1
|
Morito M, Yasuda H, Matsufuji T, Kinoshita M, Matsumori N. Identification of lipid-specific proteins with high-density lipid-immobilized beads. Analyst 2024; 149:3747-3755. [PMID: 38829210 DOI: 10.1039/d4an00579a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
In biological membranes, lipids often interact with membrane proteins (MPs), regulating the localization and activity of MPs in cells. Although elucidating lipid-MP interactions is critical to comprehend the physiological roles of lipids, a systematic and comprehensive identification of lipid-binding proteins has not been adequately established. Therefore, we report the development of lipid-immobilized beads where lipid molecules were covalently immobilized. Owing to the detergent tolerance, these beads enable screening of water-soluble proteins and MPs, the latter of which typically necessitate surfactants for solubilization. Herein, two sphingolipid species-ceramide and sphingomyelin-which are major constituents of lipid rafts, were immobilized on the beads. We first showed that the density of immobilized lipid molecules on the beads was as high as that of biological lipid membranes. Subsequently, we confirmed that these beads enabled the selective pulldown of known sphingomyelin- or ceramide-binding proteins (lysenin, p24, and CERT) from protein mixtures, including cell lysates. In contrast, commercial sphingomyelin beads, on which lipid molecules are sparsely immobilized through biotin-streptavidin linkage, failed to capture lysenin, a well-known protein that recognizes clustered sphingomyelin molecules. This clearly demonstrates the applicability of our beads for obtaining proteins that recognize not only a single lipid molecule but also lipid clusters or lipid membranes. Finally, we demonstrated the screening of lipid-binding proteins from Neuro2a cell lysates using these beads. This method is expected to significantly contribute to the understanding of interactions between lipids and proteins and to unravel the complexities of lipid diversity.
Collapse
Affiliation(s)
- Masayuki Morito
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Hiroki Yasuda
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Takaaki Matsufuji
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Masanao Kinoshita
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Friedman MJ, Wagner T, Lee H, Rosenfeld MG, Oh S. Enhancer-promoter specificity in gene transcription: molecular mechanisms and disease associations. Exp Mol Med 2024; 56:772-787. [PMID: 38658702 PMCID: PMC11058250 DOI: 10.1038/s12276-024-01233-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 04/26/2024] Open
Abstract
Although often located at a distance from their target gene promoters, enhancers are the primary genomic determinants of temporal and spatial transcriptional specificity in metazoans. Since the discovery of the first enhancer element in simian virus 40, there has been substantial interest in unraveling the mechanism(s) by which enhancers communicate with their partner promoters to ensure proper gene expression. These research efforts have benefited considerably from the application of increasingly sophisticated sequencing- and imaging-based approaches in conjunction with innovative (epi)genome-editing technologies; however, despite various proposed models, the principles of enhancer-promoter interaction have still not been fully elucidated. In this review, we provide an overview of recent progress in the eukaryotic gene transcription field pertaining to enhancer-promoter specificity. A better understanding of the mechanistic basis of lineage- and context-dependent enhancer-promoter engagement, along with the continued identification of functional enhancers, will provide key insights into the spatiotemporal control of gene expression that can reveal therapeutic opportunities for a range of enhancer-related diseases.
Collapse
Affiliation(s)
- Meyer J Friedman
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tobias Wagner
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Haram Lee
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea
| | - Michael G Rosenfeld
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Soohwan Oh
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea.
| |
Collapse
|
4
|
Escudeiro-Lopes S, Filimonenko VV, Jarolimová L, Hozák P. Lamin A/C and PI(4,5)P2-A Novel Complex in the Cell Nucleus. Cells 2024; 13:399. [PMID: 38474363 DOI: 10.3390/cells13050399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 03/14/2024] Open
Abstract
Lamins, the nuclear intermediate filaments, are important regulators of nuclear structural integrity as well as nuclear functional processes such as DNA transcription, replication and repair, and epigenetic regulations. A portion of phosphorylated lamin A/C localizes to the nuclear interior in interphase, forming a lamin A/C pool with specific properties and distinct functions. Nucleoplasmic lamin A/C molecular functions are mainly dependent on its binding partners; therefore, revealing new interactions could give us new clues on the lamin A/C mechanism of action. In the present study, we show that lamin A/C interacts with nuclear phosphoinositides (PIPs), and with nuclear myosin I (NM1). Both NM1 and nuclear PIPs have been previously reported as important regulators of gene expression and DNA damage/repair. Furthermore, phosphorylated lamin A/C forms a complex with NM1 in a phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2)-dependent manner in the nuclear interior. Taken together, our study reveals a previously unidentified interaction between phosphorylated lamin A/C, NM1, and PI(4,5)P2 and suggests new possible ways of nucleoplasmic lamin A/C regulation, function, and importance for the formation of functional nuclear microdomains.
Collapse
Affiliation(s)
- Sara Escudeiro-Lopes
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Vlada V Filimonenko
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
- Electron Microscopy Core Facility, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Lenka Jarolimová
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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: 8] [Impact Index Per Article: 8.0] [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.
Collapse
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
| |
Collapse
|
7
|
Zarreen F, Kumar K, Chakraborty S. Phosphoinositides in plant-pathogen interaction: trends and perspectives. STRESS BIOLOGY 2023; 3:4. [PMID: 37676371 PMCID: PMC10442044 DOI: 10.1007/s44154-023-00082-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 02/15/2023] [Indexed: 09/08/2023]
Abstract
Phosphoinositides are important regulatory membrane lipids, with a role in plant development and cellular function. Emerging evidence indicates that phosphoinositides play crucial roles in plant defence and are also utilized by pathogens for infection. In this review, we highlight the role of phosphoinositides in plant-pathogen interaction and the implication of this remarkable convergence in the battle against plant diseases.
Collapse
Affiliation(s)
- Fauzia Zarreen
- Molecular Virology Laboratory, School of Life Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Kamal Kumar
- Molecular Virology Laboratory, School of Life Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Science, Jawaharlal Nehru University, New Delhi, 110067, India.
| |
Collapse
|
8
|
Palmieri M, Catimel B, Mouradov D, Sakthianandeswaren A, Kapp E, Ang CS, Williamson NA, Nowell CJ, Christie M, Desai J, Gibbs P, Burgess AW, Sieber OM. PI3K-alpha translocation mediates nuclear PtdIns(3,4,5)P 3 effector signaling in colorectal cancer. Mol Cell Proteomics 2023; 22:100529. [PMID: 36931626 PMCID: PMC10130476 DOI: 10.1016/j.mcpro.2023.100529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 03/05/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The canonical view of phosphatidylinositol 3-kinase alpha (PI3Kα) signaling describes PtdIns(3,4,5)P3 generation and activation of downstream effectors at the plasma membrane or at microtubule-bound endosomes. Here, we show that colorectal cancer (CRC) cell lines exhibit a diverse plasma membrane-nuclear distribution of PI3Kα, controlling corresponding levels of subcellular PtdIns(3,4,5)P3 pools. PI3Kα nuclear translocation was mediated by the importin β-dependent nuclear import pathway. By PtdIns(3,4,5)P3 affinity capture mass spectrometry done in the presence of SDS on CRC cell lines with PI3Kα nuclear localization, we identified 867 potential nuclear PtdIns(3,4,5)P3 effector proteins. Nuclear PtdIns(3,4,5)P3 interactome proteins were characterized by non-canonical PtdIns(3,4,5)P3 binding domains and showed overrepresentation for nuclear membrane, nucleolus and nuclear speckles. The nuclear PtdIns(3,4,5)P3 interactome was enriched for proteins related to RNA metabolism, with splicing reporter assays and SC-35 foci staining suggesting a role of EGF-stimulated nuclear PI3Kα signaling in modulating pre-mRNA splicing. In patient tumors, nuclear p110α staining was associated with lower T stage and mucinous histology. These results indicate that PI3Kα translocation mediates nuclear PtdIns(3,4,5)P3 effector signaling in human CRC, modulating signaling responses.
