower T stage and mucinous histology. These results indicate that PI3Kα translocation mediates nuclear PtdIns(3,4,5)P3 effector signaling in human CRC, modulating signaling responses.
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Affiliation(s)
- Michelle Palmieri
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Bruno Catimel
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Dmitri Mouradov
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Anuratha Sakthianandeswaren
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Eugene Kapp
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia; Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nicholas A Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Cameron J Nowell
- Monash Institute for Pharmaceutical Science, Parkville, Victoria, 3052, Australia
| | - Michael Christie
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Pathology, Royal Melbourne Hospital, Parkville, Victoria, 3050, Australia
| | - Jayesh Desai
- Division of Cancer Medicine, Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia; Department of Medical Oncology, Royal Melbourne Hospital, Parkville, Victoria, 3050, Australia
| | - Peter Gibbs
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia; Department of Medical Oncology, Western Health, Footscray, Victoria, 3011, Australia
| | - Antony W Burgess
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia; Department of Surgery, The University of Melbourne, Parkville, Victoria, 3050, Australia
| | - Oliver M Sieber
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia; Department of Surgery, The University of Melbourne, Parkville, Victoria, 3050, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia.
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5
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Meraş İ, Chotard L, Liontis T, Ratemi Z, Wiles B, Seo JH, Van Raamsdonk JM, Rocheleau CE. The Rab GTPase activating protein TBC-2 regulates endosomal localization of DAF-16 FOXO and lifespan. PLoS Genet 2022; 18:e1010328. [PMID: 35913999 PMCID: PMC9371356 DOI: 10.1371/journal.pgen.1010328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/11/2022] [Accepted: 07/06/2022] [Indexed: 12/02/2022] Open
Abstract
FOXO transcription factors have been shown to regulate longevity in model organisms and are associated with longevity in humans. To gain insight into how FOXO functions to increase lifespan, we examined the subcellular localization of DAF-16 in C. elegans. We show that DAF-16 is localized to endosomes and that this endosomal localization is increased by the insulin-IGF signaling (IIS) pathway. Endosomal localization of DAF-16 is modulated by endosomal trafficking proteins. Disruption of the Rab GTPase activating protein TBC-2 increases endosomal localization of DAF-16, while inhibition of TBC-2 targets, RAB-5 or RAB-7 GTPases, decreases endosomal localization of DAF-16. Importantly, the amount of DAF-16 that is localized to endosomes has functional consequences as increasing endosomal localization through mutations in tbc-2 reduced the lifespan of long-lived daf-2 IGFR mutants, depleted their fat stores, and DAF-16 target gene expression. Overall, this work identifies endosomal localization as a mechanism regulating DAF-16 FOXO, which is important for its functions in metabolism and aging. FOXO transcription factors have been shown to modulate lifespan in multiple model organisms and to be associated with longevity in humans. Here we describe a new localization of the C. elegans FOXO transcription factor, called DAF-16. We report that DAF-16 localizes to endosomes, membrane compartments internalized from the plasma membrane at the cell surface. We demonstrate that expansion of these endosome compartments by disruption of an endosomal regulator called TBC-2 results in increased localization of DAF-16 on endosomes at the expense of nuclear localization in the intestinal cells. This results in altered expression of DAF-16 target genes, reduced fat storage and decreased lifespan. These results demonstrate the importance of endosomal trafficking for proper localization of DAF-16 and suggest that the endosome is an important site of FOXO regulation. An intriguing possibility based on our results is that storage of FOXO on endosomes facilitates the mobilization of FOXO as a rapid response to environmental stress.
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Affiliation(s)
- İçten Meraş
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, McGill University, Montreal, Canada
- Metabolic Disorders and Complications Program, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Laëtitia Chotard
- Division of Endocrinology and Metabolism, Department of Medicine, McGill University, Montreal, Canada
- Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, Canada
| | - Thomas Liontis
- Metabolic Disorders and Complications Program, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montreal, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
- Brain Repair and Integrative Neuroscience Program, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Zakaria Ratemi
- Metabolic Disorders and Complications Program, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Benjamin Wiles
- Metabolic Disorders and Complications Program, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Jung Hwa Seo
- Metabolic Disorders and Complications Program, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Jeremy M. Van Raamsdonk
- Metabolic Disorders and Complications Program, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montreal, Canada
- Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
- Brain Repair and Integrative Neuroscience Program, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Christian E. Rocheleau
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, McGill University, Montreal, Canada
- Metabolic Disorders and Complications Program, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montreal, Canada
- Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, Canada
- * E-mail:
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6
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Johansen KH, Golec DP, Huang B, Park C, Thomsen JH, Preite S, Cannons JL, Garçon F, Schrom EC, Courrèges CJF, Veres TZ, Harrison J, Nus M, Phelan JD, Bergmeier W, Kehrl JH, Okkenhaug K, Schwartzberg PL. A CRISPR screen targeting PI3K effectors identifies RASA3 as a negative regulator of LFA-1-mediated adhesion in T cells. Sci Signal 2022; 15:eabl9169. [PMID: 35857633 PMCID: PMC9637254 DOI: 10.1126/scisignal.abl9169] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The integrin lymphocyte function-associated antigen 1 (LFA-1) helps to coordinate the migration, adhesion, and activation of T cells through interactions with intercellular adhesion molecule 1 (ICAM-1) and ICAM-2. LFA-1 is activated during the engagement of chemokine receptors and the T cell receptor (TCR) through inside-out signaling, a process that is partially mediated by phosphoinositide 3-kinase (PI3K) and its product phosphatidylinositol 3,4,5-trisphosphate (PIP3). To evaluate potential roles of PI3K in LFA-1 activation, we designed a library of CRISPR/single guide RNAs targeting known and potential PIP3-binding proteins and screened for effects on the ability of primary mouse T cells to bind to ICAM-1. We identified multiple proteins that regulated the binding of LFA-1 to ICAM-1, including the Rap1 and Ras GTPase-activating protein RASA3. We found that RASA3 suppressed LFA-1 activation in T cells, that its expression was rapidly reduced upon T cell activation, and that its activity was inhibited by PI3K. Loss of RASA3 in T cells led to increased Rap1 activation, defective lymph node entry and egress, and impaired responses to T-dependent immunization in mice. Our results reveal a critical role for RASA3 in T cell migration, homeostasis, and function.
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Affiliation(s)
- Kristoffer H Johansen
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.,National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Section of Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark, Kongens Lyngby DK-2800, Denmark
| | - Dominic P Golec
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bonnie Huang
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chung Park
- B-Cell Molecular Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julie H Thomsen
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Silvia Preite
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer L Cannons
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fabien Garçon
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Edward C Schrom
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Tibor Z Veres
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - James Harrison
- Cardiovascular Division, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Meritxell Nus
- Cardiovascular Division, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - James D Phelan
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wolfgang Bergmeier
- Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - John H Kehrl
- B-Cell Molecular Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Klaus Okkenhaug
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Pamela L Schwartzberg
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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7
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Wang YH, Sheetz MP. When PIP2 Meets p53: Nuclear Phosphoinositide Signaling in the DNA Damage Response. Front Cell Dev Biol 2022; 10:903994. [PMID: 35646908 PMCID: PMC9136457 DOI: 10.3389/fcell.2022.903994] [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: 03/25/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
The mechanisms that maintain genome stability are critical for preventing tumor progression. In the past decades, many strategies were developed for cancer treatment to disrupt the DNA repair machinery or alter repair pathway selection. Evidence indicates that alterations in nuclear phosphoinositide lipids occur rapidly in response to genotoxic stresses. This implies that nuclear phosphoinositides are an upstream element involved in DNA damage signaling. Phosphoinositides constitute a new signaling interface for DNA repair pathway selection and hence a new opportunity for developing cancer treatment strategies. However, our understanding of the underlying mechanisms by which nuclear phosphoinositides regulate DNA damage repair, and particularly the dynamics of those processes, is rather limited. This is partly because there are a limited number of techniques that can monitor changes in the location and/or abundance of nuclear phosphoinositide lipids in real time and in live cells. This review summarizes our current knowledge regarding the roles of nuclear phosphoinositides in DNA damage response with an emphasis on the dynamics of these processes. Based upon recent findings, there is a novel model for p53’s role with nuclear phosphoinositides in DNA damage response that provides new targets for synthetic lethality of tumors.
