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Wen T, Chen M, Cryns VL, Anderson RA. Regulation of the poly(A) Polymerase Star-PAP by a Nuclear Phosphoinositide Signalosome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601467. [PMID: 39005346 PMCID: PMC11244925 DOI: 10.1101/2024.07.01.601467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Star-PAP is a noncanonical poly(A) polymerase that controls gene expression. Star-PAP was previously reported to bind the phosphatidylinositol 4-phosphate 5-kinase PIPKI⍺ and its product phosphatidylinositol 4,5-bisphosphate, which regulate Star-PAP poly(A) polymerase activity and expression of specific genes. Recent studies have revealed a nuclear PI signaling pathway in which the PI transfer proteins PITP⍺/β, PI kinases and phosphatases bind p53 to sequentially modify protein-linked phosphatidylinositol phosphates and regulate its function. Here we demonstrate that multiple phosphoinositides, including phosphatidylinositol 4-monophosphate and phosphatidylinositol 3,4,5-trisphosphate are also coupled to Star-PAP in response to stress. This is initiated by PITP⍺/β binding to Star-PAP, while the Star-PAP-linked phosphoinositides are modified by PI4KII⍺, PIPKI⍺, IPMK, and PTEN recruited to Star- PAP. The phosphoinositide coupling enhances the association of the small heat shock proteins HSP27/⍺B-crystallin with Star-PAP. Knockdown of the PITPs, kinases, or HSP27 reduce the expression of Star-PAP targets. Our results demonstrate that the PITPs generate Star-PAP-PIPn complexes that are then modified by PI kinases/phosphatases and small heat shock proteins that regulate the linked phosphoinositide phosphorylation and Star-PAP activity in response to stress.
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Hoboth P, Sztacho M, Hozák P. Nuclear patterns of phosphatidylinositol 4,5- and 3,4-bisphosphate revealed by super-resolution microscopy differ between the consecutive stages of RNA polymerase II transcription. FEBS J 2024. [PMID: 38734927 DOI: 10.1111/febs.17136] [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: 08/09/2023] [Revised: 12/12/2023] [Accepted: 04/05/2024] [Indexed: 05/13/2024]
Abstract
Phosphatidylinositol phosphates are powerful signaling molecules that orchestrate signaling and direct membrane trafficking in the cytosol. Interestingly, phosphatidylinositol phosphates also localize within the membrane-less compartments of the cell nucleus, where they participate in the regulation of gene expression. Nevertheless, current models of gene expression, which include condensates of proteins and nucleic acids, do not include nuclear phosphatidylinositol phosphates. This gap is partly a result of the missing detailed analysis of the subnuclear distribution of phosphatidylinositol phosphates and their relationships with gene expression. Here, we used quantitative dual-color direct stochastic optical reconstruction microscopy to analyze the nanoscale co-patterning between RNA polymerase II transcription initiation and elongation markers with respect to phosphatidylinositol 4,5- or 3,4-bisphosphate in the nucleoplasm and nuclear speckles and compared it with randomized data and cells with inhibited transcription. We found specific co-patterning of the transcription initiation marker P-S5 with phosphatidylinositol 4,5-bisphosphate in the nucleoplasm and with phosphatidylinositol 3,4-bisphosphate at the periphery of nuclear speckles. We showed the specific accumulation of the transcription elongation marker PS-2 and of nascent RNA in the proximity of phosphatidylinositol 3,4-bisphosphate associated with nuclear speckles. Taken together, this shows that the distinct spatial associations between the consecutive stages of RNA polymerase II transcription and nuclear phosphatidylinositol phosphates exhibit specificity within the gene expression compartments. Thus, in analogy to the cellular membranes, where phospholipid composition orchestrates signaling pathways and directs membrane trafficking, we propose a model in which the phospholipid identity of gene expression compartments orchestrates RNA polymerase II transcription.
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Affiliation(s)
- Peter Hoboth
- Laboratory of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Viničná Microscopy Core Facility, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Sztacho
- Laboratory of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Laboratory of Cancer Cell Architecture, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Pavel Hozák
- Laboratory of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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Carrillo ND, Chen M, Wen T, Awasthi P, Wolfe TJ, Cryns VL, Anderson RA. Lipid transfer proteins and a PI 4-kinase initiate nuclear phosphoinositide signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.08.539894. [PMID: 37214930 PMCID: PMC10197520 DOI: 10.1101/2023.05.08.539894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Phosphoinositide (PIP n ) messengers are present in non-membranous regions of nuclei, where they are assembled into a phosphatidylinositol (PI) 3-kinase (PI3K)/Akt pathway that is distinct from the cytosolic membrane-localized pathway. In the nuclear pathway, PI kinases/phosphatases bind the p53 tumor suppressor protein (wild-type and mutant) to generate p53-PIP n complexes that regulate Akt activation. However, this pathway is dependent on poorly characterized nuclear PIP n pools. Here we report that PI transfer proteins (PITPs), which transport PI between membranes to enable membrane-localized PIP n synthesis, accumulate in the nucleoplasm in response to stress and supply nuclear PIP n pools. PITPα/β and the PI 4-kinase PI4KIIα bind p53 and are required to generate p53-PI4P, which is further phosphorylated to synthesize p53-PIP n complexes that regulate nuclear Akt activation and stress-resistance. Remarkably, PITPα/β and PI4KIIα initiate PIP n -linkage to multiple proteins that are detectable by immunoblotting and [ 3 H] myo -inositol metabolic labeling and are resistant to denaturation, suggesting a posttranslational modification. In brief Phosphatidylinositol transfer proteins initiate the nuclear PIP n -linked protein network in membrane-free regions.
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Yao S, Kim SC, Li J, Tang S, Wang X. Phosphatidic acid signaling and function in nuclei. Prog Lipid Res 2024; 93:101267. [PMID: 38154743 PMCID: PMC10843600 DOI: 10.1016/j.plipres.2023.101267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 12/30/2023]
Abstract
Membrane lipidomes are dynamic and their changes generate lipid mediators affecting various biological processes. Phosphatidic acid (PA) has emerged as an important class of lipid mediators involved in a wide range of cellular and physiological responses in plants, animals, and microbes. The regulatory functions of PA have been studied primarily outside the nuclei, but an increasing number of recent studies indicates that some of the PA effects result from its action in nuclei. PA levels in nuclei are dynamic in response to stimuli. Changes in nuclear PA levels can result from activities of enzymes associated with nuclei and/or from movements of PA generated extranuclearly. PA has also been found to interact with proteins involved in nuclear functions, such as transcription factors and proteins undergoing nuclear translocation in response to stimuli. The nuclear action of PA affects various aspects of plant growth, development, and response to stress and environmental changes.
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Affiliation(s)
- Shuaibing Yao
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Sang-Chul Kim
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Jianwu Li
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Shan Tang
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Xuemin Wang
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
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Chi ES, Stivison EA, Blind RD. SF-1 Induces Nuclear PIP2. Biomolecules 2023; 13:1509. [PMID: 37892191 PMCID: PMC10604688 DOI: 10.3390/biom13101509] [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: 09/01/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
Metazoan cell nuclei contain non-membrane pools of the phosphoinositide lipid PI(4,5)P2 (PIP2), but how this hydrophobic lipid exists within the aqueous nucleoplasm remains unclear. Steroidogenic Factor-1 (NR5A1, SF-1) is a nuclear receptor that binds PIP2 in vitro, and a co-crystal structure of the complex suggests the acyl chains of PIP2 are hidden in the hydrophobic core of the SF-1 protein while the PIP2 headgroup is solvent-exposed. This binding mode explains how SF-1 can solubilize nuclear PIP2; however, cellular evidence that SF-1 expression associates with nuclear PIP2 has been lacking. Here, we examined if tetracycline induction of SF-1 expression would associate with nuclear accumulation of PIP2, using antibodies directed against the PIP2 headgroup. Indeed, tetracycline induction of wild-type SF-1 induced a signal in the nucleus of HEK cells that cross-reacts with PIP2 antibodies, but did not cross-react with antibodies against the lower abundance phosphoinositide PI(3,4,5)P3 (PIP3). The nuclear PIP2 signal co-localized with FLAG-tagged SF-1 in the nuclear compartment. To determine if the nuclear PIP2 signal was dependent on the ability of SF-1 to bind PIP2, we examined a "pocket mutant" of SF-1 (A270W, L345F) shown to be deficient in phospholipid binding by mass spectrometry. Tetracycline induction of this pocket mutant SF-1 in HEK cells failed to induce a detectable PIP2 antibody cross-reactive signal, despite similar Tet-induced expression levels of the wild-type and pocket mutant SF-1 proteins in these cells. Together, these data are the first to suggest that expression of SF-1 induces a PIP2 antibody cross-reactive signal in the nucleus, consistent with X-ray crystallographic and biochemical evidence suggesting SF-1 binds PIP2 in human cells.
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Affiliation(s)
| | | | - Raymond D. Blind
- Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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Hoboth P, Sztacho M, Quaas A, Akgül B, Hozák P. Quantitative super-resolution microscopy reveals the differences in the nanoscale distribution of nuclear phosphatidylinositol 4,5-bisphosphate in human healthy skin and skin warts. Front Cell Dev Biol 2023; 11:1217637. [PMID: 37484912 PMCID: PMC10361526 DOI: 10.3389/fcell.2023.1217637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/22/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction: Imaging of human clinical formalin-fixed paraffin-embedded (FFPE) tissue sections provides insights into healthy and diseased states and therefore represents a valuable resource for basic research, as well as for diagnostic and clinical purposes. However, conventional light microscopy does not allow to observe the molecular details of tissue and cell architecture due to the diffraction limit of light. Super-resolution microscopy overcomes this limitation and provides access to the nanoscale details of tissue and cell organization. Methods: Here, we used quantitative multicolor stimulated emission depletion (STED) nanoscopy to study the nanoscale distribution of the nuclear phosphatidylinositol 4,5-bisphosphate (nPI(4,5)P2) with respect to the nuclear speckles (NS) marker SON. Results: Increased nPI(4,5)P2 signals were previously linked to human papillomavirus (HPV)-mediated carcinogenesis, while NS-associated PI(4,5)P2 represents the largest pool of nPI(4,5)P2 visualized by staining and microscopy. The implementation of multicolor STED nanoscopy in human clinical FFPE skin and wart sections allowed us to provide here the quantitative evidence for higher levels of NS-associated PI(4,5)P2 in HPV-induced warts compared to control skin. Discussion: These data expand the previous reports of HPV-induced increase of nPI(4,5)P2 levels and reveal for the first time the functional, tissue-specific localization of nPI(4,5)P2 within NS in clinically relevant samples. Moreover, our approach is widely applicable to other human clinical FFPE tissues as an informative addition to the classical histochemistry.