Collapse
Affiliation(s)
- Michelle Palmieri
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Bruno Catimel
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Dmitri Mouradov
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Anuratha Sakthianandeswaren
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Eugene Kapp
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia; Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nicholas A Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Cameron J Nowell
- Monash Institute for Pharmaceutical Science, Parkville, Victoria, 3052, Australia
| | - Michael Christie
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Pathology, Royal Melbourne Hospital, Parkville, Victoria, 3050, Australia
| | - Jayesh Desai
- Division of Cancer Medicine, Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia; Department of Medical Oncology, Royal Melbourne Hospital, Parkville, Victoria, 3050, Australia
| | - Peter Gibbs
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia; Department of Medical Oncology, Western Health, Footscray, Victoria, 3011, Australia
| | - Antony W Burgess
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia; Department of Surgery, The University of Melbourne, Parkville, Victoria, 3050, Australia
| | - Oliver M Sieber
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia; Department of Surgery, The University of Melbourne, Parkville, Victoria, 3050, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia.
| |
Collapse
|
9
|
Edson AJ, Jacobsen RG, Lewis AE. SAF-A/hnRNP U binds polyphosphoinositides via a lysine rich polybasic motif located in the SAP domain. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000761. [PMID: 37038481 PMCID: PMC10082394 DOI: 10.17912/micropub.biology.000761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 04/12/2023]
Abstract
Polyphosphoinositides (PPIn) play essential functions as lipid signalling molecules and many of their functions have been elucidated in the cytoplasm. However, PPIn are also intranuclear where they contribute to chromatin remodelling, transcription and mRNA splicing. Using quantitative interactomics, we have previously identified PPIn-interacting proteins with roles in RNA processing/splicing including the heterogeneous nuclear ribonucleoprotein U (hnRNPU/SAF-A). In this study, hnRNPU was validated as a direct PPIn-interacting protein via 2 regions located in the N and C termini. Furthermore, deletion of the polybasic motif region located at aa 9-24 in its DNA binding SAP domain prevented PPIn interaction. In conclusion, these results are consistent with hnRNPU harbouring a polybasic region with dual functions in DNA and PPIn interaction.
Collapse
Affiliation(s)
- Amanda J Edson
- Department of Biological Sciences, University of Bergen, Bergen, Vestland, Norway
| | - Rhîan G Jacobsen
- Department of Biological Sciences, University of Bergen, Bergen, Vestland, Norway
| | - Aurélia E Lewis
- Department of Biological Sciences, University of Bergen, Bergen, Vestland, Norway
- Correspondence to: Aurélia E Lewis (
)
| |
Collapse
|
10
|
Isaac R, Vinik Y, Mikl M, Nadav-Eliyahu S, Shatz-Azoulay H, Yaakobi A, DeForest N, Majithia AR, Webster NJ, Shav-Tal Y, Elhanany E, Zick Y. A seven-transmembrane protein-TM7SF3, resides in nuclear speckles and regulates alternative splicing. iScience 2022; 25:105270. [PMID: 36304109 PMCID: PMC9593240 DOI: 10.1016/j.isci.2022.105270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 06/08/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
The seven-transmembrane superfamily member 3 protein (TM7SF3) is a p53-regulated homeostatic factor that attenuates cellular stress and the unfolded protein response. Here we show that TM7SF3 localizes to nuclear speckles; eukaryotic nuclear bodies enriched in splicing factors. This unexpected location for a trans -membranal protein enables formation of stable complexes between TM7SF3 and pre-mRNA splicing factors including DHX15, LARP7, HNRNPU, RBM14, and HNRNPK. Indeed, TM7SF3 regulates alternative splicing of >330 genes, mainly at the 3'end of introns by directly modulating the activity of splicing factors such as HNRNPK. These effects are observed both in cell lines and primary human pancreatic islets. Accordingly, silencing of TM7SF3 results in differential expression of 1465 genes (about 7% of the human genome); with 844 and 621 genes being up- or down-regulated, respectively. Our findings implicate TM7SF3, as a resident protein of nuclear speckles and suggest a role for seven-transmembrane proteins as regulators of alternative splicing.
Collapse
Affiliation(s)
- Roi Isaac
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Yaron Vinik
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Martin Mikl
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Biology, University of Haifa, Haifa, Israel
| | - Shani Nadav-Eliyahu
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Hadas Shatz-Azoulay
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Adi Yaakobi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Natalie DeForest
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Amit R. Majithia
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicholas J.G. Webster
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- VA San Diego Healthcare System, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Eytan Elhanany
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yehiel Zick
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
11
|
Wang YH, Sheetz MP. When PIP 2 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] [Key Words] [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.
Collapse
Affiliation(s)
| | - Michael P. Sheetz
- Biochemistry and Molecular Biology Dept., University of Texas Medical Branch, Galveston, TX, United States
| |
Collapse
|
12
|
Unconventional metabolites in chromatin regulation. Biosci Rep 2022; 42:230604. [PMID: 34988581 PMCID: PMC8777195 DOI: 10.1042/bsr20211558] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 11/17/2022] Open
Abstract
Chromatin, the complex of DNA and histone proteins, serves as a main integrator of cellular signals. Increasing evidence links cellular functional to chromatin state. Indeed, different metabolites are emerging as modulators of chromatin function and structure. Alterations in chromatin state are decisive for regulating all aspects of genome function and ultimately have the potential to produce phenotypic changes. Several metabolites such as acetyl-CoA, S-adenosylmethionine (SAM) or adenosine triphosphate (ATP) have now been well characterized as main substrates or cofactors of chromatin-modifying enzymes. However, there are other metabolites that can directly interact with chromatin influencing its state or that modulate the properties of chromatin regulatory factors. Also, there is a growing list of atypical enzymatic and nonenzymatic chromatin modifications that originate from different cellular pathways that have not been in the limelight of chromatin research. Here, we summarize different properties and functions of uncommon regulatory molecules originating from intermediate metabolism of lipids, carbohydrates and amino acids. Based on the various modes of action on chromatin and the plethora of putative, so far not described chromatin-regulating metabolites, we propose that there are more links between cellular functional state and chromatin regulation to be discovered. We hypothesize that these connections could provide interesting starting points for interfering with cellular epigenetic states at a molecular level.
Collapse
|
13
|
Hamed M, Antonin W. Dunking into the Lipid Bilayer: How Direct Membrane Binding of Nucleoporins Can Contribute to Nuclear Pore Complex Structure and Assembly. Cells 2021; 10:3601. [PMID: 34944108 PMCID: PMC8700311 DOI: 10.3390/cells10123601] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 02/07/2023] Open
Abstract
Nuclear pore complexes (NPCs) mediate the selective and highly efficient transport between the cytoplasm and the nucleus. They are embedded in the two membrane structure of the nuclear envelope at sites where these two membranes are fused to pores. A few transmembrane proteins are an integral part of NPCs and thought to anchor these complexes in the nuclear envelope. In addition, a number of nucleoporins without membrane spanning domains interact with the pore membrane. Here we review our current knowledge of how these proteins interact with the membrane and how this interaction can contribute to NPC assembly, stability and function as well as shaping of the pore membrane.
Collapse
Affiliation(s)
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074 Aachen, Germany;
| |
Collapse
|
14
|
Morovicz AP, Mazloumi Gavgani F, Jacobsen RG, Skuseth Slinning M, Turcu DC, Lewis AE. Phosphoinositide 3-kinase signalling in the nucleolus. Adv Biol Regul 2021; 83:100843. [PMID: 34920983 DOI: 10.1016/j.jbior.2021.100843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 11/20/2021] [Indexed: 12/26/2022]
Abstract
The phosphoinositide 3-kinase (PI3K) signalling pathway plays key roles in many cellular processes and is altered in many diseases. The function and mode of action of the pathway have mostly been elucidated in the cytoplasm. However, many of the components of the PI3K pathway are also present in the nucleus at specific sub-nuclear sites including nuclear speckles, nuclear lipid islets and the nucleolus. Nucleoli are membrane-less subnuclear structures where ribosome biogenesis occurs. Processes leading to ribosome biogenesis are tightly regulated to maintain protein translation capacity of cells. This review focuses on nucleolar PI3K signalling and how it regulates rRNA synthesis, as well as on the identification of downstream phosphatidylinositol (3,4,5)trisphosphate effector proteins.
Collapse
Affiliation(s)
| | | | - Rhîan G Jacobsen
- Department of Biological Sciences, University of Bergen, 5008, Bergen, Norway
| | | | - Diana C Turcu
- Department of Biological Sciences, University of Bergen, 5008, Bergen, Norway
| | - Aurélia E Lewis
- Department of Biological Sciences, University of Bergen, 5008, Bergen, Norway.
| |
Collapse
|
15
|
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.