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Tae H, Park S, Kim SO, Yorulmaz Avsar S, Cho NJ. Selective Recognition of Phosphatidylinositol Phosphate Receptors by C-Terminal Tail of Mitotic Kinesin-like Protein 2 (MKlp2). J Phys Chem B 2022; 126:2345-2352. [PMID: 35316051 DOI: 10.1021/acs.jpcb.1c10534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The mitotic kinesin-like protein 2 (MKlp2) plays a key role in the proper completion of cytokinetic abscission. Specifically, the C-terminal tail of MKlp2 (CTM peptides) offers a stable tethering on the plasma membrane and microtubule cytoskeleton in the midbody during abscission. However, little is known about the underlying mechanism of how the CTM peptides bind to the plasma membrane of the intercellular bridge. Herein, we identify the specific molecular interaction between the CTM peptides and phosphatidylinositol phosphate (PIP) receptors using quartz crystal microbalance-dissipation and atomic force microscopy force spectroscopic measurements. To systematically examine the effects of amino acids, we designed a series of synthetic 33-mer peptides derived from the wild-type (CTM1). First, we evaluated the peptide binding amount caused by electrostatic interactions based on 100% zwitterionic and 30% negatively charged model membranes, whereby the nonspecific attractions were nearly proportional to the net charge of peptides. Upon incubating with PIP-containing model membranes, the wild-type CTM1 and its truncated mutation showed significant PI(3)P-specific binding, which was evidenced by a 15-fold higher binding mass and 6-fold stronger adhesion force compared to other negatively charged membranes. The extent of the specific binding was predominantly dependent on the existence of S21, whereby substitution or deletion of S21 significantly hindered the binding affinity. Taken together, our findings based on a correlative measurement platform enabled the quantification of the nonelectrostatic, selective binding interactions of the C-terminal of MKlp2 to certain PIP receptors and contributed to understanding the molecular mechanisms on complete cytokinetic abscission in cells.
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Affiliation(s)
- Hyunhyuk Tae
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue 639798, Singapore
| | - Soohyun Park
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue 639798, Singapore
| | - Seong-Oh Kim
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue 639798, Singapore
| | - Saziye Yorulmaz Avsar
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue 639798, Singapore
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue 639798, Singapore.,China-Singapore International Joint Research Institute (CSIJRI), Guangzhou 510000, China
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9
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Need for more focus on lipid species in studies of biological and model membranes. Prog Lipid Res 2022; 86:101160. [DOI: 10.1016/j.plipres.2022.101160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 03/06/2022] [Indexed: 11/23/2022]
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10
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Guilherme JPLF, Semenova EA, Borisov OV, Larin AK, Moreland E, Generozov EV, Ahmetov II. Genomic predictors of testosterone levels are associated with muscle fiber size and strength. Eur J Appl Physiol 2022; 122:415-423. [PMID: 34792618 PMCID: PMC8783862 DOI: 10.1007/s00421-021-04851-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/28/2021] [Indexed: 11/29/2022]
Abstract
PURPOSE Circulating testosterone levels are a heritable trait with anabolic properties in various tissues, including skeletal muscle. So far, hundreds of single nucleotide polymorphisms (SNPs) associated with testosterone levels have been identified in nonathletic populations. The aim of the present study was to test the association of 822 testosterone-increasing SNPs with muscle-related traits (muscle fiber size, fat-free mass and handgrip strength) and to validate the identified SNPs in independent cohorts of strength and power athletes. METHODS One hundred and forty-eight physically active individuals (47 females, 101 males) were assessed for cross-sectional area (CSA) of fast-twitch muscle fibers. Significant SNPs were further assessed for fat-free mass and handgrip strength in > 354,000 participants from the UK Biobank cohort. The validation cohorts included Russian elite athletes. RESULTS From an initial panel of 822 SNPs, we identified five testosterone-increasing alleles (DOCK3 rs77031559 G, ESR1 rs190930099 G, GLIS3 rs34706136 TG, GRAMD1B rs850294 T, TRAIP rs62260729 C) nominally associated (P < 0.05) with CSA of fast-twitch muscle fibers, fat-free mass and handgrip strength. Based on these five SNPs, the number of testosterone-increasing alleles was positively associated with testosterone levels in male athletes (P = 0.048) and greater strength performance in weightlifters (P = 0.017). Moreover, the proportion of participants with ≥ 2 testosterone-increasing alleles was higher in power athletes compared to controls (68.9 vs. 55.6%; P = 0.012). CONCLUSION Testosterone-related SNPs are associated with muscle fiber size, fat-free mass and strength, which combined can partially contribute to a greater predisposition to strength/power sports.
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Affiliation(s)
- João Paulo L F Guilherme
- Laboratory of Applied Nutrition and Metabolism, School of Physical Education and Sport, University of São Paulo, São Paulo, Brazil
| | - Ekaterina A Semenova
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Research Institute of Physical Culture and Sport, Volga Region State University of Physical Culture, Sport and Tourism, Kazan, Russia
| | - Oleg V Borisov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Andrey K Larin
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Ethan Moreland
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
| | - Edward V Generozov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Ildus I Ahmetov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK.
- Department of Physical Education, Plekhanov Russian University of Economics, Moscow, Russia.
- Laboratory of Molecular Genetics, Kazan State Medical University, Kazan, Russia.
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11
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Jeung HC, Puentes R, Aleshin A, Indarte M, Correa RG, Bankston LA, Layng FIAL, Ahmed Z, Wistuba I, Yao Y, Duenas DG, Zhang S, Meuillet EJ, Marassi F, Liddington RC, Kirkpatrick L, Powis G. PLEKHA7 signaling is necessary for the growth of mutant KRAS driven colorectal cancer. Exp Cell Res 2021; 409:112930. [PMID: 34800542 DOI: 10.1016/j.yexcr.2021.112930] [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: 08/06/2021] [Revised: 10/26/2021] [Accepted: 11/14/2021] [Indexed: 10/19/2022]
Abstract
Plekha7 (Pleckstrin homology [PH] domain containing, family A member 7) regulates the assembly of proteins of the cytoplasmic apical zonula adherens junction (AJ), thus ensuring cell-cell adhesion and tight-junction barrier integrity. Little is known of Plekha7 function in cancer. In colorectal cancer (CRC) Plekha7 expression is elevated compared to adjacent normal tissue levels, increasing with clinical stage. Plekha7 was present at plasma membrane AJ with wild-type KRas (wt-KRas) but was dispersed in cells expressing mutant KRas (mut-KRas). Fluorescence lifetime imaging microscopy (FLIM) indicated a direct Plekha7 interaction with wt-KRas but scantily with mut-KRas. Inhibiting Plekha7 specifically decreased mut-KRas cell signaling, proliferation, attachment, migration, and retarded mut-KRAS CRC tumor growth. Binding of diC8-phosphoinositides (PI) to the PH domain of Plekha7 was relatively low affinity. This may be because a D175 amino acid residue plays a "sentry" role preventing PI(3,4)P2 and PI(3,4,5)P3 binding. Molecular or pharmacological inhibition of the Plekha7 PH domain prevented the growth of mut-KRas but not wt-KRas cells. Taken together the studies suggest that Plekha7, in addition to maintaining AJ structure plays a role in mut-KRas signaling and phenotype through interaction of its PH domain with membrane mut-KRas, but not wt-KRas, to increase the efficiency of mut-KRas downstream signaling.
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Affiliation(s)
- Hei-Cheul Jeung
- MD Anderson Cancer Center, Houston, TX, USA; Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-Gu, Seoul, South Korea
| | - Roisin Puentes
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | - Alexander Aleshin
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | | | - Ricardo G Correa
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | - Laurie A Bankston
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | - Fabiana I A L Layng
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | | | | | - Yong Yao
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | - Daniela G Duenas
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | | | | | - Francesca Marassi
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | - Robert C Liddington
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | | | - Garth Powis
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA; PHusis Therapeutics, La Jolla, CA, USA.
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12
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Johansen KH, Golec DP, Thomsen JH, Schwartzberg PL, Okkenhaug K. PI3K in T Cell Adhesion and Trafficking. Front Immunol 2021; 12:708908. [PMID: 34421914 PMCID: PMC8377255 DOI: 10.3389/fimmu.2021.708908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022] Open
Abstract
PI3K signalling is required for activation, differentiation, and trafficking of T cells. PI3Kδ, the dominant PI3K isoform in T cells, has been extensively characterised using PI3Kδ mutant mouse models and PI3K inhibitors. Furthermore, characterisation of patients with Activated PI3K Delta Syndrome (APDS) and mouse models with hyperactive PI3Kδ have shed light on how increased PI3Kδ activity affects T cell functions. An important function of PI3Kδ is that it acts downstream of TCR stimulation to activate the major T cell integrin, LFA-1, which controls transendothelial migration of T cells as well as their interaction with antigen-presenting cells. PI3Kδ also suppresses the cell surface expression of CD62L and CCR7 which controls the migration of T cells across high endothelial venules in the lymph nodes and S1PR1 which controls lymph node egress. Therefore, PI3Kδ can control both entry and exit of T cells from lymph nodes as well as the recruitment to and retention of T cells within inflamed tissues. This review will focus on the regulation of adhesion receptors by PI3Kδ and how this contributes to T cell trafficking and localisation. These findings are relevant for our understanding of how PI3Kδ inhibitors may affect T cell redistribution and function.