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Affiliation(s)
- Peter Hoboth
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Martin Sztacho
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Alexander Quaas
- Institute of Pathology, Medical Faculty and University Hospital Cologne, Cologne, Germany
| | - Baki Akgül
- Institute of Virology, University of Cologne, Medical Faculty and University Hospital Cologne, Cologne, Germany
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
- Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
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Vidalle MC, Sheth B, Fazio A, Marvi MV, Leto S, Koufi FD, Neri I, Casalin I, Ramazzotti G, Follo MY, Ratti S, Manzoli L, Gehlot S, Divecha N, Fiume R. Nuclear Phosphoinositides as Key Determinants of Nuclear Functions. Biomolecules 2023; 13:1049. [PMID: 37509085 PMCID: PMC10377365 DOI: 10.3390/biom13071049] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Polyphosphoinositides (PPIns) are signalling messengers representing less than five per cent of the total phospholipid concentration within the cell. Despite their low concentration, these lipids are critical regulators of various cellular processes, including cell cycle, differentiation, gene transcription, apoptosis and motility. PPIns are generated by the phosphorylation of the inositol head group of phosphatidylinositol (PtdIns). Different pools of PPIns are found at distinct subcellular compartments, which are regulated by an array of kinases, phosphatases and phospholipases. Six of the seven PPIns species have been found in the nucleus, including the nuclear envelope, the nucleoplasm and the nucleolus. The identification and characterisation of PPIns interactor and effector proteins in the nucleus have led to increasing interest in the role of PPIns in nuclear signalling. However, the regulation and functions of PPIns in the nucleus are complex and are still being elucidated. This review summarises our current understanding of the localisation, biogenesis and physiological functions of the different PPIns species in the nucleus.
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Affiliation(s)
- Magdalena C Vidalle
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Bhavwanti Sheth
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Antonietta Fazio
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Maria Vittoria Marvi
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Stefano Leto
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Foteini-Dionysia Koufi
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Irene Neri
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Irene Casalin
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Giulia Ramazzotti
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Matilde Y Follo
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Stefano Ratti
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Lucia Manzoli
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Sonakshi Gehlot
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Nullin Divecha
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Roberta Fiume
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
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8
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Chen M, Choi S, Wen T, Chen C, Thapa N, Lee JH, Cryns VL, Anderson RA. A p53-phosphoinositide signalosome regulates nuclear AKT activation. Nat Cell Biol 2022; 24:1099-1113. [PMID: 35798843 PMCID: PMC9833102 DOI: 10.1038/s41556-022-00949-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 05/26/2022] [Indexed: 01/13/2023]
Abstract
The tumour suppressor p53 and PI3K-AKT pathways have fundamental roles in the regulation of cell growth and apoptosis, and are frequently mutated in cancer. Here, we show that genotoxic stress induces nuclear AKT activation through a p53-dependent mechanism that is distinct from the canonical membrane-localized PI3K-AKT pathway. Following genotoxic stress, a nuclear PI3K binds p53 in the non-membranous nucleoplasm to generate a complex of p53 and phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3), which recruits AKT, PDK1 and mTORC2 to activate AKT and phosphorylate FOXO proteins, thereby inhibiting DNA damage-induced apoptosis. Wild-type p53 activates nuclear AKT in an on/off fashion following stress, whereas mutant p53 dose-dependently stimulates high basal AKT activity. The p53-PtdIns(3,4,5)P3 complex is dephosphorylated to p53-phosphatidylinositol 4,5-bisphosphate by PTEN to inhibit AKT activation. The nuclear p53-phosphoinositide signalosome is distinct from the canonical membrane-localized pathway and insensitive to PI3K inhibitors currently in the clinic, which underscores its therapeutic relevance.
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Affiliation(s)
- Mo Chen
- University of Wisconsin-Madison, School of Medicine and Public Health; 1300 University Avenue, Madison, WI 53706, USA
| | - Suyong Choi
- University of Wisconsin-Madison, School of Medicine and Public Health; 1300 University Avenue, Madison, WI 53706, USA
| | - Tianmu Wen
- University of Wisconsin-Madison, School of Medicine and Public Health; 1300 University Avenue, Madison, WI 53706, USA
| | - Changliang Chen
- University of Wisconsin-Madison, School of Medicine and Public Health; 1300 University Avenue, Madison, WI 53706, USA,Department of Medicine, University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, School of Medicine and Public Health; 1111 Highland Avenue, Madison, WI 53705, USA
| | - Narendra Thapa
- University of Wisconsin-Madison, School of Medicine and Public Health; 1300 University Avenue, Madison, WI 53706, USA
| | - Jeong Hyo Lee
- University of Wisconsin-Madison, School of Medicine and Public Health; 1300 University Avenue, Madison, WI 53706, USA,Department of Medicine, University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, School of Medicine and Public Health; 1111 Highland Avenue, Madison, WI 53705, USA
| | - Vincent L. Cryns
- Department of Medicine, University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, School of Medicine and Public Health; 1111 Highland Avenue, Madison, WI 53705, USA,These authors contributed equally to this work,Correspondence: (R.A.A.); (V.L.C.)
| | - Richard A. Anderson
- University of Wisconsin-Madison, School of Medicine and Public Health; 1300 University Avenue, Madison, WI 53706, USA,These authors contributed equally to this work,Correspondence: (R.A.A.); (V.L.C.)
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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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10
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Maitra N, Hammer S, Kjerfve C, Bankaitis VA, Polymenis M. Translational control of lipogenesis links protein synthesis and phosphoinositide signaling with nuclear division in Saccharomyces cerevisiae. Genetics 2022; 220:iyab171. [PMID: 34849864 PMCID: PMC8733439 DOI: 10.1093/genetics/iyab171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/23/2021] [Indexed: 12/21/2022] Open
Abstract
Continuously dividing cells coordinate their growth and division. How fast cells grow in mass determines how fast they will multiply. Yet, there are few, if any, examples of a metabolic pathway that actively drives a cell cycle event instead of just being required for it. Here, we show that translational upregulation of lipogenic enzymes in Saccharomyces cerevisiae increased the abundance of lipids and promoted nuclear elongation and division. Derepressing translation of acetyl-CoA carboxylase and fatty acid synthase also suppressed cell cycle-related phenotypes, including delayed nuclear division, associated with Sec14p phosphatidylinositol transfer protein deficiencies, and the irregular nuclear morphologies of mutants defective in phosphatidylinositol 4-OH kinase activities. Our results show that increased lipogenesis drives a critical cell cycle landmark and report a phosphoinositide signaling axis in control of nuclear division. The broad conservation of these lipid metabolic and signaling pathways raises the possibility these activities similarly govern nuclear division in other eukaryotes.
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Affiliation(s)
- Nairita Maitra
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Staci Hammer
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Clara Kjerfve
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Vytas A Bankaitis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Molecular & Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX 77843, USA
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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11
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The basis of nuclear phospholipase C in cell proliferation. Adv Biol Regul 2021; 82:100834. [PMID: 34710785 DOI: 10.1016/j.jbior.2021.100834] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/17/2021] [Accepted: 10/21/2021] [Indexed: 11/23/2022]
Abstract
Ca2+ is a highly versatile intracellular signal that regulates many biological processes such as cell death and proliferation. Broad Ca2+-signaling machinery is used to assemble signaling systems with a precise spatial and temporal resolution to achieve this versatility. Ca2+-signaling components can be organized in different regions of the cell and local increases in Ca2+ within the nucleus can regulate different cellular functions from the increases in cytosolic Ca2+. However, the mechanisms and pathways that promote localized increases in Ca2+ levels in the nucleus are still under investigation. This review presents evidence that the nucleus has its own Ca2+ stores and signaling machinery, which modulate processes such as cell proliferation and tumor growth. We focus on what is known about the functions of nuclear Phospholipase C (PLC) in the generation of nuclear Ca2+ transients that are involved in cell proliferation.
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12
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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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Hoboth P, Sztacho M, Šebesta O, Schätz M, Castano E, Hozák P. Nanoscale mapping of nuclear phosphatidylinositol phosphate landscape by dual-color dSTORM. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158890. [PMID: 33513445 DOI: 10.1016/j.bbalip.2021.158890] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/10/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
Current models of gene expression, which are based on single-molecule localization microscopy, acknowledge protein clustering and the formation of transcriptional condensates as a driving force of gene expression. However, these models largely omit the role of nuclear lipids and amongst them nuclear phosphatidylinositol phosphates (PIPs) in particular. Moreover, the precise distribution of nuclear PIPs in the functional sub-nuclear domains remains elusive. The direct stochastic optical reconstruction microscopy (dSTORM) provides an unprecedented resolution in biological imaging. Therefore, its use for imaging in the densely crowded cell nucleus is desired but also challenging. Here we present a dual-color dSTORM imaging and image analysis of nuclear PI(4,5)P2, PI(3,4)P2 and PI(4)P distribution while preserving the context of nuclear architecture. In the nucleoplasm, PI(4,5)P2 and PI(3,4)P2 co-pattern in close proximity with the subset of RNA polymerase II foci. PI(4,5)P2 is surrounded by fibrillarin in the nucleoli and all three PIPs are dispersed within the matrix formed by the nuclear speckle protein SON. PI(4,5)P2 is the most abundant nuclear PIP, while PI(4)P is a precursor for the biosynthesis of PI(4,5)P2 and PI(3,4)P2. Therefore, our data are relevant for the understanding the roles of nuclear PIPs and provide further evidence for the model in which nuclear PIPs represent a localization signal for the formation of lipo-ribonucleoprotein hubs in the nucleus. The discussed experimental pipeline is applicable for further functional studies on the role of other nuclear PIPs in the regulation of gene expression and beyond.