Collapse
|
16
|
Hoboth P, Šebesta O, Hozák P. How Single-Molecule Localization Microscopy Expanded Our Mechanistic Understanding of RNA Polymerase II Transcription. Int J Mol Sci 2021; 22:6694. [PMID: 34206594 PMCID: PMC8269275 DOI: 10.3390/ijms22136694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 11/16/2022] Open
Abstract
Classical models of gene expression were built using genetics and biochemistry. Although these approaches are powerful, they have very limited consideration of the spatial and temporal organization of gene expression. Although the spatial organization and dynamics of RNA polymerase II (RNAPII) transcription machinery have fundamental functional consequences for gene expression, its detailed studies have been abrogated by the limits of classical light microscopy for a long time. The advent of super-resolution microscopy (SRM) techniques allowed for the visualization of the RNAPII transcription machinery with nanometer resolution and millisecond precision. In this review, we summarize the recent methodological advances in SRM, focus on its application for studies of the nanoscale organization in space and time of RNAPII transcription, and discuss its consequences for the mechanistic understanding of gene expression.
Collapse
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;
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic;
| | - Ondřej Šebesta
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic;
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic;
- Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| |
Collapse
|
17
|
Ratti S, Evangelisti C, Mongiorgi S, De Stefano A, Fazio A, Bonomini F, Follo MY, Faenza I, Manzoli L, Sheth B, Vidalle MC, Kimber ST, Divecha N, Cocco L, Fiume R. "Modulating Phosphoinositide Profiles as a Roadmap for Treatment in Acute Myeloid Leukemia". Front Oncol 2021; 11:678824. [PMID: 34109125 PMCID: PMC8181149 DOI: 10.3389/fonc.2021.678824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/04/2021] [Indexed: 12/12/2022] Open
Abstract
Polyphosphoinositides (PPIns) and their modulating enzymes are involved in regulating many important cellular functions including proliferation, differentiation or gene expression, and their deregulation is involved in human diseases such as metabolic syndromes, neurodegenerative disorders and cancer, including Acute Myeloid Leukemia (AML). Given that PPIns regulating enzymes are highly druggable targets, several studies have recently highlighted the potential of targeting them in AML. For instance many inhibitors targeting the PI3K pathway are in various stages of clinical development and more recently other novel enzymes such as PIP4K2A have been implicated as AML targets. PPIns have distinct subcellular organelle profiles, in part driven by the specific localisation of enzymes that metabolise them. In particular, in the nucleus, PPIns are regulated in response to various extracellular and intracellular pathways and interact with specific nuclear proteins to control epigenetic cell state. While AML does not normally manifest with as many mutations as other cancers, it does appear in large part to be a disease of dysregulation of epigenetic signalling and many novel therapeutics are aimed at reprogramming AML cells toward a differentiated cell state or to one that is responsive to alternative successful but limited AML therapies such as ATRA. Here, we propose that by combining bioinformatic analysis with inhibition of PPIns pathways, especially within the nucleus, we might discover new combination therapies aimed at reprogramming transcriptional output to attenuate uncontrolled AML cell growth. Furthermore, we outline how different part of a PPIns signalling unit might be targeted to control selective outputs that might engender more specific and therefore less toxic inhibitory outcomes.
Collapse
Affiliation(s)
- Stefano Ratti
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Camilla Evangelisti
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Sara Mongiorgi
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Alessia De Stefano
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Antonietta Fazio
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Francesca Bonomini
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Matilde Y Follo
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Irene Faenza
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Lucia Manzoli
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Bhavwanti Sheth
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Magdalena C Vidalle
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Scott T Kimber
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Nullin Divecha
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Lucio Cocco
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Roberta Fiume
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| |
Collapse
|
18
|
The F-Actin-Binding MPRIP Forms Phase-Separated Condensates and Associates with PI(4,5)P2 and Active RNA Polymerase II in the Cell Nucleus. Cells 2021; 10:cells10040848. [PMID: 33918018 PMCID: PMC8068864 DOI: 10.3390/cells10040848] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/25/2021] [Accepted: 04/06/2021] [Indexed: 12/14/2022] Open
Abstract
Here, we provide evidence for the presence of Myosin phosphatase rho-interacting protein (MPRIP), an F-actin-binding protein, in the cell nucleus. The MPRIP protein binds to Phosphatidylinositol 4,5-bisphosphate (PIP2) and localizes to the nuclear speckles and nuclear lipid islets which are known to be involved in transcription. We identified MPRIP as a component of RNA Polymerase II/Nuclear Myosin 1 complex and showed that MPRIP forms phase-separated condensates which are able to bind nuclear F-actin fibers. Notably, the fibrous MPRIP preserves its liquid-like properties and reforms the spherical shaped condensates when F-actin is disassembled. Moreover, we show that the phase separation of MPRIP is driven by its long intrinsically disordered region at the C-terminus. We propose that the PIP2/MPRIP association might contribute to the regulation of RNAPII transcription via phase separation and nuclear actin polymerization.
Collapse
|
19
|
Mazloumi Gavgani F, Karlsson T, Tangen IL, Morovicz AP, Arnesen VS, Turcu DC, Ninzima S, Spang K, Krakstad C, Guillermet-Guibert J, Lewis AE. Nuclear upregulation of class I phosphoinositide 3-kinase p110β correlates with high 47S rRNA levels in cancer cells. J Cell Sci 2021; 134:jcs.246090. [PMID: 33536247 DOI: 10.1242/jcs.246090] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 12/24/2020] [Indexed: 12/12/2022] Open
Abstract
The class I phosphoinositide 3-kinase (PI3K) catalytic subunits p110α and p110β are ubiquitously expressed but differently targeted in tumours. In cancer, PIK3CB (encoding p110β) is seldom mutated compared with PIK3CA (encoding p110α) but can contribute to tumorigenesis in certain PTEN-deficient tumours. The underlying molecular mechanisms are, however, unclear. We have previously reported that p110β is highly expressed in endometrial cancer (EC) cell lines and at the mRNA level in primary patient tumours. Here, we show that p110β protein levels are high in both the cytoplasmic and nuclear compartments in EC cells. Moreover, high nuclear:cytoplasmic staining ratios were detected in high-grade primary tumours. High levels of phosphatidylinositol (3,4,5)-trisphosphate [PtdIns(3,4,5)P 3] were measured in the nucleus of EC cells, and pharmacological and genetic approaches showed that its production was partly dependent upon p110β activity. Using immunofluorescence staining, p110β and PtdIns(3,4,5)P 3 were localised in the nucleolus, which correlated with high levels of 47S pre-rRNA. p110β inhibition led to a decrease in both 47S rRNA levels and cell proliferation. In conclusion, these results present a nucleolar role for p110β that may contribute to tumorigenesis in EC.This article has an associated First Person interview with Fatemeh Mazloumi Gavgani, joint first author of the paper.
Collapse
Affiliation(s)
| | - Thomas Karlsson
- Department of Biological Sciences, University of Bergen, Bergen 5008, Norway
| | - Ingvild L Tangen
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen 5021, Norway.,Department of Gynaecology and Obstetrics, Haukeland University Hospital, Bergen 5021, Norway
| | | | | | - Diana C Turcu
- Department of Biological Sciences, University of Bergen, Bergen 5008, Norway
| | - Sandra Ninzima
- Department of Biological Sciences, University of Bergen, Bergen 5008, Norway
| | - Katharina Spang
- Department of Biological Sciences, University of Bergen, Bergen 5008, Norway
| | - Camilla Krakstad
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen 5021, Norway.,Department of Gynaecology and Obstetrics, Haukeland University Hospital, Bergen 5021, Norway
| | - Julie Guillermet-Guibert
- Inserm U1037, Centre de Recherches en Cancérologie de Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Université Toulouse III Paul Sabatier, 31037 Toulouse, France
| | - Aurélia E Lewis
- Department of Biological Sciences, University of Bergen, Bergen 5008, Norway
| |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Limited Proteolysis-Coupled Mass Spectrometry Identifies Phosphatidylinositol 4,5-Bisphosphate Effectors in Human Nuclear Proteome. Cells 2021; 10:cells10010068. [PMID: 33406800 PMCID: PMC7824793 DOI: 10.3390/cells10010068] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/23/2020] [Accepted: 12/29/2020] [Indexed: 12/20/2022] Open
Abstract
Specific nuclear sub-compartments that are regions of fundamental processes such as gene expression or DNA repair, contain phosphoinositides (PIPs). PIPs thus potentially represent signals for the localization of specific proteins into different nuclear functional domains. We performed limited proteolysis followed by label-free quantitative mass spectrometry and identified nuclear protein effectors of the most abundant PIP—phosphatidylinositol 4,5-bisphosphate (PIP2). We identified 515 proteins with PIP2-binding capacity of which 191 ‘exposed’ proteins represent a direct PIP2 interactors and 324 ‘hidden’ proteins, where PIP2 binding was increased upon trypsin treatment. Gene ontology analysis revealed that ‘exposed’ proteins are involved in the gene expression as regulators of Pol II, mRNA splicing, and cell cycle. They localize mainly to non-membrane bound organelles—nuclear speckles and nucleolus and are connected to the actin nucleoskeleton. ‘Hidden’ proteins are linked to the gene expression, RNA splicing and transport, cell cycle regulation, and response to heat or viral infection. These proteins localize to the nuclear envelope, nuclear pore complex, or chromatin. Bioinformatic analysis of peptides bound in both groups revealed that PIP2-binding motifs are in general hydrophilic. Our data provide an insight into the molecular mechanism of nuclear PIP2 protein interaction and advance the methodology applicable for further studies of PIPs or other protein ligands.