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Affiliation(s)
- Kristoffer H Johansen
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom.,Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, United States
| | - Dominic P Golec
- Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, United States
| | - Julie H Thomsen
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Klaus Okkenhaug
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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13
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Redefining the specificity of phosphoinositide-binding by human PH domain-containing proteins. Nat Commun 2021; 12:4339. [PMID: 34267198 PMCID: PMC8282632 DOI: 10.1038/s41467-021-24639-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/18/2021] [Indexed: 01/02/2023] Open
Abstract
Pleckstrin homology (PH) domains are presumed to bind phosphoinositides (PIPs), but specific interaction with and regulation by PIPs for most PH domain-containing proteins are unclear. Here we employ a single-molecule pulldown assay to study interactions of lipid vesicles with full-length proteins in mammalian whole cell lysates. Of 67 human PH domain-containing proteins initially examined, 36 (54%) are found to have affinity for PIPs with various specificity, the majority of which have not been reported before. Further investigation of ARHGEF3 reveals distinct structural requirements for its binding to PI(4,5)P2 and PI(3,5)P2, and functional relevance of its PI(4,5)P2 binding. We generate a recursive-learning algorithm based on the assay results to analyze the sequences of 242 human PH domains, predicting that 49% of them bind PIPs. Twenty predicted binders and 11 predicted non-binders are assayed, yielding results highly consistent with the prediction. Taken together, our findings reveal unexpected lipid-binding specificity of PH domain-containing proteins. Pleckstrin homology (PH) domains are presumed to bind phosphoinositides (PIPs) but only few specific interactions are known. Using TIRF microscopy based assays, functional studies and an experimentally validated prediction algorithm, the authors show that specific PIP binding is widespread among human PH domains.
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14
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Nuclear Phosphatidylinositol 3,4,5-Trisphosphate Interactome Uncovers an Enrichment in Nucleolar Proteins. Mol Cell Proteomics 2021; 20:100102. [PMID: 34048982 PMCID: PMC8255942 DOI: 10.1016/j.mcpro.2021.100102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/20/2021] [Indexed: 02/07/2023] Open
Abstract
Polyphosphoinositides (PPIns) play essential roles as lipid signaling molecules, and many of their functions have been elucidated in the cytoplasm. However, PPIns are also intranuclear where they contribute to chromatin remodeling, transcription, and mRNA splicing. The PPIn, phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3), has been mapped to the nucleus and nucleoli, but its role remains unclear in this subcellular compartment. To gain further insights into the nuclear functions of PtdIns(3,4,5)P3, we applied a previously developed quantitative MS-based approach to identify the targets of PtdIns(3,4,5)P3 from isolated nuclei. We identified 179 potential PtdIns(3,4,5)P3-interacting partners, and gene ontology analysis for the biological functions of this dataset revealed an enrichment in RNA processing/splicing, cytokinesis, protein folding, and DNA repair. Interestingly, about half of these interactors were common to nucleolar protein datasets, some of which had dual functions in rRNA processes and DNA repair, including poly(ADP-ribose) polymerase 1 (PARP1, now referred as ADP-ribosyltransferase 1). PARP1 was found to interact directly with PPIn via three polybasic regions in the DNA-binding domain and the linker located N-terminal of the catalytic region. PARP1 was shown to bind to PtdIns(3,4,5)P3 as well as phosphatidylinositol 3,4-bisphosphate in vitro and to colocalize with PtdIns(3,4,5)P3 in the nucleolus and with phosphatidylinositol 3,4-bisphosphate in nucleoplasmic foci. In conclusion, the PtdIns(3,4,5)P3 interactome reported here will serve as a resource to further investigate the molecular mechanisms underlying PtdIns(3,4,5)P3-mediated interactions in the nucleus and nucleolus. Phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) localizes to nucleoli. PtdIns(3,4,5)P3 interactomics from isolated nuclei identifies nucleolar proteins. PARP1 interacts directly with polyphosphoinositides via several polybasic regions. PARP1 colocalizes with PtdIns(3,4,5)P3 in the nucleolus.
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15
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The Protein Toxins Ricin and Shiga Toxin as Tools to Explore Cellular Mechanisms of Internalization and Intracellular Transport. Toxins (Basel) 2021; 13:toxins13060377. [PMID: 34070659 PMCID: PMC8227415 DOI: 10.3390/toxins13060377] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/12/2021] [Accepted: 05/22/2021] [Indexed: 12/18/2022] Open
Abstract
Protein toxins secreted by bacteria and found in plants can be threats to human health. However, their extreme toxicity can also be exploited in different ways, e.g., to produce hybrid toxins directed against cancer cells and to study transport mechanisms in cells. Investigations during the last decades have shown how powerful these molecules are as tools in cell biological research. Here, we first present a partly historical overview, with emphasis on Shiga toxin and ricin, of how such toxins have been used to characterize processes and proteins of importance for their trafficking. In the second half of the article, we describe how one can now use toxins to investigate the role of lipid classes for intracellular transport. In recent years, it has become possible to quantify hundreds of lipid species using mass spectrometry analysis. Thus, it is also now possible to explore the importance of lipid species in intracellular transport. The detailed analyses of changes in lipids seen under conditions of inhibited toxin transport reveal previously unknown connections between syntheses of lipid classes and demonstrate the ability of cells to compensate under given conditions.
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16
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Sakurai T, Kukimoto-Niino M, Kunimura K, Yamane N, Sakata D, Aihara R, Yasuda T, Yokoyama S, Shirouzu M, Fukui Y, Uruno T. A conserved PI(4,5)P2-binding domain is critical for immune regulatory function of DOCK8. Life Sci Alliance 2021; 4:4/4/e202000873. [PMID: 33574036 PMCID: PMC7893821 DOI: 10.26508/lsa.202000873] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 01/20/2021] [Accepted: 01/20/2021] [Indexed: 01/05/2023] Open
Abstract
This study uncovers a critical role of DOCK8 in coupling PI(4,5)P2 signaling with Cdc42 activation through its DHR-1 domain during interstitial leukocyte migration. DOCK8 is a Cdc42-specific guanine-nucleotide exchange factor that is essential for development and functions of various subsets of leukocytes in innate and acquired immune responses. Although DOCK8 plays a critical role in spatial control of Cdc42 activity during interstitial leukocyte migration, the mechanism remains unclear. We show that the DOCK homology region (DHR)-1 domain of DOCK8 binds specifically to phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and is required for its recruitment to the plasma membrane. Structural and biochemical analyses reveal that DOCK8 DHR-1 domain consists of a C2 domain-like core with loops creating the upper surface pocket, where three basic residues are located for stereospecific recognition of phosphoinositides. Substitution of the two basic residues, K576 and R581, with alanine abolished PI(4,5)P2 binding in vitro, ablated the ability of DOCK8 to activate Cdc42 and support leukocyte migration in three-dimensional collagen gels. Dendritic cells carrying the mutation exhibited defective interstitial migration in vivo. Thus, our study uncovers a critical role of DOCK8 in coupling PI(4,5)P2 signaling with Cdc42 activation for immune regulation.
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Affiliation(s)
- Tetsuya Sakurai
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Mutsuko Kukimoto-Niino
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Kazufumi Kunimura
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Nana Yamane
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Daiji Sakata
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Ryosuke Aihara
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Tomoharu Yasuda
- Division of Immunology and Genome Biology, Department of Molecular and Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Shigeyuki Yokoyama
- RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Yoshinori Fukui
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takehito Uruno
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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17
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Trivedi D, CM V, Bisht K, Janardan V, Pandit A, Basak B, H S, Ramesh N, Raghu P. A genome engineering resource to uncover principles of cellular organization and tissue architecture by lipid signaling. eLife 2020; 9:e55793. [PMID: 33320085 PMCID: PMC7771963 DOI: 10.7554/elife.55793] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 12/14/2020] [Indexed: 12/14/2022] Open
Abstract
Phosphoinositides (PI) are key regulators of cellular organization in eukaryotes and genes that tune PI signaling are implicated in human disease mechanisms. Biochemical analyses and studies in cultured cells have identified a large number of proteins that can mediate PI signaling. However, the role of such proteins in regulating cellular processes in vivo and development in metazoans remains to be understood. Here, we describe a set of CRISPR-based genome engineering tools that allow the manipulation of each of these proteins with spatial and temporal control during metazoan development. We demonstrate the use of these reagents to deplete a set of 103 proteins individually in the Drosophila eye and identify several new molecules that control eye development. Our work demonstrates the power of this resource in uncovering the molecular basis of tissue homeostasis during normal development and in human disease biology.