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Affiliation(s)
- Peter Hoboth
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Martin Sztacho
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Ondřej Šebesta
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic
| | - Martin Schätz
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic
| | - Enrique Castano
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic; Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico
| | - 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; Department of Epigenetics of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, division BIOCEV, Průmyslová 595, 252 20 Vestec, Czech Republic; Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
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14
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Lete MG, Tripathi A, Chandran V, Bankaitis VA, McDermott MI. Lipid transfer proteins and instructive regulation of lipid kinase activities: Implications for inositol lipid signaling and disease. Adv Biol Regul 2020; 78:100740. [PMID: 32992233 PMCID: PMC7986245 DOI: 10.1016/j.jbior.2020.100740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/16/2020] [Accepted: 06/24/2020] [Indexed: 05/17/2023]
Abstract
Cellular membranes are critical platforms for intracellular signaling that involve complex interfaces between lipids and proteins, and a web of interactions between a multitude of lipid metabolic pathways. Membrane lipids impart structural and functional information in this regulatory circuit that encompass biophysical parameters such as membrane thickness and fluidity, as well as chaperoning the interactions of protein binding partners. Phosphatidylinositol and its phosphorylated derivatives, the phosphoinositides, play key roles in intracellular membrane signaling, and these involvements are translated into an impressively diverse set of biological outcomes. The phosphatidylinositol transfer proteins (PITPs) are key regulators of phosphoinositide signaling. Found in a diverse array of organisms from plants, yeast and apicomplexan parasites to mammals, PITPs were initially proposed to be simple transporters of lipids between intracellular membranes. It now appears increasingly unlikely that the soluble versions of these proteins perform such functions within the cell. Rather, these serve to facilitate the activity of intrinsically biologically insufficient inositol lipid kinases and, in so doing, promote diversification of the biological outcomes of phosphoinositide signaling. The central engine for execution of such functions is the lipid exchange cycle that is a fundamental property of PITPs. How PITPs execute lipid exchange remains very poorly understood. Molecular dynamics simulation approaches are now providing the first atomistic insights into how PITPs, and potentially other lipid-exchange/transfer proteins, operate.
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Affiliation(s)
- Marta G Lete
- Department of Molecular and Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX, 77843-1114, USA; Institute Biofisika (UPV/EHU, CSIC) and University of the Basque Country, Leioa, Spain
| | - Ashutosh Tripathi
- Department of Molecular and Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX, 77843-1114, USA
| | - Vijay Chandran
- Department of Molecular and Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX, 77843-1114, USA
| | - Vytas A Bankaitis
- Department of Molecular and Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX, 77843-1114, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA; Department of Chemistry, Texas A&M University, College Station, TX, 77840, USA
| | - Mark I McDermott
- Department of Molecular and Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX, 77843-1114, USA.
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15
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Champeyroux C, Stoof C, Rodriguez-Villalon A. Signaling phospholipids in plant development: small couriers determining cell fate. CURRENT OPINION IN PLANT BIOLOGY 2020; 57:61-71. [PMID: 32771964 DOI: 10.1016/j.pbi.2020.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/24/2020] [Accepted: 05/23/2020] [Indexed: 05/25/2023]
Abstract
The survival of plants hinges on their ability to perceive various environmental stimuli and translate them into appropriate biochemical responses. Phospholipids, a class of membrane lipid compounds that are asymmetrically distributed within plant cells, stand out among signal transmitters for their diversity of mechanisms by which they modulate stress and developmental processes. By modifying the chemo-physical properties of the plasma membrane (PM) as well as vesicle trafficking, phospholipids contribute to changes in the protein membrane landscape, and hence, signaling responses. In this article, we review the distinct signaling mechanisms phospholipids are involved in, with a special focus on the nuclear role of these compounds. Additionally, we summarize exemplary developmental processes greatly influenced by phospholipids.
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Affiliation(s)
- Chloe Champeyroux
- Group of Plant Vascular Development, Swiss Federal Institute of Technology (ETH) Zurich, 8092 Zurich, Switzerland
| | - Claudia Stoof
- Group of Plant Vascular Development, Swiss Federal Institute of Technology (ETH) Zurich, 8092 Zurich, Switzerland
| | - Antia Rodriguez-Villalon
- Group of Plant Vascular Development, Swiss Federal Institute of Technology (ETH) Zurich, 8092 Zurich, Switzerland.
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16
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Super-Resolution Localisation of Nuclear PI(4)P and Identification of Its Interacting Proteome. Cells 2020; 9:cells9051191. [PMID: 32403279 PMCID: PMC7291030 DOI: 10.3390/cells9051191] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/03/2020] [Accepted: 05/05/2020] [Indexed: 12/23/2022] Open
Abstract
Phosphoinositides are glycerol-based phospholipids, and they play essential roles in cellular signalling, membrane and cytoskeletal dynamics, cell movement, and the modulation of ion channels and transporters. Phosphoinositides are also associated with fundamental nuclear processes through their nuclear protein-binding partners, even though membranes do not exist inside of the nucleus. Phosphatidylinositol 4-phosphate (PI(4)P) is one of the most abundant cellular phosphoinositides; however, its functions in the nucleus are still poorly understood. In this study, we describe PI(4)P localisation in the cell nucleus by super-resolution light and electron microscopy, and employ immunoprecipitation with a specific anti-PI(4)P antibody and subsequent mass spectrometry analysis to determine PI(4)P’s interaction partners. We show that PI(4)P is present at the nuclear envelope, in nuclear lamina, in nuclear speckles and in nucleoli and also forms multiple small foci in the nucleoplasm. Nuclear PI(4)P undergoes re-localisation to the cytoplasm during cell division; it does not localise to chromosomes, nucleolar organising regions or mitotic interchromatin granules. When PI(4)P and PI(4,5)P2 are compared, they have different nuclear localisations during interphase and mitosis, pointing to their functional differences in the cell nucleus. Mass spectrometry identified hundreds of proteins, including 12 potentially novel PI(4)P interactors, most of them functioning in vital nuclear processes such as pre-mRNA splicing, transcription or nuclear transport, thus extending the current knowledge of PI(4)P’s interaction partners. Based on these data, we propose that PI(4)P also plays a role in essential nuclear processes as a part of protein–lipid complexes. Altogether, these observations provide a novel insight into the role of PI(4)P in nuclear functions and provide a direction for further investigation.
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17
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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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18
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Chen M, Wen T, Horn HT, Chandrahas VK, Thapa N, Choi S, Cryns VL, Anderson RA. The nuclear phosphoinositide response to stress. Cell Cycle 2020; 19:268-289. [PMID: 31902273 PMCID: PMC7028212 DOI: 10.1080/15384101.2019.1711316] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Accumulating evidence reveals that nuclear phosphoinositides (PIs) serve as central signaling hubs that control a multitude of nuclear processes by regulating the activity of nuclear proteins. In response to cellular stressors, PIs accumulate in the nucleus and multiple PI isomers are synthesized by the actions of PI-metabolizing enzymes, kinases, phosphatases and phospholipases. By directly interacting with effector proteins, phosphoinositide signals transduce changes in cellular functions. Here we describe nuclear phosphoinositide signaling in multiple sub-nuclear compartments and summarize the literature that demonstrates roles for specific kinases, phosphatases, and phospholipases in the orchestration of nuclear phosphoinositide signaling in response to cellular stress. Additionally, we discuss the specific PI-protein complexes through which these lipids execute their functions by regulating the configuration, stability, and transcription activity of their effector proteins. Overall, our review provides a detailed landscape of the current understanding of the nuclear PI-protein interactome and its role in shaping the coordinated response to cellular stress.
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Affiliation(s)
- Mo Chen
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Tianmu Wen
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Hudson T. Horn
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Narendra Thapa
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Suyong Choi
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Vincent L. Cryns
- Department of Medicine, University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Richard A. Anderson
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
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19
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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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20
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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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21
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Phosphatidylinositol 5 Phosphate (PI5P): From Behind the Scenes to the Front (Nuclear) Stage. Int J Mol Sci 2019; 20:ijms20092080. [PMID: 31035587 PMCID: PMC6539119 DOI: 10.3390/ijms20092080] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/20/2019] [Accepted: 04/23/2019] [Indexed: 12/11/2022] Open
Abstract
Phosphatidylinositol (PI)-related signaling plays a pivotal role in many cellular aspects, including survival, cell proliferation, differentiation, DNA damage, and trafficking. PI is the core of a network of proteins represented by kinases, phosphatases, and lipases which are able to add, remove or hydrolyze PI, leading to different phosphoinositide products. Among the seven known phosphoinositides, phosphatidylinositol 5 phosphate (PI5P) was the last to be discovered. PI5P presence in cells is very low compared to other PIs. However, much evidence collected throughout the years has described the role of this mono-phosphoinositide in cell cycles, stress response, T-cell activation, and chromatin remodeling. Interestingly, PI5P has been found in different cellular compartments, including the nucleus. Here, we will review the nuclear role of PI5P, describing how it is synthesized and regulated, and how changes in the levels of this rare phosphoinositide can lead to different nuclear outputs.