Collapse
|
22
|
Santos AP, Gaudin V, Mozgová I, Pontvianne F, Schubert D, Tek AL, Dvořáčková M, Liu C, Fransz P, Rosa S, Farrona S. Tidying-up the plant nuclear space: domains, functions, and dynamics. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5160-5178. [PMID: 32556244 PMCID: PMC8604271 DOI: 10.1093/jxb/eraa282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/12/2020] [Indexed: 05/07/2023]
Abstract
Understanding how the packaging of chromatin in the nucleus is regulated and organized to guide complex cellular and developmental programmes, as well as responses to environmental cues is a major question in biology. Technological advances have allowed remarkable progress within this field over the last years. However, we still know very little about how the 3D genome organization within the cell nucleus contributes to the regulation of gene expression. The nuclear space is compartmentalized in several domains such as the nucleolus, chromocentres, telomeres, protein bodies, and the nuclear periphery without the presence of a membrane around these domains. The role of these domains and their possible impact on nuclear activities is currently under intense investigation. In this review, we discuss new data from research in plants that clarify functional links between the organization of different nuclear domains and plant genome function with an emphasis on the potential of this organization for gene regulation.
Collapse
Affiliation(s)
- Ana Paula Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova
de Lisboa, Oeiras, Portugal
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université
Paris-Saclay, Versailles, France
| | - Iva Mozgová
- Biology Centre of the Czech Academy of Sciences, České
Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České
Budějovice, Czech Republic
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de
Perpignan Via Domitia, Perpignan, France
| | - Daniel Schubert
- Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Ahmet L Tek
- Agricultural Genetic Engineering Department, Niğde Ömer Halisdemir
University, Niğde, Turkey
| | | | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of
Tübingen, Tübingen, Germany
- Institute of Biology, University of Hohenheim, Stuttgart,
Germany
| | - Paul Fransz
- University of Amsterdam, Amsterdam, The
Netherlands
| | - Stefanie Rosa
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, NUI Galway,
Galway, Ireland
| |
Collapse
|
23
|
Fang F, Ye S, Tang J, Bennett MJ, Liang W. DWT1/DWL2 act together with OsPIP5K1 to regulate plant uniform growth in rice. THE NEW PHYTOLOGIST 2020; 225:1234-1246. [PMID: 31550392 DOI: 10.1111/nph.16216] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 09/14/2019] [Indexed: 05/27/2023]
Abstract
Uniform growth of the main shoot and tillers significantly influences rice plant architecture and grain yield. The WUSCHEL-related homeobox transcription factor DWT1 is a key regulator of this important agronomic trait, disruption of which causes enhanced main shoot dominance and tiller dwarfism by an unknown mechanism. Here, we have used yeast-two-hybrid screening to identify OsPIP5K1, a member of the rice phosphatidylinositol-4-phosphate 5-kinase family, as a protein that interacts with DWT1. Cytological analyses confirmed that DWT1 induces accumulation of OsPIP5K1 and its product PI(4,5)P2 , a phosphoinositide secondary messenger, in nuclear bodies. Mutation of OsPIP5K1 compounds the dwarf dwt1 phenotype but abolishes the main shoot dominance. Conversely, overexpression of OsPIP5K1 partially rescues dwt1 developmental defects. Furthermore, we showed that DWL2, the homologue of DWT1, is also able to interact with OsPIP5K1 and shares partial functional redundancy with DWT1 in controlling rice uniformity. Overall, our data suggest that nuclear localised OsPIP5K1 acts with DWT1 and/or DWL2 to coordinate the uniform growth of rice shoots, likely to be through nuclear phosphoinositide signals, and provides insights into the regulation of rice uniformity via a largely unexplored plant nuclear signalling pathway.
Collapse
Affiliation(s)
- Fang Fang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Shiwei Ye
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Jingyao Tang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| |
Collapse
|
24
|
Jakubec M, Bariås E, Kryuchkov F, Hjørnevik LV, Halskau Ø. Fast and Quantitative Phospholipidomic Analysis of SH-SY5Y Neuroblastoma Cell Cultures Using Liquid Chromatography-Tandem Mass Spectrometry and 31P Nuclear Magnetic Resonance. ACS OMEGA 2019; 4:21596-21603. [PMID: 31867556 PMCID: PMC6921604 DOI: 10.1021/acsomega.9b03463] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 11/08/2019] [Indexed: 05/04/2023]
Abstract
Global lipid analysis still lags behind proteomics with respect to the availability of databases, experimental protocols, and specialized software. Determining the lipidome of cellular model systems in common use is of particular importance, especially when research questions involve lipids directly. In Parkinson's disease research, there is a growing awareness for the role of the biological membrane, where individual lipids may contribute to provoking α-synuclein oligomerisation and fibrillation. We present an analysis of the whole cell and plasma membrane lipid isolates of a neuroblastoma cell line, SH-SY5Y, a commonly used model system for research on this and other neurodegenerative diseases. We have used two complementary lipidomics methods. The relative quantities of PC, PE, SMs, CL, PI, PG, and PS were determined by 31P NMR. Fatty acid chain composition and their relative abundances within each phospholipid group were evaluated by liquid chromatography-tandem mass spectrometry. For this part of the analysis, we have developed and made available a set of Matlab scripts, LipMat. Our approach allowed us to observe several deviations of lipid abundances when compared to published reports regarding phospholipid analysis of cell cultures or brain matter. The most striking was the high abundance of PC (54.7 ± 1.9%) and low abundance of PE (17.8 ± 4.8%) and SMs (2.7 ± 1.2%). In addition, the observed abundance of PS was smaller than expected (4.7 ± 2.7%), similar to the observed abundance of PG (4.5 ± 1.8%). The observed fatty acid chain distribution was similar to the whole brain content with some notable differences: a higher abundance of 16:1 PC FA (17.4 ± 3.4% in PC whole cell content), lower abundance of 22:6 PE FA (15.9 ± 2.2% in plasma membrane fraction), and a complete lack of 22:6 PS FA.
Collapse
Affiliation(s)
- Martin Jakubec
- Faculty of Mathematics
and Natural Sciences, Department of Biological Sciences, University of Bergen, PB 7803, Bergen NO 5020, Norway
| | - Espen Bariås
- Faculty of Mathematics
and Natural Sciences, Department of Biological Sciences, University of Bergen, PB 7803, Bergen NO 5020, Norway
| | - Fedor Kryuchkov
- Faculty of Veterinary and Biosciences, Norwegian University of Life Sciences, Ullevålsveien 68, Oslo, Akershus NO 0033, Norway
| | - Linda Veka Hjørnevik
- Faculty of Mathematics
and Natural Sciences, Department of Biological Sciences, University of Bergen, PB 7803, Bergen NO 5020, Norway
| | - Øyvind Halskau
- Faculty of Mathematics
and Natural Sciences, Department of Biological Sciences, University of Bergen, PB 7803, Bergen NO 5020, Norway
- E-mail:
| |
Collapse
|
25
|
Lin TC, Kuo HH, Wu YC, Pan TS, Yih LH. Phosphatidylinositol-5-phosphate 4-kinase gamma accumulates at the spindle pole and prevents microtubule depolymerization. Cell Div 2019; 14:9. [PMID: 31452676 PMCID: PMC6702725 DOI: 10.1186/s13008-019-0053-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 08/13/2019] [Indexed: 11/10/2022] Open
Abstract
Background A previous screen of a human kinase and phosphatase shRNA library to select genes that mediate arsenite induction of spindle abnormalities resulted in the identification of phosphatidylinositol-5-phosphate 4-kinase type-2 gamma (PIP4KIIγ), a phosphatidylinositol 4,5-bisphosphate (PIP2)-synthesizing enzyme. In this study, we explored how PIP4KIIγ regulates the assembly of mitotic spindles. Results PIP4KIIγ accumulates at the spindle pole before anaphase, and is required for the assembly of functional bipolar spindles. Depletion of PIP4KIIγ enhanced the spindle pole accumulation of mitotic centromere-associated kinesin (MCAK), a microtubule (MT)-depolymerizing kinesin, and resulted in a less stable spindle pole-associated MT. Depletion of MCAK can ameliorate PIP4KIIγ depletion-induced spindle abnormalities. In addition, PIP2 binds to polo-like kinase (PLK1) and reduces PLK1-mediated phosphorylation of MCAK. These results indicate that PIP4KIIγ and PIP2 may negatively regulate the MT depolymerization activity of MCAK by reducing PLK1-mediated phosphorylation of MCAK. Consequently, depletion of PLK1 has been shown to counteract the PIP4KIIγ depletion-induced instability of spindle pole-associated MT and cell resistance to arsenite. Conclusions Our current results imply that PIP4KIIγ may restrain MT depolymerization at the spindle pole through attenuating PLK1-mediated activation of MCAK before anaphase onset.