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Affiliation(s)
- Deepti Trivedi
- National Centre for Biological Sciences-TIFR, GKVK CampusBangaloreIndia
| | - Vinitha CM
- National Centre for Biological Sciences-TIFR, GKVK CampusBangaloreIndia
| | - Karishma Bisht
- National Centre for Biological Sciences-TIFR, GKVK CampusBangaloreIndia
| | - Vishnu Janardan
- National Centre for Biological Sciences-TIFR, GKVK CampusBangaloreIndia
| | - Awadhesh Pandit
- National Centre for Biological Sciences-TIFR, GKVK CampusBangaloreIndia
| | - Bishal Basak
- National Centre for Biological Sciences-TIFR, GKVK CampusBangaloreIndia
| | - Shwetha H
- National Centre for Biological Sciences-TIFR, GKVK CampusBangaloreIndia
| | - Navyashree Ramesh
- National Centre for Biological Sciences-TIFR, GKVK CampusBangaloreIndia
| | - Padinjat Raghu
- National Centre for Biological Sciences-TIFR, GKVK CampusBangaloreIndia
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18
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Cestari I, Stuart K. The phosphoinositide regulatory network in Trypanosoma brucei: Implications for cell-wide regulation in eukaryotes. PLoS Negl Trop Dis 2020; 14:e0008689. [PMID: 33119588 PMCID: PMC7595295 DOI: 10.1371/journal.pntd.0008689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The unicellular eukaryote Trypanosoma brucei undergoes extensive cellular and developmental changes during its life cycle. These include regulation of mammalian stage surface antigen variation and surface composition changes between life stages; switching between glycolysis and oxidative phosphorylation; differential mRNA editing; and changes in posttranscriptional gene expression, protein trafficking, organellar function, and cell morphology. These diverse events are coordinated and controlled throughout parasite development, maintained in homeostasis at each life stage, and are essential for parasite survival in both the host and insect vector. Described herein are the enzymes and metabolites of the phosphatidylinositol (PI) cellular regulatory network, its integration with other cellular regulatory systems that collectively control and coordinate these numerous cellular processes, including cell development and differentiation and the many associated complex processes in multiple subcellular compartments. We conclude that this regulation is the product of the organization of these enzymes within the cellular architecture, their activities, metabolite fluxes, and responses to environmental changes via signal transduction and other processes. We describe a paradigm for how these enzymes and metabolites could function to control and coordinate multiple cellular functions. The significance of the PI system's regulatory functions in single-celled eukaryotes to metazoans and their potential as chemotherapeutic targets are indicated.
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Affiliation(s)
- Igor Cestari
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
- * E-mail: (IC); (KS)
| | - Kenneth Stuart
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- * E-mail: (IC); (KS)
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19
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Nuclear Inositides and Inositide-Dependent Signaling Pathways in Myelodysplastic Syndromes. Cells 2020; 9:cells9030697. [PMID: 32178280 PMCID: PMC7140618 DOI: 10.3390/cells9030697] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/04/2020] [Accepted: 03/11/2020] [Indexed: 12/21/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of hematological malignancies characterized by peripheral blood cytopenia and abnormal myeloproliferation, as well as a variable risk of evolution into acute myeloid leukemia (AML). The nucleus is a highly organized organelle with several distinct domains where nuclear inositides localize to mediate essential cellular events. Nuclear inositides play a critical role in the modulation of erythropoiesis or myelopoiesis. Here, we briefly review the nuclear structure, the localization of inositides and their metabolic enzymes in subnuclear compartments, and the molecular aspects of nuclear inositides in MDS.
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20
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Durrant TN, Moore SF, Bayliss AL, Jiang Y, Aitken EW, Wilson MC, Heesom KJ, Hers I. Identification of PtdIns(3,4)P2 effectors in human platelets using quantitative proteomics. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158575. [DOI: 10.1016/j.bbalip.2019.158575] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 09/20/2019] [Accepted: 10/29/2019] [Indexed: 12/26/2022]
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21
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Jose GP, Gopan S, Bhattacharyya S, Pucadyil TJ. A facile, sensitive and quantitative membrane-binding assay for proteins. Traffic 2019; 21:297-305. [PMID: 31846132 DOI: 10.1111/tra.12719] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 01/07/2023]
Abstract
Soluble proteins that bind membranes function in numerous cellular pathways yet facile, sensitive and quantitative methods that complement and improve sensitivity of widely used liposomes-based assays remain unavailable. Here, we describe the utility of a photoactivable fluorescent lipid as a generic reporter of protein-membrane interactions. When incorporated into liposomes and exposed to ultraviolet (UV), proteins bound to liposomes become crosslinked with the fluorescent lipid and can be readily detected and quantitated by in-gel fluorescence analysis. This modification obviates the requirement for high-speed centrifugation spins common to most liposome-binding assays. We refer to this assay as Proximity-based Labeling of Membrane-Associated Proteins (PLiMAP).
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Affiliation(s)
- Gregor P Jose
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Shilpa Gopan
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Soumya Bhattacharyya
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Thomas J Pucadyil
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
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22
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Raghu P, Joseph A, Krishnan H, Singh P, Saha S. Phosphoinositides: Regulators of Nervous System Function in Health and Disease. Front Mol Neurosci 2019; 12:208. [PMID: 31507376 PMCID: PMC6716428 DOI: 10.3389/fnmol.2019.00208] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 08/07/2019] [Indexed: 12/11/2022] Open
Abstract
Phosphoinositides, the seven phosphorylated derivatives of phosphatidylinositol have emerged as regulators of key sub-cellular processes such as membrane transport, cytoskeletal function and plasma membrane signaling in eukaryotic cells. All of these processes are also present in the cells that constitute the nervous system of animals and in this setting too, these are likely to tune key aspects of cell biology in relation to the unique structure and function of neurons. Phosphoinositides metabolism and function are mediated by enzymes and proteins that are conserved in evolution, and analysis of knockouts of these in animal models implicate this signaling system in neural function. Most recently, with the advent of human genome analysis, mutations in genes encoding components of the phosphoinositide signaling pathway have been implicated in human diseases although the cell biological basis of disease phenotypes in many cases remains unclear. In this review we evaluate existing evidence for the involvement of phosphoinositide signaling in human nervous system diseases and discuss ways of enhancing our understanding of the role of this pathway in the human nervous system's function in health and disease.
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Affiliation(s)
- Padinjat Raghu
- National Centre for Biological Sciences-TIFR, Bengaluru, India
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23
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Nuclear Phosphoinositides-Versatile Regulators of Genome Functions. Cells 2019; 8:cells8070649. [PMID: 31261688 PMCID: PMC6678639 DOI: 10.3390/cells8070649] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/21/2019] [Accepted: 06/25/2019] [Indexed: 12/17/2022] Open
Abstract
The many functions of phosphoinositides in cytosolic signaling were extensively studied; however, their activities in the cell nucleus are much less clear. In this review, we summarize data about their nuclear localization and metabolism, and review the available literature on their involvements in chromatin remodeling, gene transcription, and RNA processing. We discuss the molecular mechanisms via which nuclear phosphoinositides, in particular phosphatidylinositol (4,5)-bisphosphate (PI(4,5)P2), modulate nuclear processes. We focus on PI(4,5)P2’s role in the modulation of RNA polymerase I activity, and functions of the nuclear lipid islets—recently described nucleoplasmic PI(4,5)P2-rich compartment involved in RNA polymerase II transcription. In conclusion, the high impact of the phosphoinositide–protein complexes on nuclear organization and genome functions is only now emerging and deserves further thorough studies.
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24
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Nuclear Phosphoinositides: Their Regulation and Roles in Nuclear Functions. Int J Mol Sci 2019; 20:ijms20122991. [PMID: 31248120 PMCID: PMC6627530 DOI: 10.3390/ijms20122991] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/22/2019] [Accepted: 06/17/2019] [Indexed: 12/29/2022] Open
Abstract
Polyphosphoinositides (PPIns) are a family of seven lipid messengers that regulate a vast array of signalling pathways to control cell proliferation, migration, survival and differentiation. PPIns are differentially present in various sub-cellular compartments and, through the recruitment and regulation of specific proteins, are key regulators of compartment identity and function. Phosphoinositides and the enzymes that synthesise and degrade them are also present in the nuclear membrane and in nuclear membraneless compartments such as nuclear speckles. Here we discuss how PPIns in the nucleus are modulated in response to external cues and how they function to control downstream signalling. Finally we suggest a role for nuclear PPIns in liquid phase separations that are involved in the formation of membraneless compartments within the nucleus.