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22
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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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23
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Follo MY, Ratti S, Manzoli L, Ramazzotti G, Faenza I, Fiume R, Mongiorgi S, Suh PG, McCubrey JA, Cocco L. Inositide-Dependent Nuclear Signalling in Health and Disease. Handb Exp Pharmacol 2019; 259:291-308. [PMID: 31889219 DOI: 10.1007/164_2019_321] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Nuclear inositides have a specific subcellular distribution that is linked to specific functions; thus their regulation is fundamental both in health and disease. Emerging evidence shows that alterations in multiple inositide signalling pathways are involved in pathophysiology, not only in cancer but also in other diseases. Here, we give an overview of the main features of inositides in the cell, and we discuss their potential as new molecular therapeutic targets.
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Affiliation(s)
- Matilde Y Follo
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Stefano Ratti
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Lucia Manzoli
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Giulia Ramazzotti
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Irene Faenza
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Roberta Fiume
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Sara Mongiorgi
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Pann Ghill Suh
- Korea Brain Research Institute, Daegu, Republic of Korea.,School of Life Sciences, UNIST, Ulsan, Republic of Korea
| | - James A McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Lucio Cocco
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy.
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24
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Bryant JM, Blind RD. Signaling through non-membrane nuclear phosphoinositide binding proteins in human health and disease. J Lipid Res 2018; 60:299-311. [PMID: 30201631 DOI: 10.1194/jlr.r088518] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/22/2018] [Indexed: 12/22/2022] Open
Abstract
Phosphoinositide membrane signaling is critical for normal physiology, playing well-known roles in diverse human pathologies. The basic mechanisms governing phosphoinositide signaling within the nucleus, however, have remained deeply enigmatic owing to their presence outside the nuclear membranes. Over 40% of nuclear phosphoinositides can exist in this non-membrane state, held soluble in the nucleoplasm by nuclear proteins that remain largely unidentified. Recently, two nuclear proteins responsible for solubilizing phosphoinositides were identified, steroidogenic factor-1 (SF-1; NR5A1) and liver receptor homolog-1 (LRH-1; NR5A2), along with two enzymes that directly remodel these phosphoinositide/protein complexes, phosphatase and tensin homolog (PTEN; MMAC) and inositol polyphosphate multikinase (IPMK; ipk2). These new footholds now permit the assignment of physiological functions for nuclear phosphoinositides in human diseases, such as endometriosis, nonalcoholic fatty liver disease/steatohepatitis, glioblastoma, and hepatocellular carcinoma. The unique nature of nuclear phosphoinositide signaling affords extraordinary clinical opportunities for new biomarkers, diagnostics, and therapeutics. Thus, phosphoinositide biology within the nucleus may represent the next generation of low-hanging fruit for new drugs, not unlike what has occurred for membrane phosphatidylinositol 3-kinase drug development. This review connects recent basic science discoveries in nuclear phosphoinositide signaling to clinical pathologies, with the hope of inspiring development of new therapies.
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Affiliation(s)
- Jamal M Bryant
- Departments of Pharmacology, Biochemistry, and Medicine, Division of Diabetes, Endocrinology, and Metabolism, Vanderbilt Diabetes Research and Training Center, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Raymond D Blind
- Departments of Pharmacology, Biochemistry, and Medicine, Division of Diabetes, Endocrinology, and Metabolism, Vanderbilt Diabetes Research and Training Center, Vanderbilt University School of Medicine, Nashville, TN 37232
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25
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Sobol M, Krausová A, Yildirim S, Kalasová I, Fáberová V, Vrkoslav V, Philimonenko V, Marášek P, Pastorek L, Čapek M, Lubovská Z, Uličná L, Tsuji T, Lísa M, Cvačka J, Fujimoto T, Hozak P. Nuclear phosphatidylinositol 4,5-bisphosphate islets contribute to efficient RNA polymerase II-dependent transcription. J Cell Sci 2018; 131:jcs.211094. [PMID: 29507116 DOI: 10.1242/jcs.211094] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/22/2018] [Indexed: 12/18/2022] Open
Abstract
This paper describes a novel type of nuclear structure - nuclear lipid islets (NLIs). They are of 40-100 nm with a lipidic interior, and phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] molecules comprise a significant part of their surface. Most of NLIs have RNA at the periphery. Consistent with that, RNA is required for their integrity. The NLI periphery is associated with Pol II transcription machinery, including the largest Pol II subunit, transcription factors and NM1 (also known as NMI). The PtdIns(4,5)P2-NM1 interaction is important for Pol II transcription, since NM1 knockdown reduces the Pol II transcription level, and the overexpression of wild-type NM1 [but not NM1 mutated in the PtdIns(4,5)P2-binding site] rescues the transcription. Importantly, Pol II transcription is dependent on NLI integrity, because an enzymatic reduction of the PtdIns(4,5)P2 level results in a decrease of the Pol II transcription level. Furthermore, about half of nascent transcripts localise to NLIs, and transcriptionally active transgene loci preferentially colocalise with NLIs. We hypothesize that NLIs serve as a structural platform that facilitates the formation of Pol II transcription factories, thus participating in the formation of nuclear architecture competent for transcription.
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Affiliation(s)
- Margarita Sobol
- Institute of Molecular Genetics, CAS, v.v.i., Department of Biology of the Cell Nucleus, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Alžběta Krausová
- Institute of Molecular Genetics, CAS, v.v.i., Department of Biology of the Cell Nucleus, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Sukriye Yildirim
- Institute of Molecular Genetics, CAS, v.v.i., Department of Biology of the Cell Nucleus, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Ilona Kalasová
- Institute of Molecular Genetics, CAS, v.v.i., Department of Biology of the Cell Nucleus, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Veronika Fáberová
- Institute of Molecular Genetics, CAS, v.v.i., Department of Biology of the Cell Nucleus, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Vladimír Vrkoslav
- Institute of Organic Chemistry and Biochemistry, CAS, v.v.i., Research Service Group of Mass Spectrometry, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic
| | - Vlada Philimonenko
- Institute of Molecular Genetics, CAS, v.v.i., Department of Biology of the Cell Nucleus, Vídeňská 1083, 142 20, Prague 4, Czech Republic.,Institute of Molecular Genetics, CAS, v.v.i., Electron Microscopy Core Facility, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Pavel Marášek
- Institute of Molecular Genetics, CAS, v.v.i., Department of Biology of the Cell Nucleus, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Lukáš Pastorek
- Institute of Molecular Genetics, CAS, v.v.i., Department of Biology of the Cell Nucleus, Vídeňská 1083, 142 20, Prague 4, Czech Republic.,Institute of Molecular Genetics, CAS, v.v.i., Electron Microscopy Core Facility, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Martin Čapek
- Institute of Molecular Genetics, CAS, v.v.i., Light Microscopy Core Facility, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Zuzana Lubovská
- Institute of Molecular Genetics, CAS, v.v.i., Electron Microscopy Core Facility, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Lívia Uličná
- Institute of Molecular Genetics, CAS, v.v.i., Department of Biology of the Cell Nucleus, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Takuma Tsuji
- Nagoya University Graduate School of Medicine, Department of Molecular Cell Biology, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Miroslav Lísa
- University of Pardubice, Faculty of Chemical Technology, Department of Analytical Chemistry, Studentská 573, 532 10, Pardubice, Czech Republic
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry, CAS, v.v.i., Research Service Group of Mass Spectrometry, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic
| | - Toyoshi Fujimoto
- Nagoya University Graduate School of Medicine, Department of Molecular Cell Biology, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Pavel Hozak
- Institute of Molecular Genetics, CAS, v.v.i., Department of Biology of the Cell Nucleus, Vídeňská 1083, 142 20, Prague 4, Czech Republic .,Institute of Molecular Genetics, CAS, v.v.i., Division BIOCEV, Laboratory of Epigenetics of the Cell Nucleus, Průmyslová 595, 252 50, Vestec, Czech Republic.,Institute of Molecular Genetics, CAS, v.v.i., Microscopy Centre, Vídeňská 1083, 142 20, Prague 4, Czech Republic
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Hamann BL, Blind RD. Nuclear phosphoinositide regulation of chromatin. J Cell Physiol 2017; 233:107-123. [PMID: 28256711 DOI: 10.1002/jcp.25886] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/01/2017] [Indexed: 12/26/2022]
Abstract
Phospholipid signaling has clear connections to a wide array of cellular processes, particularly in gene expression and in controlling the chromatin biology of cells. However, most of the work elucidating how phospholipid signaling pathways contribute to cellular physiology have studied cytoplasmic membranes, while relatively little attention has been paid to the role of phospholipid signaling in the nucleus. Recent work from several labs has shown that nuclear phospholipid signaling can have important roles that are specific to this cellular compartment. This review focuses on the nuclear phospholipid functions and the activities of phospholipid signaling enzymes that regulate metazoan chromatin and gene expression. In particular, we highlight the roles that nuclear phosphoinositides play in several nuclear-driven physiological processes, such as differentiation, proliferation, and gene expression. Taken together, the recent discovery of several specifically nuclear phospholipid functions could have dramatic impact on our understanding of the fundamental mechanisms that enable tight control of cellular physiology.