Collapse
Affiliation(s)
- Tz-Chi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Hsiao-Hui Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Yi-Chen Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Tiffany S Pan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Ling-Huei Yih
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115 Taiwan
| |
Collapse
|
26
|
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.
Collapse
|
27
|
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.
Collapse
|
28
|
Maraldi NM. In search of a primitive signaling code. Biosystems 2019; 183:103984. [PMID: 31201829 DOI: 10.1016/j.biosystems.2019.103984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 10/26/2022]
Abstract
Cells must have preceded by simpler chemical systems (protocells) that had the capacity of a spontaneous self-assembly process and the ability to confine chemical reaction networks together with a form of information. The presence of lipid molecules in the early Earth conditions is sufficient to ensure the occurrence of spontaneous self-assembly processes, not defined by genetic information, but related to their chemical amphiphilic nature. Ribozymes are plausible molecules for early life, being the first small polynucleotides made up of random oligomers or formed by non-enzymatic template copying. Compartmentalization represents a strategy for the evolution of ribozymes; the attachment of ribozymes to surfaces, such as formed by lipid micellar aggregates may be particular relevant if the surface itself catalyzes RNA polymerization.It is conceivable that the transition from pre-biotic molecular aggregates to cellular life required the coevolution of the RNA world, capable of synthesizing specific, instead of statistical proteins, and of the Lipid world, with a transition from micellar aggregates to semipermeable vesicles. Small molecules available in the prebiotic inventory might promote RNA stability and the evolution of hydrophobic micellar aggregates into membrane-delimited vesicles. The transition from ribozymes catalyzing the assembly of statistical polypeptides to the synthesis of proteins, required the appearance of the genetic code; the transition from hydrophobic platforms favoring the stability of ribozymes and of nascent polypeptides to the selective transport of reagents through a membrane, required the appearance of the signal transduction code.A further integration between the RNA and Lipid worlds can be advanced, taking into account the emerging roles of phospholipid aggregates not only in ensuring stability to ribozymes by compartmentalization, but also in a crucial step of evolution through natural selection mechanisms, based on signal transduction pathways that convert environmental changes into biochemical responses that could vary according to the context. Here I present evidences on the presence of traces of the evolution of a signal transduction system in extant cells, which utilize a phosphoinositide signaling system located both at nucleoplasmic level as well as at the plasma membrane, based on the very same molecules but responding to different rules. The model herewith proposed is based on the following assumptions on the biomolecules of extant organisms: i) amphiphils can be converted into structured aggregates by hydrophobic forces thus giving rise to functional platforms for the interaction of other biomolecules and to their compartmentalization; ii) fundamental biochemical pathways, including protein synthesis, can be sustained by natural ribozymes of ancient origin; iii) ribozymes and nucleotide-derived coenzymes could have existed long before protein enzymes emerged; iv) signaling molecules, both derived from phospholipids and from RNAs could have guided the evolution of complex metabolic processes before the emergence of proteins.
Collapse
Affiliation(s)
- Nadir M Maraldi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| |
Collapse
|
29
|
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.
Collapse
|
30
|
Choi S, Chen M, Cryns VL, Anderson RA. A nuclear phosphoinositide kinase complex regulates p53. Nat Cell Biol 2019; 21:462-475. [PMID: 30886346 DOI: 10.1038/s41556-019-0297-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 02/11/2019] [Indexed: 12/29/2022]
Abstract
The tumour suppressor p53 (encoded by TP53) protects the genome against cellular stress and is frequently mutated in cancer. Mutant p53 acquires gain-of-function oncogenic activities that are dependent on its enhanced stability. However, the mechanisms by which nuclear p53 is stabilized are poorly understood. Here, we demonstrate that the stability of stress-induced wild-type and mutant p53 is regulated by the type I phosphatidylinositol phosphate kinase (PIPKI-α (also known as PIP5K1A)) and its product phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2). Nuclear PIPKI-α binds to p53 upon stress, resulting in the production and association of PtdIns(4,5)P2 with p53. PtdIns(4,5)P2 binding promotes the interaction between p53 and the small heat shock proteins HSP27 (also known as HSPB1) and αB-crystallin (also known as HSPB5), which stabilize nuclear p53. Moreover, inhibition of PIPKI-α or PtdIns(4,5)P2 association results in p53 destabilization. Our results point to a previously unrecognized role of nuclear phosphoinositide signalling in regulating p53 stability and implicate this pathway as a promising therapeutic target in cancer.
Collapse
Affiliation(s)
- Suyong Choi
- University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Mo Chen
- University of Wisconsin-Madison, School of Medicine and Public Health, 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
- University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA.
| |
Collapse
|
31
|
Phosphoinositides: multipurpose cellular lipids with emerging roles in cell death. Cell Death Differ 2019; 26:781-793. [PMID: 30742090 DOI: 10.1038/s41418-018-0269-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 02/07/2023] Open
Abstract
Phosphorylated phosphatidylinositol lipids, or phosphoinositides, critically regulate diverse cellular processes, including signalling transduction, cytoskeletal reorganisation, membrane dynamics and cellular trafficking. However, phosphoinositides have been inadequately investigated in the context of cell death, where they are mainly regarded as signalling secondary messengers. However, recent studies have begun to highlight the importance of phosphoinositides in facilitating cell death execution. Here, we cover the latest phosphoinositide research with a particular focus on phosphoinositides in the mechanisms of cell death. This progress article also raises key questions regarding the poorly defined role of phosphoinositides, particularly during membrane-associated events in cell death such as apoptosis and secondary necrosis. The review then further discusses important future directions for the phosphoinositide field, including therapeutically targeting phosphoinositides to modulate cell death.
Collapse
|
32
|
Bucki R, Wang YH, Yang C, Kandy SK, Fatunmbi O, Bradley R, Pogoda K, Svitkina T, Radhakrishnan R, Janmey PA. Lateral distribution of phosphatidylinositol 4,5-bisphosphate in membranes regulates formin- and ARP2/3-mediated actin nucleation. J Biol Chem 2019; 294:4704-4722. [PMID: 30692198 DOI: 10.1074/jbc.ra118.005552] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/13/2019] [Indexed: 11/06/2022] Open
Abstract
Spatial and temporal control of actin polymerization is fundamental for many cellular processes, including cell migration, division, vesicle trafficking, and response to agonists. Many actin-regulatory proteins interact with phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and are either activated or inactivated by local PI(4,5)P2 concentrations that form transiently at the cytoplasmic face of cell membranes. The molecular mechanisms of these interactions and how the dozens of PI(4,5)P2-sensitive actin-binding proteins are selectively recruited to membrane PI(4,5)P2 pools remains undefined. Using a combination of biochemical, imaging, and cell biologic studies, combined with molecular dynamics and analytical theory, we test the hypothesis that the lateral distribution of PI(4,5)P2 within lipid membranes and native plasma membranes alters the capacity of PI(4,5)P2 to nucleate actin assembly in brain and neutrophil extracts and show that activities of formins and the Arp2/3 complex respond to PI(4,5)P2 lateral distribution. Simulations and analytical theory show that cholesterol promotes the cooperative interaction of formins with multiple PI(4,5)P2 headgroups in the membrane to initiate actin nucleation. Masking PI(4,5)P2 with neomycin or disrupting PI(4,5)P2 domains in the plasma membrane by removing cholesterol decreases the ability of these membranes to nucleate actin assembly in cytoplasmic extracts.