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25
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Cholesterol transport through the peroxisome-ER membrane contacts tethered by PI(4,5)P 2 and extended synaptotagmins. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1117-1135. [PMID: 31144242 DOI: 10.1007/s11427-019-9569-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/20/2019] [Indexed: 10/26/2022]
Abstract
Most mammalian cells take up cholesterol from low-density lipoproteins (LDLs) via receptor-mediated endocytosis. After reaching lysosomes, LDL-derived cholesterol continues to transport to downstream organelles including the ER for specific structural and functional needs. Peroxisomes are recently found to receive cholesterol from lysosomes through lysosome-peroxisome membrane contacts. However, whether and how cholesterol is conveyed from peroxisomes to the ER remain unknown. Here, by combining high-resolution microscopic analyses and in vitro reconstitution of highly purified organelles or artificial liposomes, we demonstrate that peroxisomes form membrane contacts with the ER through the interaction between peroxisomal PI(4,5)P2 and ER-resident extended synaptotagmin-1, 2 and 3 (E-Syts). Depletion of peroxisomal PI(4,5)P2 or E-Syts markedly decreases peroxisome-ER membrane contacts and induces cholesterol accumulation in lysosomes. Furthermore, we show that cholesterol is delivered from 3H-labeled peroxisomes or PI(4,5)P2-containing liposomes to the ER in vitro, and that the presence of peroxisomes augments cholesterol transfer from lysosomes to the ER. Together, our study reveals a new cholesterol transport pathway along the lysosome-peroxisome-ER membrane contacts in the cell.
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Shami Shah A, Batrouni AG, Kim D, Punyala A, Cao W, Han C, Goldberg ML, Smolka MB, Baskin JM. PLEKHA4/kramer Attenuates Dishevelled Ubiquitination to Modulate Wnt and Planar Cell Polarity Signaling. Cell Rep 2019; 27:2157-2170.e8. [PMID: 31091453 PMCID: PMC6594551 DOI: 10.1016/j.celrep.2019.04.060] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 02/26/2019] [Accepted: 04/11/2019] [Indexed: 12/13/2022] Open
Abstract
Wnt signaling pathways direct key physiological decisions in development. Here, we establish a role for a pleckstrin homology domain-containing protein, PLEKHA4, as a modulator of signaling strength in Wnt-receiving cells. PLEKHA4 oligomerizes into clusters at PI(4,5)P2-rich regions of the plasma membrane and recruits the Cullin-3 (CUL3) E3 ubiquitin ligase substrate adaptor Kelch-like protein 12 (KLHL12) to these assemblies. This recruitment decreases CUL3-KLHL12-mediated polyubiquitination of Dishevelled, a central intermediate in canonical and non-canonical Wnt signaling. Knockdown of PLEKHA4 in mammalian cells demonstrates that PLEKHA4 positively regulates canonical and non-canonical Wnt signaling via these effects on the Dishevelled polyubiquitination machinery. In vivo knockout of the Drosophila melanogaster PLEKHA4 homolog, kramer, selectively affects the non-canonical, planar cell polarity (PCP) signaling pathway. We propose that PLEKHA4 tunes the sensitivities of cells toward the stimulation of Wnt or PCP signaling by sequestering a key E3 ligase adaptor controlling Dishevelled polyubiquitination within PI(4,5)P2-rich plasma membrane clusters.
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Affiliation(s)
- Adnan Shami Shah
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Alex G Batrouni
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Dongsung Kim
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Amith Punyala
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Wendy Cao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Chun Han
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Michael L Goldberg
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Marcus B Smolka
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
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Polyphosphoinositides in the nucleus: Roadmap of their effectors and mechanisms of interaction. Adv Biol Regul 2019; 72:7-21. [PMID: 31003946 DOI: 10.1016/j.jbior.2019.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 01/01/2023]
Abstract
Biomolecular interactions between proteins and polyphosphoinositides (PPIn) are essential in the regulation of the vast majority of cellular processes. Consequently, alteration of these interactions is implicated in the development of many diseases. PPIn are phosphorylated derivatives of phosphatidylinositol and consist of seven species with different phosphate combinations. PPIn signal by recruiting proteins via canonical domains or short polybasic motifs. Although their actions are predominantly documented on cytoplasmic membranes, six of the seven PPIn are present within the nucleus together with the PPIn kinases, phosphatases and phospholipases that regulate their turnover. Importantly, the contribution of nuclear PPIn in the regulation of nuclear processes has led to an increased recognition of their importance compared to their more accepted cytoplasmic roles. This review summarises our knowledge on the identification and functional characterisation of nuclear PPIn-effector proteins as well as their mode of interactions, which tend to favour polybasic motifs.
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Abstract
Polyphosphoinositides (PPIn) are essential signaling phospholipids that make remarkable contributions to the identity of all cellular membranes and signaling cascades in mammalian cells. They exert regulatory control over membrane homeostasis via selective interactions with cellular proteins at the membrane–cytoplasm interface. This review article briefly summarizes our current understanding of the key roles that PPIn play in orchestrating and regulating crucial electrical and chemical signaling events in mammalian neurons and the significant neuro-pathophysiological conditions that arise following alterations in their metabolism.
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Affiliation(s)
- Eamonn James Dickson
- Department Physiology and Membrane Biology, University of California, Davis, CA, 95616, USA
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29
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Hawse WF, Cattley RT. T cells transduce T-cell receptor signal strength by generating different phosphatidylinositols. J Biol Chem 2019; 294:4793-4805. [PMID: 30692200 DOI: 10.1074/jbc.ra118.006524] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/14/2019] [Indexed: 12/26/2022] Open
Abstract
T-cell receptor (TCR) signaling strength is a dominant factor regulating T-cell differentiation, thymic development, and cytokine signaling. The molecular mechanisms by which TCR signal strength is transduced to downstream signaling networks remains ill-defined. Using computational modeling, biochemical assays, and imaging flow cytometry, we found here that TCR signal strength differentially generates phosphatidylinositol species. Weak TCR signals generated elevated phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and reduced phosphatidylinositol (3,4,5)-trisphosphate (PIP3) levels, whereas strong TCR signals reduced PI(4,5)P2 and elevated PIP3 levels. A proteomics screen revealed that focal adhesion kinase bound PI(4,5)P2, biochemical assays disclosed that focal adhesion kinase is preferentially activated by weak TCR signals and is required for optimal Treg induction, and further biochemical experiments revealed how TCR signaling strength regulates AKT activation. Low PIP3 levels generated by weak TCR signals were sufficient to activate phosphoinositide-dependent kinase-1 to phosphorylate AKT on Thr-308 but insufficient to activate mTOR complex 2 (mTORC2), whereas elevated PIP3 levels generated by a strong TCR signal were required to activate mTORC2 to phosphorylate Ser-473 on AKT. Our results provide support for a model that links TCR signaling to mTORC2 activation via phosphoinositide 3-kinase signaling. Together, the findings in this work establish that T cells measure TCR signal strength by generating different levels of phosphatidylinositol species that engage alternate signaling networks to control cell fate decisions.
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Affiliation(s)
- William F Hawse
- From the Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
| | - Richard T Cattley
- From the Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
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Bucki R, Wang YH, Yang C, Kandy SK, Fatunmbi O, Bradley R, Pogoda K, Svitkina T, Radhakrishnan R, Janmey PA. Lateral distribution of phosphatidylinositol 4,5-bisphosphate in membranes regulates formin- and ARP2/3-mediated actin nucleation. J Biol Chem 2019; 294:4704-4722. [PMID: 30692198 DOI: 10.1074/jbc.ra118.005552] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/13/2019] [Indexed: 11/06/2022] Open
Abstract
Spatial and temporal control of actin polymerization is fundamental for many cellular processes, including cell migration, division, vesicle trafficking, and response to agonists. Many actin-regulatory proteins interact with phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and are either activated or inactivated by local PI(4,5)P2 concentrations that form transiently at the cytoplasmic face of cell membranes. The molecular mechanisms of these interactions and how the dozens of PI(4,5)P2-sensitive actin-binding proteins are selectively recruited to membrane PI(4,5)P2 pools remains undefined. Using a combination of biochemical, imaging, and cell biologic studies, combined with molecular dynamics and analytical theory, we test the hypothesis that the lateral distribution of PI(4,5)P2 within lipid membranes and native plasma membranes alters the capacity of PI(4,5)P2 to nucleate actin assembly in brain and neutrophil extracts and show that activities of formins and the Arp2/3 complex respond to PI(4,5)P2 lateral distribution. Simulations and analytical theory show that cholesterol promotes the cooperative interaction of formins with multiple PI(4,5)P2 headgroups in the membrane to initiate actin nucleation. Masking PI(4,5)P2 with neomycin or disrupting PI(4,5)P2 domains in the plasma membrane by removing cholesterol decreases the ability of these membranes to nucleate actin assembly in cytoplasmic extracts.