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Affiliation(s)
- Bree L Hamann
- Division of Diabetes Endocrinology and Metabolism, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Raymond D Blind
- Division of Diabetes Endocrinology and Metabolism, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee.,Departments of Medicine, Biochemistry and Pharmacology, Division of Diabetes Endocrinology and Metabolism, The Vanderbilt Diabetes Research and Training Center and the Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
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27
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Ratti S, Mongiorgi S, Ramazzotti G, Follo MY, Mariani GA, Suh PG, McCubrey JA, Cocco L, Manzoli L. Nuclear Inositide Signaling Via Phospholipase C. J Cell Biochem 2017; 118:1969-1978. [PMID: 28106288 DOI: 10.1002/jcb.25894] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 01/18/2017] [Indexed: 12/22/2022]
Abstract
The existence of an independent nuclear inositide pathway distinct from the cytoplasmic one has been demonstrated in different physiological systems and in diseases. In this prospect we analyze the role of PI-PLCβ1 nuclear isoform in relation to the cell cycle regulation, the cell differentiation, and different physiopathological pathways focusing on the importance of the nuclear localization from both molecular and clinical point of view. PI-PLCβ1 is essential for G1/S transition through DAG and Cyclin D3 and plays also a central role in G2/M progression through Cyclin B1 and PKCα. In the differentiation process of C2C12 cells PI-PLCβ1 increases in both myogenic differentiation and osteogenic differentiation. PI-PLCβ1 and Cyclin D3 reduction has been observed in Myotonic Dystrophy (DM) suggesting a pivotal role of these enzymes in DM physiopathology. PI-PLCβ1 is also involved in adipogenesis through a double phase mechanism. Moreover, PI-PLCβ1 plays a key role in the normal hematopoietic differentiation where it seems to decrease in erythroid differentiation and increase in myeloid differentiation. In Myelodysplastic Syndromes (MDS) PI-PLCβ1 has a genetic and epigenetic relevance and it is related to MDS patients' risk of Acute Myeloid Leukemia (AML) evolution. In MDS patients PI-PLCβ1 seems to be also a therapeutic predictive outcome marker. In the central nervous system, PI-PLCβ1 seems to be involved in different pathways in both brain cortex development and synaptic plasticity related to different diseases. Another PI-PLC isozyme that could be related to nuclear activities is PI-PLCζ that is involved in infertility processes. J. Cell. Biochem. 118: 1969-1978, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Stefano Ratti
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, via Irnerio 48, 40126 Bologna, Italy
| | - Sara Mongiorgi
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, via Irnerio 48, 40126 Bologna, Italy
| | - Giulia Ramazzotti
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, via Irnerio 48, 40126 Bologna, Italy
| | - Matilde Y Follo
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, via Irnerio 48, 40126 Bologna, Italy
| | - Giulia A Mariani
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, via Irnerio 48, 40126 Bologna, Italy
| | - Pann-Ghill Suh
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - James A McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville 27834, North Carolina
| | - Lucio Cocco
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, via Irnerio 48, 40126 Bologna, Italy
| | - Lucia Manzoli
- Cellular Signalling Laboratory, Department of Biomedical and Neuromotor Sciences, University of Bologna, via Irnerio 48, 40126 Bologna, Italy
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Abstract
The diverse family of inositol lipids is now known to be central to many aspects of cell biology. The route from the first discovery of inositol to our present day knowledge of inositol lipids spans more than 150 years and is long and complex. This is a brief account of some of the most important stages along that route.
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Affiliation(s)
- Robin F Irvine
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, United Kingdom
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Phosphoinositides in the nucleus and myogenic differentiation: how a nuclear turtle with a PHD builds muscle. Biochem Soc Trans 2016; 44:299-306. [PMID: 26862219 DOI: 10.1042/bst20150238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Phosphoinositides are a family of phospholipid messenger molecules that control various aspects of cell biology in part by interacting with and regulating downstream protein partners. Importantly, phosphoinositides are present in the nucleus. They form part of the nuclear envelope and are present within the nucleus in nuclear speckles, intra nuclear chromatin domains, the nuclear matrix and in chromatin. What their exact role is within these compartments is not completely clear, but the identification of nuclear specific proteins that contain phosphoinositide interaction domains suggest that they are important regulators of DNA topology, chromatin conformation and RNA maturation and export. The plant homeo domain (PHD) finger is a phosphoinositide binding motif that is largely present in nuclear proteins that regulate chromatin conformation. In the present study I outline how changes in the levels of the nuclear phosphoinositide PtdIns5P impact on muscle cell differentiation through the PHD finger of TAF3 (TAF, TATA box binding protein (TBP)-associated factor), which is a core component of a number of different basal transcription complexes.
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30
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Epand RM. Features of the Phosphatidylinositol Cycle and its Role in Signal Transduction. J Membr Biol 2016; 250:353-366. [PMID: 27278236 DOI: 10.1007/s00232-016-9909-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 05/26/2016] [Indexed: 01/03/2023]
Abstract
The phosphatidylinositol cycle (PI-cycle) has a central role in cell signaling. It is the major pathway for the synthesis of phosphatidylinositol and its phosphorylated forms. In addition, some lipid intermediates of the PI-cycle, including diacylglycerol and phosphatidic acid, are also important lipid signaling agents. The PI-cycle has some features that are important for the understanding of its role in the cell. As a cycle, the intermediates will be regenerated. The PI-cycle requires a large amount of metabolic energy. There are different steps of the cycle that occur in two different membranes, the plasma membrane and the endoplasmic reticulum. In order to complete the PI-cycle lipid must be transferred between the two membranes. The role of the Nir proteins in the process has recently been elucidated. The lipid intermediates of the PI-cycle are normally highly enriched with 1-stearoyl-2-arachidonoyl molecular species in mammals. This enrichment will be retained as long as the intermediates are segregated from other lipids of the cell. However, there is a significant fraction (>15 %) of lipids in the PI-cycle of normal cells that have other acyl chains. Phosphatidylinositol largely devoid of arachidonoyl chains are found in cancer cells. Phosphatidylinositol species with less unsaturation will not be as readily converted to phosphatidylinositol-3,4,5-trisphosphate, the lipid required for the activation of Akt with resulting effects on cell proliferation. Thus, the cyclical nature of the PI-cycle, its dependence on acyl chain composition and its requirement for lipid transfer between two membranes, explain many of the biological properties of this cycle.
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Affiliation(s)
- Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada.
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31
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Tribble EK, Ivanova PT, Grabon A, Alb JG, Faenza I, Cocco L, Brown HA, Bankaitis VA. Quantitative profiling of the endonuclear glycerophospholipidome of murine embryonic fibroblasts. J Lipid Res 2016; 57:1492-506. [PMID: 27256690 DOI: 10.1194/jlr.m068734] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Indexed: 01/18/2023] Open
Abstract
A reliable method for purifying envelope-stripped nuclei from immortalized murine embryonic fibroblasts (iMEFs) was established. Quantitative profiling of the glycerophospholipids (GPLs) in envelope-free iMEF nuclei yields several conclusions. First, we find the endonuclear glycerophospholipidome differs from that of bulk membranes, and phosphatidylcholine (PtdCho) and phosphatidylethanolamine species are the most abundant endonuclear GPLs by mass. By contrast, phosphatidylinositol (PtdIns) represents a minor species. We also find only a slight enrichment of saturated versus unsaturated GPL species in iMEF endonuclear fractions. Moreover, much lower values for GPL mass were measured in the iMEF nuclear matrix than those reported for envelope-stripped IMF-32 nuclei. The collective results indicate that the nuclear matrix in these cells is a GPL-poor environment where GPL occupies only approximately 0.1% of the total nuclear matrix volume. This value suggests GPL accommodation in this compartment can be satisfied by binding to resident proteins. Finally, we find no significant role for the PtdIns/PtdCho-transfer protein, PITPα, in shuttling PtdIns into the iMEF nuclear matrix.
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Affiliation(s)
- Emily K Tribble
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Pavlina T Ivanova
- Departments of Pharmacology and Biochemistry, Vanderbilt University School of Medicine, Vanderbilt Institute of Chemical Biology, Nashville, TN
| | - Aby Grabon
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX
| | - James G Alb
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Irene Faenza
- Cellular Signaling Laboratory, Department of Biomedical Sciences, University of Bologna, Bologna, Italy
| | - Lucio Cocco
- Cellular Signaling Laboratory, Department of Biomedical Sciences, University of Bologna, Bologna, Italy
| | - H Alex Brown
- Departments of Pharmacology and Biochemistry, Vanderbilt University School of Medicine, Vanderbilt Institute of Chemical Biology, Nashville, TN
| | - Vytas A Bankaitis
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX
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A polybasic motif in ErbB3-binding protein 1 (EBP1) has key functions in nucleolar localization and polyphosphoinositide interaction. Biochem J 2016; 473:2033-47. [PMID: 27118868 PMCID: PMC4941749 DOI: 10.1042/bcj20160274] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 04/26/2016] [Indexed: 12/29/2022]
Abstract
We reveal the identification of a polybasic motif necessary for polyphosphoinositide interaction and nucleolar targeting of ErbB3 binding protein 1 (EBP1). EBP1 interacts directly with phosphatidylinositol(3,4,5)-triphosphate and their association is detected in the nucleolus, implying regulatory roles of nucleolar processes. Polyphosphoinositides (PPIns) are present in the nucleus where they participate in crucial nuclear processes, such as chromatin remodelling, transcription and mRNA processing. In a previous interactomics study, aimed to gain further insight into nuclear PPIns functions, we identified ErbB3 binding protein 1 (EBP1) as a potential nuclear PPIn-binding protein in a lipid pull-down screen. EBP1 is a ubiquitous and conserved protein, located in both the cytoplasm and nucleolus, and associated with cell proliferation and survival. In the present study, we show that EBP1 binds directly to several PPIns via two distinct PPIn-binding sites consisting of clusters of lysine residues and positioned at the N- and C-termini of the protein. Using interaction mutants, we show that the C-terminal PPIn-binding motif contributes the most to the localization of EBP1 in the nucleolus. Importantly, a K372N point mutation, located within the C-terminal motif and found in endometrial tumours, is sufficient to alter the nucleolar targeting of EBP1. Our study reveals also the presence of the class I phosphoinositide 3-kinase (PI3K) catalytic subunit p110β and its product PtdIns(3,4,5)P3 together with EBP1 in the nucleolus. Using NMR, we further demonstrate an association between EBP1 and PtdIns(3,4,5)P3 via both electrostatic and hydrophobic interactions. Taken together, these results show that EBP1 interacts directly with PPIns and associate with PtdIns(3,4,5)P3 in the nucleolus. The presence of p110β and PtdIns(3,4,5)P3 in the nucleolus indicates their potential role in regulating nucleolar processes, at least via EBP1.