Collapse
Affiliation(s)
- Robert Bucki
- From the Departments of Physiology, .,the Department of Microbiological and Nanobiomedical Engineering, Medical University of Białystok, 15-089 Białystok, Poland
| | - Yu-Hsiu Wang
- Chemistry.,the Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | | | - Sreeja Kutti Kandy
- Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Ololade Fatunmbi
- Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Ryan Bradley
- Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Katarzyna Pogoda
- From the Departments of Physiology.,the Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland, and
| | | | - Ravi Radhakrishnan
- Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Paul A Janmey
- From the Departments of Physiology.,the Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| |
Collapse
|
33
|
Marx B, Hufbauer M, Zigrino P, Majewski S, Markiefka B, Sachsenheimer T, Brügger B, Akgül B. Phospholipidation of nuclear proteins by the human papillomavirus E6 oncoprotein: implication in carcinogenesis. Oncotarget 2018; 9:34142-34158. [PMID: 30344928 PMCID: PMC6183346 DOI: 10.18632/oncotarget.26140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 09/06/2018] [Indexed: 12/16/2022] Open
Abstract
Phospholipids regulate numerous cellular functions and their deregulation is known to be associated with cancer development. Here, we show for the first time that expression of the E6 oncoprotein of human papillomavirus type 8 (HPV8) leads to a profound increase in nuclear phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) lipid levels in monolayer cultures, that led to an aberrant phospholipidation of cellular proteins. Elevated PI(4,5)P2 levels in organotypic skin cultures, skin tumors of K14-HPV8-E6 transgenic mice as well as HPV8 positive skin carcinomas highly suggest a decisive role of PI(4,5)P2 in HPV associated squamous-cell-carcinoma development. Furthermore, mass-spectrometric analysis confirmed an increase of PI(4,5)P2, which was characterized by a shift in the distribution of lipid species. PI(4,5)P2 upregulation was independent of E6 interference with MAML1. However, E6 does interfere with the PI(4,5)P2 metabolic pathway by upregulation of phosphatidylinositol-4-phosphate-5-kinase type I and phosphatidylinositol-5-phosphate 4-kinase type II as well as the binding to 5'-phosphatase OCRL and phosphatidylinositol. All of these mechanisms combined may contribute to PI(4,5)P2 elevation in E6 positive cells. The identification of CAND1 and SND1 - two proteins known to be involved in carcinogenic processes - were significantly stronger phospholipidized in the presence of E6. In conclusion we provide evidence that the modulation of the PI(4,5)P2 metabolism is a novel oncogenic mechanism relevant for HPV-induced carcinogenesis.
Collapse
Affiliation(s)
- Benjamin Marx
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Martin Hufbauer
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Paola Zigrino
- Department of Dermatology and Venereology, University Hospital Cologne, Cologne, Germany
| | - Slawomir Majewski
- Department of Dermatology and Venereology, Medical University of Warsaw, Warsaw, Poland
| | - Birgid Markiefka
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Baki Akgül
- Institute of Virology, University of Cologne, Cologne, Germany
| |
Collapse
|
34
|
Sztacho M, Sobol M, Balaban C, Escudeiro Lopes SE, Hozák P. Nuclear phosphoinositides and phase separation: Important players in nuclear compartmentalization. Adv Biol Regul 2018; 71:111-117. [PMID: 30249540 DOI: 10.1016/j.jbior.2018.09.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/14/2018] [Accepted: 09/15/2018] [Indexed: 02/08/2023]
Abstract
Nuclear phosphoinositides are recognized as regulators of many nuclear processes including chromatin remodeling, splicing, transcription, DNA repair and epigenetics. These processes are spatially organized in different nuclear compartments. Phase separation is involved in the formation of various nuclear compartments and molecular condensates separated from surrounding environment. The surface of such structures spatiotemporally coordinates formation of protein complexes. PI(4,5)P2 (PIP2) integration into phase-separated structures might provide an additional step in their spatial diversification by attracting certain proteins with affinity to PIP2. Our laboratory has recently identified novel membrane-free PIP2-containing structures, so called Nuclear Lipid Islets (NLIs). We provide an evidence that these structures are evolutionary conserved in different organisms. We hypothesize that NLIs serve as a scaffolding platform which facilitates the formation of transcription factories, thus participating in the formation of nuclear architecture competent for transcription. In this review we speculate on a possible role of NLIs in the integration of various processes linked to RNAPII transcription, chromatin remodeling, actin-myosin interaction, alternative splicing and lamin structures.
Collapse
Affiliation(s)
- Martin Sztacho
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic
| | - Margarita Sobol
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic
| | - Can Balaban
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic
| | - Sara Eliana Escudeiro Lopes
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic; Department of Epigenetics of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., division BIOCEV, 25250, Vestec, Czech Republic; Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic.
| |
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
Phospholipids and inositol phosphates linked to the epigenome. Histochem Cell Biol 2018; 150:245-253. [DOI: 10.1007/s00418-018-1690-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2018] [Indexed: 12/17/2022]
|
37
|
PIP2 epigenetically represses rRNA genes transcription interacting with PHF8. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:266-275. [DOI: 10.1016/j.bbalip.2017.12.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/05/2017] [Accepted: 12/09/2017] [Indexed: 02/01/2023]
|
38
|
DNA damage causes rapid accumulation of phosphoinositides for ATR signaling. Nat Commun 2017; 8:2118. [PMID: 29242514 PMCID: PMC5730617 DOI: 10.1038/s41467-017-01805-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 10/13/2017] [Indexed: 12/11/2022] Open
Abstract
Phosphoinositide lipids (PPIs) are enriched in the nucleus and are accumulated at DNA damage sites. Here, we investigate roles of nuclear PPIs in DNA damage response by sequestering specific PPIs with the expression of nuclear-targeted PH domains, which inhibits recruitment of Ataxia telangiectasia and Rad3-related protein (ATR) and reduces activation of Chk1. PPI-binding domains rapidly (< 1 s) accumulate at damage sites with local enrichment of PPIs. Accumulation of PIP3 in complex with the nuclear receptor protein, SF1, at damage sites requires phosphorylation by inositol polyphosphate multikinase (IPMK) and promotes nuclear actin assembly that is required for ATR recruitment. Suppressed ATR recruitment/activation is confirmed with latrunculin A and wortmannin treatment as well as IPMK or SF1 depletion. Other DNA repair pathways involving ATM and DNA-PKcs are unaffected by PPI sequestration. Together, these findings reveal that nuclear PPI metabolism mediates an early damage response through the IPMK-dependent pathway to specifically recruit ATR. Phosphoinositides are enriched in the nucleus and accumulate upon DNA damage but their role in responding to DNA damage is poorly defined. Here, the authors show that phosphoinositides rapidly accumulate at DNA damage sites and are required for ATR recruitment and subsequent Chk1 activation.
Collapse
|
39
|
Hoffmann C, Weigert C. Skeletal Muscle as an Endocrine Organ: The Role of Myokines in Exercise Adaptations. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a029793. [PMID: 28389517 DOI: 10.1101/cshperspect.a029793] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Exercise stimulates the release of proteins with autocrine, paracrine, or endocrine functions produced in skeletal muscle, termed myokines. Based on the current state of knowledge, the major physiological function of myokines is to protect the functionality and to enhance the exercise capacity of skeletal muscle. Myokines control adaptive processes in skeletal muscle by acting as paracrine regulators of fuel oxidation, hypertrophy, angiogenesis, inflammatory processes, and regulation of the extracellular matrix. Endocrine functions attributed to myokines are involved in body weight regulation, low-grade inflammation, insulin sensitivity, suppression of tumor growth, and improvement of cognitive function. Muscle-derived regulatory RNAs and metabolites, as well as the design of modified myokines, are promising novel directions for treatment of chronic diseases.