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Affiliation(s)
- Robert Bucki
- From the Departments of Physiology, .,the Department of Microbiological and Nanobiomedical Engineering, Medical University of Białystok, 15-089 Białystok, Poland
| | - Yu-Hsiu Wang
- Chemistry.,the Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | | | - Sreeja Kutti Kandy
- Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Ololade Fatunmbi
- Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Ryan Bradley
- Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Katarzyna Pogoda
- From the Departments of Physiology.,the Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland, and
| | | | - Ravi Radhakrishnan
- Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Paul A Janmey
- From the Departments of Physiology.,the Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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31
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Understanding phosphoinositides: rare, dynamic, and essential membrane phospholipids. Biochem J 2019; 476:1-23. [PMID: 30617162 DOI: 10.1042/bcj20180022] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/03/2018] [Accepted: 12/07/2018] [Indexed: 12/15/2022]
Abstract
Polyphosphoinositides (PPIs) are essential phospholipids located in the cytoplasmic leaflet of eukaryotic cell membranes. Despite contributing only a small fraction to the bulk of cellular phospholipids, they make remarkable contributions to practically all aspects of a cell's life and death. They do so by recruiting cytoplasmic proteins/effectors or by interacting with cytoplasmic domains of membrane proteins at the membrane-cytoplasm interface to organize and mold organelle identity. The present study summarizes aspects of our current understanding concerning the metabolism, manipulation, measurement, and intimate roles these lipids play in regulating membrane homeostasis and vital cell signaling reactions in health and disease.
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Pemberton JG, Balla T. Polyphosphoinositide-Binding Domains: Insights from Peripheral Membrane and Lipid-Transfer Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1111:77-137. [PMID: 30483964 DOI: 10.1007/5584_2018_288] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Within eukaryotic cells, biochemical reactions need to be organized on the surface of membrane compartments that use distinct lipid constituents to dynamically modulate the functions of integral proteins or influence the selective recruitment of peripheral membrane effectors. As a result of these complex interactions, a variety of human pathologies can be traced back to improper communication between proteins and membrane surfaces; either due to mutations that directly alter protein structure or as a result of changes in membrane lipid composition. Among the known structural lipids found in cellular membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the membrane-anchored precursor of low-abundance regulatory lipids, the polyphosphoinositides (PPIn), which have restricted distributions within specific subcellular compartments. The ability of PPIn lipids to function as signaling platforms relies on both non-specific electrostatic interactions and the selective stereospecific recognition of PPIn headgroups by specialized protein folds. In this chapter, we will attempt to summarize the structural diversity of modular PPIn-interacting domains that facilitate the reversible recruitment and conformational regulation of peripheral membrane proteins. Outside of protein folds capable of capturing PPIn headgroups at the membrane interface, recent studies detailing the selective binding and bilayer extraction of PPIn species by unique functional domains within specific families of lipid-transfer proteins will also be highlighted. Overall, this overview will help to outline the fundamental physiochemical mechanisms that facilitate localized interactions between PPIn lipids and the wide-variety of PPIn-binding proteins that are essential for the coordinate regulation of cellular metabolism and membrane dynamics.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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Sztacho M, Sobol M, Balaban C, Escudeiro Lopes SE, Hozák P. Nuclear phosphoinositides and phase separation: Important players in nuclear compartmentalization. Adv Biol Regul 2018; 71:111-117. [PMID: 30249540 DOI: 10.1016/j.jbior.2018.09.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/14/2018] [Accepted: 09/15/2018] [Indexed: 02/08/2023]
Abstract
Nuclear phosphoinositides are recognized as regulators of many nuclear processes including chromatin remodeling, splicing, transcription, DNA repair and epigenetics. These processes are spatially organized in different nuclear compartments. Phase separation is involved in the formation of various nuclear compartments and molecular condensates separated from surrounding environment. The surface of such structures spatiotemporally coordinates formation of protein complexes. PI(4,5)P2 (PIP2) integration into phase-separated structures might provide an additional step in their spatial diversification by attracting certain proteins with affinity to PIP2. Our laboratory has recently identified novel membrane-free PIP2-containing structures, so called Nuclear Lipid Islets (NLIs). We provide an evidence that these structures are evolutionary conserved in different organisms. We hypothesize that NLIs serve as a scaffolding platform which facilitates the formation of transcription factories, thus participating in the formation of nuclear architecture competent for transcription. In this review we speculate on a possible role of NLIs in the integration of various processes linked to RNAPII transcription, chromatin remodeling, actin-myosin interaction, alternative splicing and lamin structures.
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Affiliation(s)
- Martin Sztacho
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic
| | - Margarita Sobol
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic
| | - Can Balaban
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic
| | - Sara Eliana Escudeiro Lopes
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic; Department of Epigenetics of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., division BIOCEV, 25250, Vestec, Czech Republic; Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic.
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Ulicna L, Rohozkova J, Hozak P. Multiple Aspects of PIP2 Involvement in C. elegans Gametogenesis. Int J Mol Sci 2018; 19:ijms19092679. [PMID: 30201859 PMCID: PMC6163852 DOI: 10.3390/ijms19092679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/28/2018] [Accepted: 09/05/2018] [Indexed: 12/20/2022] Open
Abstract
One of the most studied phosphoinositides is phosphatidylinositol 4,5-bisphosphate (PIP2), which localizes to the plasma membrane, nuclear speckles, small foci in the nucleoplasm, and to the nucleolus in mammalian cells. Here, we show that PIP2 also localizes to the nucleus in prophase I, during the gametogenesis of C. elegans hermaphrodite. The depletion of PIP2 by type I PIP kinase (PPK-1) kinase RNA interference results in an altered chromosome structure and leads to various defects during meiotic progression. We observed a decreased brood size and aneuploidy in progeny, defects in synapsis, and crossover formation. The altered chromosome structure is reflected in the increased transcription activity of a tightly regulated process in prophase I. To elucidate the involvement of PIP2 in the processes during the C. elegans development, we identified the PIP2-binding partners, leucine-rich repeat (LRR-1) protein and proteasome subunit beta 4 (PBS-4), pointing to its involvement in the ubiquitin–proteasome pathway.
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Affiliation(s)
- Livia Ulicna
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prague 142 20, Czech Republic.
| | - Jana Rohozkova
- Department of Epigenetics of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Division BIOCEV, Vestec 252 50, Czech Republic.
| | - Pavel Hozak
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prague 142 20, Czech Republic.
- Department of Epigenetics of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Division BIOCEV, Vestec 252 50, Czech Republic.
- Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., Prague 142 20, Czech Republic.
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35
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Phospholipids and inositol phosphates linked to the epigenome. Histochem Cell Biol 2018; 150:245-253. [DOI: 10.1007/s00418-018-1690-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2018] [Indexed: 12/17/2022]
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Cestari I, Anupama A, Stuart K. Inositol polyphosphate multikinase regulation of Trypanosoma brucei life stage development. Mol Biol Cell 2018. [PMID: 29514930 PMCID: PMC5921579 DOI: 10.1091/mbc.e17-08-0515] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The regulation of Trypanosoma brucei life stage development remains unclear. Inositol polyphosphate multikinase regulates the development of mammalian bloodforms to insect stages that normally develop in flies. Specific inositol phosphates, perhaps as second messengers, interact with proteins of the regulatory network that controls development. Many cellular processes change during the Trypanosoma brucei life cycle as this parasite alternates between the mammalian host and tsetse fly vector. We show that the inositol phosphate pathway helps regulate these developmental changes. Knockdown of inositol polyphosphate multikinase (IPMK), which phosphorylates Ins(1,4,5)P3 and Ins(1,3,4,5)P4, resulted in changes in bloodstream forms that are characteristic of insect stage procyclic forms. These changes include expression of the procyclic surface coat, up-regulation of RNA-binding proteins that we show to regulate stage-specific transcripts, and activation of oxidative phosphorylation with increased ATP production in bloodstream forms. These changes were accompanied by development of procyclic morphology, which also occurred by the expression of a catalytically inactive IPMK, implying that regulation of these processes entails IPMK activity. Proteins involved in signaling, protein synthesis and turnover, and metabolism were affinity-enriched with the IPMK substrate or product. Developmental changes associated with IPMK knockdown or catalytic inactivation reflected processes that are enriched with inositol phosphates, and chemical and genetic perturbation of these processes affected T. brucei development. Hence, IPMK helps regulate T. brucei development, perhaps by affecting inositol phosphate interactions with proteins of the regulatory network that controls energy metabolism and development.