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33
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Smrcka AV. Regulation of phosphatidylinositol-specific phospholipase C at the nuclear envelope in cardiac myocytes. J Cardiovasc Pharmacol 2016; 65:203-10. [PMID: 25658460 DOI: 10.1097/fjc.0000000000000195] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Phosphatidylinositol 4,5-bisphosphate hydrolysis at the plasma membrane by phospholipase C is one of the major hormone regulated intracellular signaling systems. The system generates the diffusible second messenger IP3 and the membrane bound messenger diacylglycerol. Spatial regulation of this system has been thought to be through specific subcellular distributions of the IP3 receptor or PKC. As is becoming increasingly apparent, receptor-stimulated signaling systems are also found at intracellular membranes. As discussed in this issue, G protein-coupled receptors have been identified at the nuclear envelope implying intracellular localization of the signaling systems that respond to G protein-coupled receptors. Here, we discuss the evidence for the existence of PLC signals that regulate nuclear processes, as well as the evidence for nuclear and nuclear envelope localization of PLC signaling components, and their implications for cardiac physiology and disease.
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Affiliation(s)
- Alan V Smrcka
- Department of Pharmacology and Physiology, University of Rochester School of Medicine and Dentistry, Rochester, NY
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34
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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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35
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Poli A, Billi AM, Mongiorgi S, Ratti S, McCubrey JA, Suh PG, Cocco L, Ramazzotti G. Nuclear Phosphatidylinositol Signaling: Focus on Phosphatidylinositol Phosphate Kinases and Phospholipases C. J Cell Physiol 2015; 231:1645-55. [DOI: 10.1002/jcp.25273] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 12/01/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Alessandro Poli
- Department of Biomedical Sciences; University of Bologna; Bologna Italy
| | - Anna Maria Billi
- Department of Biomedical Sciences; University of Bologna; Bologna Italy
| | - Sara Mongiorgi
- Department of Biomedical Sciences; University of Bologna; Bologna Italy
| | - Stefano Ratti
- Department of Biomedical Sciences; University of Bologna; Bologna Italy
| | - James A. McCubrey
- Department of Microbiology and Immunology; Brody School of Medicine; East Carolina University; Greenville North Carolina
| | - Pann-Ghill Suh
- School of Life Sciences; Ulsan National Institute of Science and Technology; Ulsan Republic of Korea
| | - Lucio Cocco
- Department of Biomedical Sciences; University of Bologna; Bologna Italy
| | - Giulia Ramazzotti
- Department of Biomedical Sciences; University of Bologna; Bologna Italy
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36
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Mongiorgi S, Finelli C, Yang YR, Clissa C, McCubrey JA, Billi AM, Manzoli L, Suh PG, Cocco L, Follo MY. Inositide-dependent signaling pathways as new therapeutic targets in myelodysplastic syndromes. Expert Opin Ther Targets 2015; 20:677-87. [PMID: 26610046 DOI: 10.1517/14728222.2016.1125885] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
INTRODUCTION Nuclear inositide signaling pathways specifically regulate cell proliferation and differentiation. Interestingly, the modulation of nuclear inositides in hematological malignancies can differentially affect erythropoiesis or myelopoiesis. This is particularly important in patients with myelodysplastic syndromes (MDS), who show both defective erythroid and myeloid differentiation, as well as an increased risk of evolution into acute myeloid leukemia (AML). AREAS COVERED This review focuses on the structure and function of specific nuclear inositide enzymes, whose impairment could be linked with disease pathogenesis and cancer. The authors, stemming from literature and published data, discuss and describe the role of nuclear inositides, focusing on specific enzymes and demonstrating that targeting these molecules could be important to develop innovative therapeutic approaches, with particular reference to MDS treatment. EXPERT OPINION Demethylating therapy, alone or in combination with other drugs, is the most common and current therapy for MDS patients. Nuclear inositide signaling molecules have been demonstrated to be important in hematopoietic differentiation and are promising new targets for developing a personalized MDS therapy. Indeed, these enzymes can be ideal targets for drug design and their modulation can have several important downstream effects to regulate MDS pathogenesis and prevent MDS progression to AML.
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Affiliation(s)
- Sara Mongiorgi
- a Cellular Signalling Laboratory, Institute of Human Anatomy, Department of Biomedical and Neuromotor Sciences , University of Bologna , Bologna , Italy
| | - Carlo Finelli
- b Institute of Hematology "L e A Seràgnoli" , S. Orsola-Malpighi Hospital , Bologna , Italy
| | - Yong Ryoul Yang
- c School of Life Sciences , Ulsan National Institute of Science and Technology , Ulsan , Republic of Korea
| | - Cristina Clissa
- b Institute of Hematology "L e A Seràgnoli" , S. Orsola-Malpighi Hospital , Bologna , Italy.,d Hematology and Transplant Center , AORMN , Pesaro , Italy
| | - James A McCubrey
- e Department of Microbiology & Immunology, Brody School of Medicine , East Carolina University , Greenville , NC , USA
| | - Anna Maria Billi
- a Cellular Signalling Laboratory, Institute of Human Anatomy, Department of Biomedical and Neuromotor Sciences , University of Bologna , Bologna , Italy
| | - Lucia Manzoli
- a Cellular Signalling Laboratory, Institute of Human Anatomy, Department of Biomedical and Neuromotor Sciences , University of Bologna , Bologna , Italy
| | - Pann-Ghill Suh
- c School of Life Sciences , Ulsan National Institute of Science and Technology , Ulsan , Republic of Korea
| | - Lucio Cocco
- a Cellular Signalling Laboratory, Institute of Human Anatomy, Department of Biomedical and Neuromotor Sciences , University of Bologna , Bologna , Italy
| | - Matilde Y Follo
- a Cellular Signalling Laboratory, Institute of Human Anatomy, Department of Biomedical and Neuromotor Sciences , University of Bologna , Bologna , Italy
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37
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Lete MG, Sot J, Gil D, Valle M, Medina M, Goñi FM, Alonso A. Histones cause aggregation and fusion of lipid vesicles containing phosphatidylinositol-4-phosphate. Biophys J 2015; 108:863-871. [PMID: 25692591 DOI: 10.1016/j.bpj.2014.12.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/07/2014] [Accepted: 12/09/2014] [Indexed: 12/13/2022] Open
Abstract
In a previous article, we demonstrated that histones (H1 or histone octamers) interact with negatively charged bilayers and induce extensive aggregation of vesicles containing phosphatidylinositol-4-phosphate (PIP) and, to a lesser extent, vesicles containing phosphatidylinositol (PI). Here, we found that vesicles containing PIP, but not those containing PI, can undergo fusion induced by histones. Fusion was demonstrated through the observation of intervesicular mixing of total lipids and inner monolayer lipids, and by ultrastructural and confocal microscopy studies. Moreover, in both PI- and PIP-containing vesicles, histones caused permeabilization and release of vesicular aqueous contents, but the leakage mechanism was different (all-or-none for PI and graded release for PIP vesicles). These results indicate that histones could play a role in the remodeling of the nuclear envelope that takes place during the mitotic cycle.
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Affiliation(s)
- Marta G Lete
- Unidad de Biofísica (CSIC, UPV/EHU), Universidad del País Vasco, Leioa, Spain; Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain
| | - Jesus Sot
- Unidad de Biofísica (CSIC, UPV/EHU), Universidad del País Vasco, Leioa, Spain; Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain
| | - David Gil
- Structural Biology Unit, Center for Cooperative Research in Biosciences, CIC bioGUNE, Derio, Spain
| | - Mikel Valle
- Structural Biology Unit, Center for Cooperative Research in Biosciences, CIC bioGUNE, Derio, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos, Unidad Asociada BIFI-IQFR, Universidad de Zaragoza, Zaragoza, Spain
| | - Felix M Goñi
- Unidad de Biofísica (CSIC, UPV/EHU), Universidad del País Vasco, Leioa, Spain; Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain
| | - Alicia Alonso
- Unidad de Biofísica (CSIC, UPV/EHU), Universidad del País Vasco, Leioa, Spain; Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain.
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Davis WJ, Lehmann PZ, Li W. Nuclear PI3K signaling in cell growth and tumorigenesis. Front Cell Dev Biol 2015; 3:24. [PMID: 25918701 PMCID: PMC4394695 DOI: 10.3389/fcell.2015.00024] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 03/27/2015] [Indexed: 12/12/2022] Open
Abstract
The PI3K/Akt signaling pathway is a major driving force in a variety of cellular functions. Dysregulation of this pathway has been implicated in many human diseases including cancer. While the activity of the cytoplasmic PI3K/Akt pathway has been extensively studied, the functions of these molecules and their effector proteins within the nucleus are poorly understood. Harboring key cellular processes such as DNA replication and repair as well as nascent messenger RNA transcription, the nucleus provides a unique compartmental environment for protein–protein and protein–DNA/RNA interactions required for cell survival, growth, and proliferation. Here we summarize recent advances made toward elucidating the nuclear PI3K/Akt signaling cascade and its key components within the nucleus as they pertain to cell growth and tumorigenesis. This review covers the spatial and temporal localization of the major nuclear kinases having PI3K activities and the counteracting phosphatases as well as the role of nuclear PI3K/Akt signaling in mRNA processing and exportation, DNA replication and repair, ribosome biogenesis, cell survival, and tumorigenesis.