Collapse
Affiliation(s)
- Christoph Hoffmann
- Division of Pathobiochemistry and Clinical Chemistry, Department of Internal Medicine IV, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Cora Weigert
- Division of Pathobiochemistry and Clinical Chemistry, Department of Internal Medicine IV, University Hospital Tübingen, 72076 Tübingen, Germany.,Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum München at the University of Tübingen, 72076 Tübingen, Germany.,German Center for Diabetes Research (DZD), 85764 München-Neuherberg, Germany
| |
Collapse
|
40
|
Marx B, Miller-Lazic D, Doorbar J, Majewski S, Hofmann K, Hufbauer M, Akgül B. HPV8-E6 Interferes with Syntenin-2 Expression through Deregulation of Differentiation, Methylation and Phosphatidylinositide-Kinase Dependent Mechanisms. Front Microbiol 2017; 8:1724. [PMID: 28970821 PMCID: PMC5609557 DOI: 10.3389/fmicb.2017.01724] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/24/2017] [Indexed: 12/01/2022] Open
Abstract
The E6 oncoproteins of high-risk human papillomaviruses (HPV) of genus alpha contain a short peptide sequence at the carboxy-terminus, the PDZ binding domain, with which they interact with the corresponding PDZ domain of cellular proteins. Interestingly, E6 proteins from papillomaviruses of genus beta (betaPV) do not encode a comparable PDZ binding domain. Irrespective of this fact, we previously showed that the E6 protein of HPV8 (betaPV type) could circumvent this deficit by targeting the PDZ protein Syntenin-2 through transcriptional repression (Lazic et al., 2012). Despite its high binding affinity to phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2), very little is known about Syntenin-2. This study aimed to extend the knowledge on Syntenin-2 and how its expression is controlled. We now identified that Syntenin-2 is expressed at high levels in differentiating and in lower amounts in keratinocytes cultured in serum-free media containing low calcium concentration. HPV8-E6 led to a further reduction of Syntenin-2 expression only in cells cultured in low calcium. In the skin of patients suffering from Epidermodysplasia verruciformis, who are predisposed to betaPV infection, Syntenin-2 was expressed in differentiating keratinocytes of non-lesional skin, but was absent in virus positive squamous tumors. Using 5-Aza-2′-deoxycytidine, which causes DNA demethylation, Syntenin-2 transcription was profoundly activated and fully restored in the absence and presence of HPV8-E6, implicating that E6 mediated repression of Syntenin-2 transcription is due to promoter hypermethylation. Since Syntenin-2 binds to PI(4,5)P2, we further tested whether the PI(4,5)P2 metabolic pathway might govern Syntenin-2 expression. PI(4,5)P2 is generated by the activity of phosphatidylinositol-4-phosphate-5-kinase type I (PIP5KI) or phosphatidylinositol-5-phosphate-4-kinase type II (PIP4KII) isoforms α, β and γ. Phosphatidylinositide kinases have recently been identified as regulators of gene transcription. Surprisingly, transfection of siRNAs directed against PIP5KI and PIP4KII resulted in higher Syntenin-2 expression with the highest effect mediated by siPIP5KIα. HPV8-E6 was able to counteract siPIP4KIIα, siPIP4KIIβ and siPIP5KIγ mediated Syntenin-2 re-expression but not siPIP5KIα. Finally, we identified Syntenin-2 as a key factor regulating PIP5KIα expression. Collectively, our data demonstrates that Syntenin-2 is regulated through multiple mechanisms and that downregulation of Syntenin-2 expression may contribute to E6 mediated dedifferentiation of infected skin cells.
Collapse
Affiliation(s)
- Benjamin Marx
- Institute of Virology, University of CologneCologne, Germany
| | | | - John Doorbar
- Department of Pathology, University of CambridgeCambridge, United Kingdom
| | - Slawomir Majewski
- Department of Dermatology and Venereology, Medical University of WarsawWarsaw, Poland
| | - Kay Hofmann
- Institute for Genetics, University of CologneCologne, Germany
| | - Martin Hufbauer
- Institute of Virology, University of CologneCologne, Germany
| | - Baki Akgül
- Institute of Virology, University of CologneCologne, Germany
| |
Collapse
|
41
|
Kostrhon S, Kontaxis G, Kaufmann T, Schirghuber E, Kubicek S, Konrat R, Slade D. A histone-mimicking interdomain linker in a multidomain protein modulates multivalent histone binding. J Biol Chem 2017; 292:17643-17657. [PMID: 28864776 PMCID: PMC5663869 DOI: 10.1074/jbc.m117.801464] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/28/2017] [Indexed: 01/18/2023] Open
Abstract
N-terminal histone tails are subject to many posttranslational modifications that are recognized by and interact with designated reader domains in histone-binding proteins. BROMO domain adjacent to zinc finger 2B (BAZ2B) is a multidomain histone-binding protein that contains two histone reader modules, a plant homeodomain (PHD) and a bromodomain (BRD), linked by a largely disordered linker. Although previous studies have reported specificity of the PHD domain for the unmodified N terminus of histone H3 and of the BRD domain for H3 acetylated at Lys14 (H3K14ac), the exact mode of H3 binding by BAZ2B and its regulation are underexplored. Here, using isothermal titration calorimetry and NMR spectroscopy, we report that acidic residues in the BAZ2B PHD domain are essential for H3 binding and that BAZ2B PHD–BRD establishes a polyvalent interaction with H3K14ac. Furthermore, we provide evidence that the disordered interdomain linker modulates the histone-binding affinity by interacting with the PHD domain. In particular, lysine-rich stretches in the linker, which resemble the positively charged N terminus of histone H3, reduce the binding affinity of the PHD finger toward the histone substrate. Phosphorylation, acetylation, or poly(ADP-ribosyl)ation of the linker residues may therefore act as a cellular mechanism to transiently tune BAZ2B histone-binding affinity. Our findings further support the concept of interdomain linkers serving a dual role in substrate binding by appropriately positioning the adjacent domains and by electrostatically modulating substrate binding. Moreover, inhibition of histone binding by a histone-mimicking interdomain linker represents another example of regulation of protein–protein interactions by intramolecular mimicry.
Collapse
Affiliation(s)
- Sebastian Kostrhon
- From the Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Georg Kontaxis
- the Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Tanja Kaufmann
- From the Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Erika Schirghuber
- the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1030 Vienna, Austria, and.,the Christian Doppler Laboratory for Chemical Epigenetics and Antiinfectives, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Stefan Kubicek
- the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1030 Vienna, Austria, and.,the Christian Doppler Laboratory for Chemical Epigenetics and Antiinfectives, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Robert Konrat
- the Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Dea Slade
- From the Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria,
| |
Collapse
|
42
|
Finelli MJ, Oliver PL. TLDc proteins: new players in the oxidative stress response and neurological disease. Mamm Genome 2017; 28:395-406. [PMID: 28707022 PMCID: PMC5614904 DOI: 10.1007/s00335-017-9706-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/03/2017] [Indexed: 12/14/2022]
Abstract
Oxidative stress (OS) arises from an imbalance in the cellular redox state, which can lead to intracellular damage and ultimately cell death. OS occurs as a result of normal ageing, but it is also implicated as a common etiological factor in neurological disease; thus identifying novel proteins that modulate the OS response may facilitate the design of new therapeutic approaches applicable to many disorders. In this review, we describe the recent progress that has been made using a range of genetic approaches to understand a family of proteins that share the highly conserved TLDc domain. We highlight their shared ability to prevent OS-related cell death and their unique functional characteristics, as well as discussing their potential application as new neuroprotective factors. Furthermore, with an increasing number of pathogenic mutations leading to epilepsy and hearing loss being discovered in the TLDc protein TBC1D24, understanding the function of this family has important implications for a range of inherited neurological diseases.
Collapse
Affiliation(s)
- Mattéa J Finelli
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, UK
| | - Peter L Oliver
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, UK.
| |
Collapse
|
43
|
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.
Collapse
|
44
|
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.
Collapse
|
45
|
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]
|
46
|
Tauber M, Fischle W. Conserved linker regions and their regulation determine multiple chromatin-binding modes of UHRF1. Nucleus 2016; 6:123-32. [PMID: 25891992 PMCID: PMC4615792 DOI: 10.1080/19491034.2015.1026022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Ubiquitin-like with PHD and RING Finger domains 1 (UHRF1) is an important nuclear protein that is mutated and aberrantly expressed in many tumors. The protein integrates different chromatin modifications and is essential for their maintenance throughout the cell cycle. Separate chromatin-binding modules of UHRF1 have been studied on a functional and structural level. The unmodified N-terminus of histone H3 is recognized by a PHD domain, while a TTD domain specifically interacts with histone H3 Lysine 9 trimethylation. A SRA region binds hemimethylatd DNA. Emerging evidence indicates that the modules of UHRF1 do not act independently of each other but establish complex modes of interaction with patterns of chromatin modifications. This multivalent readout is regulated by allosteric binding of phosphatidylinositol 5-phosphate to a region outside the PHD, TTD and SRA domains as well as by phosphorylation of one of the linker regions connecting these modules. Here, we summarize the current knowledge on UHRF1 chromatin interaction and introduce a novel model of conformational transitions of the protein that are directed by the flexible and highly charged linker regions. We propose that these are essential in setting up defined structural states of the protein where different domains or combinations thereof are available for binding chromatin modifications or are prevented from doing so. Lastly, we suggest that controlled tuning of intramolecular linker interactions by ligands and posttranslational modifications establishes a rational framework for comprehending UHRF1 regulation and putatively the working mode of other chromatin factors in different physiological contexts.