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Affiliation(s)
- Igor Cestari
- Center for Infectious Disease Research, Seattle, WA 98109
| | - Atashi Anupama
- Center for Infectious Disease Research, Seattle, WA 98109
| | - Kenneth Stuart
- Center for Infectious Disease Research, Seattle, WA 98109.,Department of Global Health, University of Washington, Seattle, WA 98195
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PIP2 epigenetically represses rRNA genes transcription interacting with PHF8. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:266-275. [DOI: 10.1016/j.bbalip.2017.12.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/05/2017] [Accepted: 12/09/2017] [Indexed: 02/01/2023]
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DNA damage causes rapid accumulation of phosphoinositides for ATR signaling. Nat Commun 2017; 8:2118. [PMID: 29242514 PMCID: PMC5730617 DOI: 10.1038/s41467-017-01805-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 10/13/2017] [Indexed: 12/11/2022] Open
Abstract
Phosphoinositide lipids (PPIs) are enriched in the nucleus and are accumulated at DNA damage sites. Here, we investigate roles of nuclear PPIs in DNA damage response by sequestering specific PPIs with the expression of nuclear-targeted PH domains, which inhibits recruitment of Ataxia telangiectasia and Rad3-related protein (ATR) and reduces activation of Chk1. PPI-binding domains rapidly (< 1 s) accumulate at damage sites with local enrichment of PPIs. Accumulation of PIP3 in complex with the nuclear receptor protein, SF1, at damage sites requires phosphorylation by inositol polyphosphate multikinase (IPMK) and promotes nuclear actin assembly that is required for ATR recruitment. Suppressed ATR recruitment/activation is confirmed with latrunculin A and wortmannin treatment as well as IPMK or SF1 depletion. Other DNA repair pathways involving ATM and DNA-PKcs are unaffected by PPI sequestration. Together, these findings reveal that nuclear PPI metabolism mediates an early damage response through the IPMK-dependent pathway to specifically recruit ATR. Phosphoinositides are enriched in the nucleus and accumulate upon DNA damage but their role in responding to DNA damage is poorly defined. Here, the authors show that phosphoinositides rapidly accumulate at DNA damage sites and are required for ATR recruitment and subsequent Chk1 activation.
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Baranov MV, Revelo NH, Dingjan I, Maraspini R, Ter Beest M, Honigmann A, van den Bogaart G. SWAP70 Organizes the Actin Cytoskeleton and Is Essential for Phagocytosis. Cell Rep 2017; 17:1518-1531. [PMID: 27806292 PMCID: PMC5149533 DOI: 10.1016/j.celrep.2016.10.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/05/2016] [Accepted: 10/06/2016] [Indexed: 10/25/2022] Open
Abstract
Actin plays a critical role during the early stages of pathogenic microbe internalization by immune cells. In this study, we identified a key mechanism of actin filament tethering and stabilization to the surface of phagosomes in human dendritic cells. We found that the actin-binding protein SWAP70 is specifically recruited to nascent phagosomes by binding to the lipid phosphatidylinositol (3,4)-bisphosphate. Multi-color super-resolution stimulated emission depletion (STED) microscopy revealed that the actin cage surrounding early phagosomes is formed by multiple concentric rings containing SWAP70. SWAP70 colocalized with and stimulated activation of RAC1, a known activator of actin polymerization, on phagosomes. Genetic ablation of SWAP70 impaired actin polymerization around phagosomes and resulted in a phagocytic defect. These data show a key role for SWAP70 as a scaffold for tethering the peripheral actin cage to phagosomes.
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Affiliation(s)
- Maksim V Baranov
- Department of Tumor Immunology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28, 6525GA Nijmegen, the Netherlands
| | - Natalia H Revelo
- Department of Tumor Immunology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28, 6525GA Nijmegen, the Netherlands
| | - Ilse Dingjan
- Department of Tumor Immunology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28, 6525GA Nijmegen, the Netherlands
| | - Riccardo Maraspini
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Martin Ter Beest
- Department of Tumor Immunology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28, 6525GA Nijmegen, the Netherlands
| | - Alf Honigmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Geert van den Bogaart
- Department of Tumor Immunology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28, 6525GA Nijmegen, the Netherlands.
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40
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Hosp F, Mann M. A Primer on Concepts and Applications of Proteomics in Neuroscience. Neuron 2017; 96:558-571. [DOI: 10.1016/j.neuron.2017.09.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/29/2017] [Accepted: 09/14/2017] [Indexed: 02/06/2023]
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41
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Choy CH, Han BK, Botelho RJ. Phosphoinositide Diversity, Distribution, and Effector Function: Stepping Out of the Box. Bioessays 2017; 39. [PMID: 28977683 DOI: 10.1002/bies.201700121] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/31/2017] [Indexed: 12/26/2022]
Abstract
Phosphoinositides (PtdInsPs) modulate a plethora of functions including signal transduction and membrane trafficking. PtdInsPs are thought to consist of seven interconvertible species that localize to a specific organelle, to which they recruit a set of cognate effector proteins. Here, in reviewing the literature, we argue that this model needs revision. First, PtdInsPs can carry a variety of acyl chains, greatly boosting their molecular diversity. Second, PtdInsPs are more promiscuous in their localization than is usually acknowledged. Third, PtdInsP interconversion is likely achieved through kinase-phosphatase enzyme complexes that coordinate their activities and channel substrates without affecting bulk substrate population. Additionally, we contend that despite hundreds of PtdInsP effectors, our attention is biased toward few proteins. Lastly, we recognize that PtdInsPs can act to nucleate coincidence detection at the effector level, as in PDK1 and Akt. Overall, better integrated models of PtdInsP regulation and function are not only possible but needed.
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Affiliation(s)
- Christopher H Choy
- Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada M5B2K3.,Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada M5B2K3
| | - Bong-Kwan Han
- The Intelligent Synthetic Biology Center, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Roberto J Botelho
- Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada M5B2K3.,Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada M5B2K3
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Wood MN, Ishiyama N, Singaram I, Chung CM, Flozak AS, Yemelyanov A, Ikura M, Cho W, Gottardi CJ. α-Catenin homodimers are recruited to phosphoinositide-activated membranes to promote adhesion. J Cell Biol 2017; 216:3767-3783. [PMID: 28874417 PMCID: PMC5674881 DOI: 10.1083/jcb.201612006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/22/2017] [Accepted: 07/28/2017] [Indexed: 11/22/2022] Open
Abstract
A unique feature of α-catenin localized outside the cadherin-catenin complex is its capacity to form homodimers, but the subcellular localization and functions of this form of α-catenin remain incompletely understood. We identified a cadherin-free form of α-catenin that is recruited to the leading edge of migrating cells in a phosphatidylinositol 3-kinase-dependent manner. Surface plasmon resonance analysis shows that α-catenin homodimers, but not monomers, selectively bind phosphatidylinositol-3,4,5-trisphosphate-containing lipid vesicles with high affinity, where three basic residues, K488, K493, and R496, contribute to binding. Chemical-induced dimerization of α-catenin containing a synthetic dimerization domain promotes its accumulation within lamellipodia and elaboration of protrusions with extended filopodia, which are attenuated in the α-cateninKKR<3A mutant. Cells restored with a full-length, natively homodimerizing form of α-cateninKKR<3A display reduced membrane recruitment, altered epithelial sheet migrations, and weaker cell-cell adhesion compared with WT α-catenin. These findings show that α-catenin homodimers are recruited to phosphoinositide-activated membranes to promote adhesion and migration, suggesting that phosphoinositide binding may be a defining feature of α-catenin function outside the cadherin-catenin complex.
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Affiliation(s)
- Megan N Wood
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL.,The Driskill Graduate Training Program in Life Sciences, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Noboru Ishiyama
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Indira Singaram
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL
| | - Connie M Chung
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Annette S Flozak
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Alex Yemelyanov
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL.,Department of Chemistry of Life Processes, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Mitsu Ikura
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada.,Division of Signaling Biology, Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada
| | - Wonhwa Cho
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL.,Department of Genetic Engineering, Kyung Hee University, Yongin, Republic of Korea
| | - Cara J Gottardi
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL .,Department of Cellular and Molecular Biology, Northwestern University, Feinberg School of Medicine, Chicago, IL
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43
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Prostate cancer, PI3K, PTEN and prognosis. Clin Sci (Lond) 2017; 131:197-210. [PMID: 28057891 DOI: 10.1042/cs20160026] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 11/12/2016] [Accepted: 11/21/2016] [Indexed: 12/22/2022]
Abstract
Loss of function of the PTEN tumour suppressor, resulting in dysregulated activation of the phosphoinositide 3-kinase (PI3K) signalling network, is recognized as one of the most common driving events in prostate cancer development. The observed mechanisms of PTEN loss are diverse, but both homozygous and heterozygous genomic deletions including PTEN are frequent, and often accompanied by loss of detectable protein as assessed by immunohistochemistry (IHC). The occurrence of PTEN loss is highest in aggressive metastatic disease and this has driven the development of PTEN as a prognostic biomarker, either alone or in combination with other factors, to distinguish indolent tumours from those likely to progress. Here, we discuss these factors and the consequences of PTEN loss, in the context of its role as a lipid phosphatase, as well as current efforts to use available inhibitors of specific components of the PI3K/PTEN/TOR signalling network in prostate cancer treatment.