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Affiliation(s)
- William J Davis
- College of Medical Sciences, Washington State University Spokane, WA, USA
| | - Peter Z Lehmann
- College of Medical Sciences, Washington State University Spokane, WA, USA
| | - Weimin Li
- College of Medical Sciences, Washington State University Spokane, WA, USA
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39
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Fiume R, Stijf-Bultsma Y, Shah ZH, Keune WJ, Jones DR, Jude JG, Divecha N. PIP4K and the role of nuclear phosphoinositides in tumour suppression. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1851:898-910. [PMID: 25728392 DOI: 10.1016/j.bbalip.2015.02.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 02/03/2015] [Accepted: 02/17/2015] [Indexed: 12/27/2022]
Abstract
Phosphatidylinositol-5-phosphate (PtdIns5P)-4-kinases (PIP4Ks) are stress-regulated lipid kinases that phosphorylate PtdIns5P to generate PtdIns(4,5)P₂. There are three isoforms of PIP4Ks: PIP4K2A, 2B and 2C, which localise to different subcellular compartments with the PIP4K2B isoform being localised predominantly in the nucleus. Suppression of PIP4K expression selectively prevents tumour cell growth in vitro and prevents tumour development in mice that have lost the tumour suppressor p53. p53 is lost or mutated in over 70% of all human tumours. These studies suggest that inhibition of PIP4K signalling constitutes a novel anti-cancer therapeutic target. In this review we will discuss the role of PIP4K in tumour suppression and speculate on how PIP4K modulates nuclear phosphoinositides (PPIns) and how this might impact on nuclear functions to regulate cell growth. This article is part of a Special Issue entitled Phosphoinositides.
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Affiliation(s)
- Roberta Fiume
- Cellular Signalling Laboratory, DIBINEM, University of Bologna, Bologna, Italy.
| | - Yvette Stijf-Bultsma
- Inositide Laboratory, Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, Life Sciences Building 85, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Zahid H Shah
- Inositide Laboratory, Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, Life Sciences Building 85, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Willem Jan Keune
- The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - David R Jones
- Oncology iMED, AstraZeneca, Alderley Park, Macclesfield SK10 4TF, UK
| | - Julian Georg Jude
- IMP - Institute of Molecular Pathology, Vienna Biocenter, Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Nullin Divecha
- Inositide Laboratory, Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, Life Sciences Building 85, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK.
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40
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Lete MG, Sot J, Ahyayauch H, Fernández-Rivero N, Prado A, Goñi FM, Alonso A. Histones and DNA compete for binding polyphosphoinositides in bilayers. Biophys J 2014; 106:1092-100. [PMID: 24606933 DOI: 10.1016/j.bpj.2014.01.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 01/08/2014] [Accepted: 01/17/2014] [Indexed: 12/28/2022] Open
Abstract
Recent discoveries on the presence and location of phosphoinositides in the eukaryotic cell nucleoplasm and nuclear membrane prompted us to study the putative interaction of chromatin components with these lipids in model membranes (liposomes). Turbidimetric studies revealed that a variety of histones and histone combinations (H1, H2AH2B, H3H4, octamers) caused a dose-dependent aggregation of phosphatidylcholine vesicles (large unilamellar vesicle or small unilamellar vesicle) containing negatively charged phospholipids. 5 mol % phosphatidylinositol-4-phosphate (PIP) was enough to cause extensive aggregation under our conditions, whereas with phosphatidylinositol (PI) at least 20 mol % was necessary to obtain a similar effect. Histone binding to giant unilamellar vesicle and vesicle aggregation was visualized by confocal microscopy. Histone did not cause vesicle aggregation in the presence of DNA, and the latter was able to disassemble the histone-vesicle aggregates. At DNA/H1 weight ratios 0.1-0.5 DNA- and PIP-bound H1 appear to coexist. Isothermal calorimetry studies revealed that the PIP-H1 association constant was one order of magnitude higher than that of PI-H1, and the corresponding lipid/histone stoichiometries were ~0.5 and ~1, respectively. The results suggest that, in the nucleoplasm, a complex interplay of histones, DNA, and phosphoinositides may be taking place, particularly at the nucleoplasmic reticula that reach deep within the nucleoplasm, or during somatic and nonsomatic nuclear envelope assembly. The data described here provide a minimal model for analyzing and understanding the mechanism of these interactions.
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Affiliation(s)
- Marta G Lete
- Unidad de Biofísica (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain
| | - Jesús Sot
- Unidad de Biofísica (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain
| | - Hasna Ahyayauch
- Unidad de Biofísica (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain; Institut de Formation aux Carrieres de Sante de Rabat (IFCSR), Rabat, Morocco
| | - Noelia Fernández-Rivero
- Unidad de Biofísica (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain
| | - Adelina Prado
- Unidad de Biofísica (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain
| | - Félix M Goñi
- Unidad de Biofísica (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain
| | - Alicia Alonso
- Unidad de Biofísica (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain.
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García del Caño G, Aretxabala X, González-Burguera I, Montaña M, López de Jesús M, Barrondo S, Barrio RJ, Sampedro C, Goicolea MA, Sallés J. Nuclear diacylglycerol lipase-α in rat brain cortical neurons: evidence of 2-arachidonoylglycerol production in concert with phospholipase C-β activity. J Neurochem 2014; 132:489-503. [PMID: 25308538 DOI: 10.1111/jnc.12963] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/22/2014] [Accepted: 10/07/2014] [Indexed: 01/12/2023]
Abstract
In this report, we describe the localization of diacylglycerol lipase-α (DAGLα) in nuclei from adult cortical neurons, as assessed by double-immunofluorescence staining of rat brain cortical sections and purified intact nuclei and by western blot analysis of subnuclear fractions. Double-labeling assays using the anti-DAGLα antibody and NeuN combined with Hoechst staining showed that only nuclei of neuronal origin were DAGLα positive. At high resolution, DAGLα-signal displayed a punctate pattern in nuclear subdomains poor in Hoechst's chromatin and lamin B1 staining. In contrast, SC-35- and NeuN-signals (markers of the nuclear speckles) showed a high overlap with DAGLα within specific subdomains of the nuclear matrix. Among the members of the phospholipase C-β (PLCβ) family, PLCβ1, PLCβ2, and PLCβ4 exhibited the same distribution with respect to chromatin, lamin B1, SC-35, and NeuN as that described for DAGLα. Furthermore, by quantifying the basal levels of 2-arachidonoylglycerol (2-AG) by liquid chromatography and mass spectrometry (LC-MS), and by characterizing the pharmacology of its accumulation, we describe the presence of a mechanism for 2-AG production, and its PLCβ/DAGLα-dependent biosynthesis in isolated nuclei. These results extend our knowledge about subcellular distribution of neuronal DAGLα, providing biochemical grounds to hypothesize a role for 2-AG locally produced within the neuronal nucleus.
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Affiliation(s)
- Gontzal García del Caño
- Departamento de Neurociencias, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - Xabier Aretxabala
- Departamento de Neurociencias, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - Imanol González-Burguera
- Departamento de Farmacología, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - Mario Montaña
- Departamento de Farmacología, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - Maider López de Jesús
- Departamento de Farmacología, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - Sergio Barrondo
- Departamento de Farmacología, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - Ramón J Barrio
- Departamento de Química Analítica, Facultad de Farmacia, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - Carmen Sampedro
- Servicio General de Análisis, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - M Arantzazu Goicolea
- Departamento de Química Analítica, Facultad de Farmacia, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - Joan Sallés
- Departamento de Farmacología, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
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The signaling phospholipid PIP3 creates a new interaction surface on the nuclear receptor SF-1. Proc Natl Acad Sci U S A 2014; 111:15054-9. [PMID: 25288771 DOI: 10.1073/pnas.1416740111] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The signaling phosphatidylinositol lipids PI(4,5)P2 (PIP2) and PI(3,4,5)P3 (PIP3) bind nuclear receptor 5A family (NR5As), but their regulatory mechanisms remain unknown. Here, the crystal structures of human NR5A1 (steroidogenic factor-1, SF-1) ligand binding domain (LBD) bound to PIP2 and PIP3 show the lipid hydrophobic tails sequestered in the hormone pocket, as predicted. However, unlike classic nuclear receptor hormones, the phosphoinositide head groups are fully solvent-exposed and complete the LBD fold by organizing the receptor architecture at the hormone pocket entrance. The highest affinity phosphoinositide ligand PIP3 stabilizes the coactivator binding groove and increases coactivator peptide recruitment. This receptor-ligand topology defines a previously unidentified regulatory protein-lipid surface on SF-1 with the phosphoinositide head group at its nexus and poised to interact with other proteins. This surface on SF-1 coincides with the predicted binding site of the corepressor DAX-1 (dosage-sensitive sex reversal, adrenal hypoplasia critical region on chromosome X), and importantly harbors missense mutations associated with human endocrine disorders. Our data provide the structural basis for this poorly understood cluster of human SF-1 mutations and demonstrates how signaling phosphoinositides function as regulatory ligands for NR5As.
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c-Fos-activated synthesis of nuclear phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P₂] promotes global transcriptional changes. Biochem J 2014; 461:521-30. [PMID: 24819416 DOI: 10.1042/bj20131376] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
c-Fos is a well-recognized member of the AP-1 (activator protein-1) family of transcription factors. In addition to this canonical activity, we previously showed that cytoplasmic c-Fos activates phospholipid synthesis through a mechanism independent of its genomic AP-1 activity. c-Fos associates with particular enzymes of the lipid synthesis pathway at the endoplasmic reticulum and increases the Vmax of the reactions without modifying the Km values. This lipid synthesis activation is associated with events of differentiation and proliferation that require high rates of membrane biogenesis. Since lipid synthesis also occurs in the nucleus, and different phospholipids have been assigned transcription regulatory functions, in the present study we examine if c-Fos also acts as a regulator of phospholipid synthesis in the nucleus. Furthermore, we examine if c-Fos modulates transcription through its phospholipid synthesis activator capacity. We show that nuclear-localized c-Fos associates with and activates PI4P5K (phosphatidylinositol-4-monophosphate 5-kinase), but not with PI4KIIIβ (type IIIβ phosphatidylinositol 4-kinase) thus promoting PtdIns(4,5)P₂ (phosphatidylinositol 4,5-bisphosphate) formation, which, in turn, promotes transcriptional changes. We propose c-Fos as a key regulator of nuclear PtdIns(4,5)P₂ synthesis in response to growth signals that results in c-Fos-dependent transcriptional changes promoted by the newly synthesized lipids.