Collapse
Affiliation(s)
- Maria Tauber
- a Laboratory of Chromatin Biochemistry ; Max Planck Institute for Biophysical Chemistry ; Göttingen , Germany
| | | |
Collapse
|
47
|
Choi S, Anderson RA. IQGAP1 is a phosphoinositide effector and kinase scaffold. Adv Biol Regul 2015; 60:29-35. [PMID: 26554303 DOI: 10.1016/j.jbior.2015.10.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 10/05/2015] [Accepted: 10/06/2015] [Indexed: 01/16/2023]
Abstract
Phosphatidylinositol 4,5-bisphosphate (PI4,5P2) is a lipid messenger that regulates a wide variety of cellular functions. The majority of cellular PI4,5P2 is generated by isoforms of the type I phosphatidylinositol phosphate kinases (PIPKI) that are generated from three genes, and each PIPKI isoform has a unique distribution and function in cells. It has been shown that the signaling specificity of PI4,5P2 can be determined by a physical association of PIPKs with PI4,5P2 effectors. IQGAP1 is newly identified as an interactor of multiple isoforms of PIPKs. Considering the versatile roles of IQGAP1 in cellular signaling pathways, IQGAP1 may confer isoform-specific roles of PIPKs in distinct cellular locations. In this mini review, the emerging roles of PIPKs that are regulated by an association with IQGAP1 will be summarized. Focuses will be on cell migration, vesicle trafficking, cell signaling, and nuclear events.
Collapse
Affiliation(s)
- Suyong Choi
- University of Wisconsin-Madison, School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
| | - Richard A Anderson
- University of Wisconsin-Madison, School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA.
| |
Collapse
|
48
|
Choi S, Thapa N, Tan X, Hedman AC, Anderson RA. PIP kinases define PI4,5P₂signaling specificity by association with effectors. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1851:711-23. [PMID: 25617736 PMCID: PMC4380618 DOI: 10.1016/j.bbalip.2015.01.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 01/14/2015] [Accepted: 01/16/2015] [Indexed: 12/21/2022]
Abstract
Phosphatidylinositol 4,5-bisphosphate (PI4,5P₂) is an essential lipid messenger with roles in all eukaryotes and most aspects of human physiology. By controlling the targeting and activity of its effectors, PI4,5P₂modulates processes, such as cell migration, vesicular trafficking, cellular morphogenesis, signaling and gene expression. In cells, PI4,5P₂has a much higher concentration than other phosphoinositide species and its total content is largely unchanged in response to extracellular stimuli. The discovery of a vast array of PI4,5P₂ binding proteins is consistent with data showing that the majority of cellular PI4,5P₂is sequestered. This supports a mechanism where PI4,5P₂functions as a localized and highly specific messenger. Further support of this mechanism comes from the de novo synthesis of PI4,5P₂which is often linked with PIP kinase interaction with PI4,5P₂effectors and is a mechanism to define specificity of PI4,5P₂signaling. The association of PI4,5P₂-generating enzymes with PI4,5P₂effectors regulate effector function both temporally and spatially in cells. In this review, the PI4,5P₂effectors whose functions are tightly regulated by associations with PI4,5P₂-generating enzymes will be discussed. This article is part of a Special Issue entitled Phosphoinositides.
Collapse
Affiliation(s)
- Suyong Choi
- Cellular and Molecular Biology Program, University of Wisconsin-Madison, School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
| | - Narendra Thapa
- Molecular and Cellular Pharmacology Program, University of Wisconsin-Madison, School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
| | - Xiaojun Tan
- Molecular and Cellular Pharmacology Program, University of Wisconsin-Madison, School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
| | - Andrew C Hedman
- Molecular and Cellular Pharmacology Program, University of Wisconsin-Madison, School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
| | - Richard A Anderson
- Cellular and Molecular Biology Program, University of Wisconsin-Madison, School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA; Molecular and Cellular Pharmacology Program, University of Wisconsin-Madison, School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA.
| |
Collapse
|
49
|
Stijf-Bultsma Y, Sommer L, Tauber M, Baalbaki M, Giardoglou P, Jones DR, Gelato KA, van Pelt J, Shah Z, Rahnamoun H, Toma C, Anderson KE, Hawkins P, Lauberth SM, Haramis APG, Hart D, Fischle W, Divecha N. The basal transcription complex component TAF3 transduces changes in nuclear phosphoinositides into transcriptional output. Mol Cell 2015; 58:453-67. [PMID: 25866244 PMCID: PMC4429956 DOI: 10.1016/j.molcel.2015.03.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 01/20/2015] [Accepted: 03/06/2015] [Indexed: 12/17/2022]
Abstract
Phosphoinositides (PI) are important signaling molecules in the nucleus that influence gene expression. However, if and how nuclear PI directly affects the transcriptional machinery is not known. We report that the lipid kinase PIP4K2B regulates nuclear PI5P and the expression of myogenic genes during myoblast differentiation. A targeted screen for PI interactors identified the PHD finger of TAF3, a TATA box binding protein-associated factor with important roles in transcription regulation, pluripotency, and differentiation. We show that the PI interaction site is distinct from the known H3K4me3 binding region of TAF3 and that PI binding modulates association of TAF3 with H3K4me3 in vitro and with chromatin in vivo. Analysis of TAF3 mutants indicates that TAF3 transduces PIP4K2B-mediated alterations in PI into changes in specific gene transcription. Our study reveals TAF3 as a direct target of nuclear PI and further illustrates the importance of basal transcription components as signal transducers.
Collapse
Affiliation(s)
- Yvette Stijf-Bultsma
- The Inositide Laboratory, Centre for Biological Sciences, Highfield Campus, University of Southampton, Southampton SO171BJ, UK; The Inositide Laboratory, the CRUK Manchester Institute, the University of Manchester, Wilmslow Road, Manchester M204BX, UK
| | - Lilly Sommer
- The Inositide Laboratory, the CRUK Manchester Institute, the University of Manchester, Wilmslow Road, Manchester M204BX, UK
| | - Maria Tauber
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Mai Baalbaki
- University of California, San Francisco, Mail Code 3120, Smith Cardiovascular Research Building, 555 Mission Bay Boulevard, South San Francisco, CA 94158-9001, USA
| | - Panagiota Giardoglou
- Institute of Biology (IBL), Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - David R Jones
- The Inositide Laboratory, the CRUK Manchester Institute, the University of Manchester, Wilmslow Road, Manchester M204BX, UK
| | - Kathy A Gelato
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jason van Pelt
- Institute of Biology (IBL), Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Zahid Shah
- The Inositide Laboratory, Centre for Biological Sciences, Highfield Campus, University of Southampton, Southampton SO171BJ, UK
| | - Homa Rahnamoun
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Clara Toma
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Karen E Anderson
- Signaling Laboratory, The Babraham Institute, Cambridge, Cambridgeshire CB22 3AT, UK
| | - Philip Hawkins
- Signaling Laboratory, The Babraham Institute, Cambridge, Cambridgeshire CB22 3AT, UK
| | - Shannon M Lauberth
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anna-Pavlina G Haramis
- Institute of Biology (IBL), Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Daniel Hart
- University of California, San Francisco, Mail Code 3120, Smith Cardiovascular Research Building, 555 Mission Bay Boulevard, South San Francisco, CA 94158-9001, USA
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Nullin Divecha
- The Inositide Laboratory, Centre for Biological Sciences, Highfield Campus, University of Southampton, Southampton SO171BJ, UK; The Inositide Laboratory, the CRUK Manchester Institute, the University of Manchester, Wilmslow Road, Manchester M204BX, UK.
| |
Collapse
|
50
|
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.
Collapse
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
| |
Collapse
|