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In-depth PtdIns(3,4,5)P 3 signalosome analysis identifies DAPP1 as a negative regulator of GPVI-driven platelet function. Blood Adv 2017; 1:918-932. [PMID: 29242851 DOI: 10.1182/bloodadvances.2017005173] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The class I phosphoinositide 3-kinase (PI3K) isoforms play important roles in platelet priming, activation, and stable thrombus formation. Class I PI3Ks predominantly regulate cell function through their catalytic product, the signaling phospholipid phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P3], which coordinates the localization and/or activity of a diverse range of binding proteins. Notably, the complete repertoire of these class I PI3K effectors in platelets remains unknown, limiting mechanistic understanding of class I PI3K-mediated control of platelet function. We measured robust agonist-driven PtdIns (3,4,5)P3 generation in human platelets by lipidomic mass spectrometry (MS), and then used affinity-capture coupled to high-resolution proteomic MS to identify the targets of PtdIns (3,4,5)P3 in these cells. We reveal for the first time a diverse platelet PtdIns(3,4,5)P3 interactome, including kinases, signaling adaptors, and regulators of small GTPases, many of which are previously uncharacterized in this cell type. Of these, we show dual adaptor for phosphotyrosine and 3-phosphoinositides (DAPP1) to be regulated by Src-family kinases and PI3K, while platelets from DAPP1-deficient mice display enhanced thrombus formation on collagen in vitro. This was associated with enhanced platelet α/δ granule secretion and αIIbβ3 integrin activation downstream of the collagen receptor glycoprotein VI. Thus, we present the first comprehensive analysis of the PtdIns(3,4,5)P3 signalosome of human platelets and identify DAPP1 as a novel negative regulator of platelet function. This work provides important new insights into how class I PI3Ks shape platelet function.
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Marat AL, Wallroth A, Lo WT, Müller R, Norata GD, Falasca M, Schultz C, Haucke V. mTORC1 activity repression by late endosomal phosphatidylinositol 3,4-bisphosphate. Science 2017; 356:968-972. [DOI: 10.1126/science.aaf8310] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 11/22/2016] [Accepted: 05/08/2017] [Indexed: 12/15/2022]
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Gulluni F, Martini M, Hirsch E. Cytokinetic Abscission: Phosphoinositides and ESCRT
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Direct the Final Cut. J Cell Biochem 2017; 118:3561-3568. [DOI: 10.1002/jcb.26066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 04/14/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Federico Gulluni
- Department of Molecular Biotechnology and Health SciencesUniversity of TurinTurinItaly
| | - Miriam Martini
- Department of Molecular Biotechnology and Health SciencesUniversity of TurinTurinItaly
| | - Emilio Hirsch
- Department of Molecular Biotechnology and Health SciencesUniversity of TurinTurinItaly
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Inositol polyphosphates intersect with signaling and metabolic networks via two distinct mechanisms. Proc Natl Acad Sci U S A 2016; 113:E6757-E6765. [PMID: 27791083 DOI: 10.1073/pnas.1606853113] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Inositol-based signaling molecules are central eukaryotic messengers and include the highly phosphorylated, diffusible inositol polyphosphates (InsPs) and inositol pyrophosphates (PP-InsPs). Despite the essential cellular regulatory functions of InsPs and PP-InsPs (including telomere maintenance, phosphate sensing, cell migration, and insulin secretion), the majority of their protein targets remain unknown. Here, the development of InsP and PP-InsP affinity reagents is described to comprehensively annotate the interactome of these messenger molecules. By using the reagents as bait, >150 putative protein targets were discovered from a eukaryotic cell lysate (Saccharomyces cerevisiae). Gene Ontology analysis of the binding partners revealed a significant overrepresentation of proteins involved in nucleotide metabolism, glucose metabolism, ribosome biogenesis, and phosphorylation-based signal transduction pathways. Notably, we isolated and characterized additional substrates of protein pyrophosphorylation, a unique posttranslational modification mediated by the PP-InsPs. Our findings not only demonstrate that the PP-InsPs provide a central line of communication between signaling and metabolic networks, but also highlight the unusual ability of these molecules to access two distinct modes of action.
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48
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Ceccato L, Chicanne G, Nahoum V, Pons V, Payrastre B, Gaits-Iacovoni F, Viaud J. PLIF: A rapid, accurate method to detect and quantitatively assess protein-lipid interactions. Sci Signal 2016; 9:rs2. [PMID: 27025878 DOI: 10.1126/scisignal.aad4337] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Phosphoinositides are a type of cellular phospholipid that regulate signaling in a wide range of cellular and physiological processes through the interaction between their phosphorylated inositol head group and specific domains in various cytosolic proteins. These lipids also influence the activity of transmembrane proteins. Aberrant phosphoinositide signaling is associated with numerous diseases, including cancer, obesity, and diabetes. Thus, identifying phosphoinositide-binding partners and the aspects that define their specificity can direct drug development. However, current methods are costly, time-consuming, or technically challenging and inaccessible to many laboratories. We developed a method called PLIF (for "protein-lipid interaction by fluorescence") that uses fluorescently labeled liposomes and tethered, tagged proteins or peptides to enable fast and reliable determination of protein domain specificity for given phosphoinositides in a membrane environment. We validated PLIF against previously known phosphoinositide-binding partners for various proteins and obtained relative affinity profiles. Moreover, PLIF analysis of the sorting nexin (SNX) family revealed not only that SNXs bound most strongly to phosphatidylinositol 3-phosphate (PtdIns3P or PI3P), which is known from analysis with other methods, but also that they interacted with other phosphoinositides, which had not previously been detected using other techniques. Different phosphoinositide partners, even those with relatively weak binding affinity, could account for the diverse functions of SNXs in vesicular trafficking and protein sorting. Because PLIF is sensitive, semiquantitative, and performed in a high-throughput manner, it may be used to screen for highly specific protein-lipid interaction inhibitors.
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Affiliation(s)
- Laurie Ceccato
- INSERM, U1048 and Université Toulouse 3, I2MC, Avenue Jean Poulhès BP84225, 31432 Toulouse Cedex 04, France
| | - Gaëtan Chicanne
- INSERM, U1048 and Université Toulouse 3, I2MC, Avenue Jean Poulhès BP84225, 31432 Toulouse Cedex 04, France
| | - Virginie Nahoum
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS), 31000 Toulouse, France. Université de Toulouse, UPS (Université Paul Sabatier), IPBS, 31000 Toulouse, France
| | - Véronique Pons
- INSERM, U1048 and Université Toulouse 3, I2MC, Avenue Jean Poulhès BP84225, 31432 Toulouse Cedex 04, France
| | - Bernard Payrastre
- INSERM, U1048 and Université Toulouse 3, I2MC, Avenue Jean Poulhès BP84225, 31432 Toulouse Cedex 04, France. CHU (Centre Hospitalier Universitaire) de Toulouse, Laboratoire d'Hématologie, 31059 Toulouse Cedex 03, France
| | - Frédérique Gaits-Iacovoni
- INSERM, U1048 and Université Toulouse 3, I2MC, Avenue Jean Poulhès BP84225, 31432 Toulouse Cedex 04, France
| | - Julien Viaud
- INSERM, U1048 and Université Toulouse 3, I2MC, Avenue Jean Poulhès BP84225, 31432 Toulouse Cedex 04, France.
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Marat AL, Haucke V. Phosphatidylinositol 3-phosphates-at the interface between cell signalling and membrane traffic. EMBO J 2016; 35:561-79. [PMID: 26888746 DOI: 10.15252/embj.201593564] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 01/26/2016] [Indexed: 12/31/2022] Open
Abstract
Phosphoinositides (PIs) form a minor class of phospholipids with crucial functions in cell physiology, ranging from cell signalling and motility to a role as signposts of compartmental membrane identity. Phosphatidylinositol 3-phosphates are present at the plasma membrane and within the endolysosomal system, where they serve as key regulators of both cell signalling and of intracellular membrane traffic. Here, we provide an overview of the metabolic pathways that regulate cellular synthesis of PI 3-phosphates at distinct intracellular sites and discuss the mechanisms by which these lipids regulate cell signalling and membrane traffic. Finally, we provide a framework for how PI 3-phosphate metabolism is integrated into the cellular network.
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Affiliation(s)
- Andrea L Marat
- Leibniz Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Volker Haucke
- Leibniz Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
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50
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Tools for visualization of phosphoinositides in the cell nucleus. Histochem Cell Biol 2016; 145:485-96. [DOI: 10.1007/s00418-016-1409-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2016] [Indexed: 01/09/2023]
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