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Abstract
The phosphoinositide 3-kinase (PI 3-K) signal relay pathway represents arguably one of the most intensely studied mechanisms by which extracellular signals elicit cellular responses through the generation of second messengers that are associated with cell growth and transformation. This chapter reviews the many landmark discoveries in the PI 3-K signaling pathway in biology and disease, from the identification of a novel phosphoinositide kinase activity associated with transforming oncogenes in the 1980s, to the identification of oncogenic mutations in the catalytic subunit of PI 3-K in the mid 2000s. Two and a half decades of intense research have provided clear evidence that the PI 3-K pathway controls virtually all aspects of normal cellular physiology, and that deregulation of one or more proteins that regulate or transduce the PI 3-K signal ultimately leads to human pathology. The most recent efforts have focused on the development of specific PI 3-K inhibitors that are currently being evaluated in clinical trials for a range of disease states.This chapter is devoted to a historical review of the landmark findings in the PI 3-K from its relatively humble beginnings in the early to mid 1980s up until the present day. When considering the key findings in the history of PI 3-K, it is essential to recognize the landmark studies by Lowell and Mabel Hokin in the 1950s who were the first to describe that extracellular agonists such as acetylcholine could stimulate the incorporation of radiolabeled phosphate into phospholipids (Hokin and Hokin 1953). Their work initiated an entirely new field of lipid signaling, and subsequent studies in the 1970s by Michell and Lapetina who linked phosphoinositide turnover to membrane-associated receptors that initiate intracellular calcium mobilization (Lapetina and Michell 1973). Later studies revealed that the phospholipase-mediated breakdown of the same minor membrane phospholipids such as PtdIns-4,5-P(2) (phosphatidylinositol-4,5-bisphosphate) is responsible for the release of two additional key second messengers, diacylglycerol (DG) and IP(3) (inositol-1,4,5-trisphosphate) (Kirk et al. 1981; Berridge 1983; Berridge et al. 1983). Berridge, Irvine and Schulz then revealed that one of the byproducts of this lipid signal relay pathway is the release of calcium from intracellular stores such as the endoplasmic reticulum (Streb et al. 1983). Finally, pioneering studies by Nishizuka in the late 1970s identified PKC (protein kinase C) as a phospholipid and diacylglycerol-activated serine/threonine protein kinase (Inoue et al. 1977; Takai et al. 1977). At this point, it probably seemed to most at the time that the story was complete, such that hydrolysis of phosphoinositides such as PtdIns-4,5-P(2) and PtdIns-4-P would account for the major mechanisms of agonist-stimulated lipid signaling leading to physiological responses. On the contrary, the story was far from complete and was about to become a lot more complex.
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Affiliation(s)
- Alex Toker
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, EC/CLS-633A, 02130, Boston, MA, USA,
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Shah ZH, Jones DR, Sommer L, Foulger R, Bultsma Y, D'Santos C, Divecha N. Nuclear phosphoinositides and their impact on nuclear functions. FEBS J 2013; 280:6295-310. [PMID: 24112514 DOI: 10.1111/febs.12543] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/11/2013] [Accepted: 09/16/2013] [Indexed: 12/23/2022]
Abstract
Polyphosphoinositides (PPIn) are important lipid molecules whose levels are de-regulated in human diseases such as cancer, neurodegenerative disorders and metabolic syndromes. PPIn are synthesized and degraded by an array of kinases, phosphatases and lipases which are localized to various subcellular compartments and are subject to regulation in response to both extra- and intracellular cues. Changes in the activities of enzymes that metabolize PPIn lead to changes in the profiles of PPIn in various subcellular compartments. Understanding how subcellular PPIn are regulated and how they affect downstream signaling is critical to understanding their roles in human diseases. PPIn are present in the nucleus, and their levels are changed in response to various stimuli, suggesting that they may serve to regulate specific nuclear functions. However, the lack of nuclear downstream targets has hindered the definition of which pathways nuclear PPIn affect. Over recent years, targeted and global proteomic studies have identified a plethora of potential PPIn-interacting proteins involved in many aspects of transcription, chromatin remodelling and mRNA maturation, suggesting that PPIn signalling within the nucleus represents a largely unexplored novel layer of complexity in the regulation of nuclear functions.
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Affiliation(s)
- Zahid H Shah
- Cancer Research UK Inositide Laboratory, Paterson Institute for Cancer Research, Manchester, UK
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Rhee SG. Reflections on the days of phospholipase C. Adv Biol Regul 2013; 53:223-231. [PMID: 24054839 DOI: 10.1016/j.jbior.2013.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 08/20/2013] [Accepted: 08/20/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Sue Goo Rhee
- Yonsei Biomedical Research Institute, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea.
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Faenza I, Fiume R, Piazzi M, Colantoni A, Cocco L. Nuclear inositide specific phospholipase C signalling - interactions and activity. FEBS J 2013; 280:6311-21. [PMID: 23890371 DOI: 10.1111/febs.12450] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 06/26/2013] [Accepted: 07/18/2013] [Indexed: 01/07/2023]
Abstract
Evidence accumulated over the past 20 years has highlighted the presence of an autonomous nuclear inositol lipid metabolism, and suggests that lipid signalling molecules are important components of signalling pathways operating within the nucleus. Nuclear polyphosphoinositide (PI) signalling relies on the synthesis and metabolism of phosphatidylinositol 4,5-bisphosphate, which can modulate the activity of effector proteins and is a substrate of signalling enzymes. The regulation of the nuclear PI pool is totally independent from the plasma membrane counterpart, suggesting that the nucleus constitutes a functionally distinct compartment of inositol lipids metabolism. Among the nuclear enzymes involved in PI metabolism, inositide specific phospholipase C (PI-PLC) has been one of the most extensively studied. Several isoforms of PI-PLCs have been identified in the nucleus, namely PI-PLC-β1, γ1, δ1 and ζ; however, the β1 isozyme is the best characterized. In the present review, we focus on the signal transduction-related metabolism of nuclear PI-PLC and review the most convincing evidence for PI-PLC expression and activity being involved in differentiation and proliferation programmes in several cell systems. Moreover, nuclear PI-PLC is an intermediate effector and interactor for nuclear inositide signalling. The inositide cycle exists and shows a biological role inside the nucleus. It is an autonomous lipid-dependent signalling system, independently regulated with respect to the one at the plasma membrane counterpart, and is involved in cell cycle progression and differentiation.
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Affiliation(s)
- Irene Faenza
- Cell Signaling Laboratory, Department of Biomedical Science (DIBINEM), University of Bologna, Italy
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48
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Abstract
Phosphoinositides (PIs) make up only a small fraction of cellular phospholipids, yet they control almost all aspects of a cell's life and death. These lipids gained tremendous research interest as plasma membrane signaling molecules when discovered in the 1970s and 1980s. Research in the last 15 years has added a wide range of biological processes regulated by PIs, turning these lipids into one of the most universal signaling entities in eukaryotic cells. PIs control organelle biology by regulating vesicular trafficking, but they also modulate lipid distribution and metabolism via their close relationship with lipid transfer proteins. PIs regulate ion channels, pumps, and transporters and control both endocytic and exocytic processes. The nuclear phosphoinositides have grown from being an epiphenomenon to a research area of its own. As expected from such pleiotropic regulators, derangements of phosphoinositide metabolism are responsible for a number of human diseases ranging from rare genetic disorders to the most common ones such as cancer, obesity, and diabetes. Moreover, it is increasingly evident that a number of infectious agents hijack the PI regulatory systems of host cells for their intracellular movements, replication, and assembly. As a result, PI converting enzymes began to be noticed by pharmaceutical companies as potential therapeutic targets. This review is an attempt to give an overview of this enormous research field focusing on major developments in diverse areas of basic science linked to cellular physiology and disease.
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Affiliation(s)
- Tamas Balla
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA.
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Siniossoglou S. Phospholipid metabolism and nuclear function: Roles of the lipin family of phosphatidic acid phosphatases. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1831:575-81. [DOI: 10.1016/j.bbalip.2012.09.014] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/19/2012] [Accepted: 09/24/2012] [Indexed: 01/22/2023]
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50
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Yildirim S, Castano E, Sobol M, Philimonenko VV, Dzijak R, Venit T, Hozák P. Involvement of PIP2 in RNA Polymerase I transcription. J Cell Sci 2013; 126:2730-9. [DOI: 10.1242/jcs.123661] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA polymerase I (Pol I) transcription is essential for the cell cycle, growth, and overall protein synthesis in eukaryotes. We found that phosphatidylinositol 4,5-bisphosphate (PIP2) is a part of the protein complex on the active ribosomal promoter during the transcription. PIP2 makes a complex with Pol I and Pol I transcription factor UBF in the nucleolus. PIP2 depletion reduces Pol I transcription which can be rescued by the addition of exogenous PIP2. In addition, PIP2 also binds directly to the pre-rRNA processing factor, fibrillarin (Fib), and co-localizes with nascent transcripts in the nucleolus. PIP2 binding to UBF and Fib modulates their binding to DNA and RNA, respectively. In conclusion, PIP2 interacts with a subset of Pol I transcription machinery, and promotes Pol I transcription.
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