1
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Vidalle MC, Sheth B, Fazio A, Marvi MV, Leto S, Koufi FD, Neri I, Casalin I, Ramazzotti G, Follo MY, Ratti S, Manzoli L, Gehlot S, Divecha N, Fiume R. Nuclear Phosphoinositides as Key Determinants of Nuclear Functions. Biomolecules 2023; 13:1049. [PMID: 37509085 PMCID: PMC10377365 DOI: 10.3390/biom13071049] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Polyphosphoinositides (PPIns) are signalling messengers representing less than five per cent of the total phospholipid concentration within the cell. Despite their low concentration, these lipids are critical regulators of various cellular processes, including cell cycle, differentiation, gene transcription, apoptosis and motility. PPIns are generated by the phosphorylation of the inositol head group of phosphatidylinositol (PtdIns). Different pools of PPIns are found at distinct subcellular compartments, which are regulated by an array of kinases, phosphatases and phospholipases. Six of the seven PPIns species have been found in the nucleus, including the nuclear envelope, the nucleoplasm and the nucleolus. The identification and characterisation of PPIns interactor and effector proteins in the nucleus have led to increasing interest in the role of PPIns in nuclear signalling. However, the regulation and functions of PPIns in the nucleus are complex and are still being elucidated. This review summarises our current understanding of the localisation, biogenesis and physiological functions of the different PPIns species in the nucleus.
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Affiliation(s)
- Magdalena C Vidalle
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Bhavwanti Sheth
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Antonietta Fazio
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Maria Vittoria Marvi
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Stefano Leto
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Foteini-Dionysia Koufi
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Irene Neri
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Irene Casalin
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Giulia Ramazzotti
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Matilde Y Follo
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Stefano Ratti
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Lucia Manzoli
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Sonakshi Gehlot
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Nullin Divecha
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Roberta Fiume
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
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2
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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.
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Affiliation(s)
- Nadir M Maraldi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
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3
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Ramamurthy B, Cohen S, Canales M, Coffman FD. Three-Dimensional Cellular Raman Analysis: Evidence of Highly Ordered Lipids Within Cell Nuclei. J Histochem Cytochem 2018; 66:889-902. [PMID: 30138043 DOI: 10.1369/0022155418794125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Striking levels of spatial organization exist among and within interphase cell chromosomes, raising the possibility that other nuclear molecular components may also be organized in ways that facilitate nuclear function. To further examine molecular distributions and organization within cell nuclei, we utilized Raman spectroscopy to map distributions of molecular components, with a focus on cellular lipids. Although the vast majority of cellular lipids are associated with membranes, mapping the 2870/2850 cm-1 lipid peak ratios revealed that the most highly ordered lipids within interphase cells are found within cell nuclei. This finding was seen in cells from multiple tissue types, noncancerous cells, and in cancer cell lines of different metastatic potential. These highly ordered lipids colocalize with nuclear chromatin, are present throughout the nuclear volume, and remain colocalized with chromatin through mitosis, when the nuclear envelope has dissociated. Phosphatidylinositol is a major component of the highly ordered lipids. The presence of phosphatidylinositol and other lipids in the nuclear interior is well established, but their highly ordered packing has not been reported and represents a unique finding. The molecular interactions involved in the formation and maintenance of these highly ordered lipids, and their potential effects on nuclear activities, remain to be discovered.
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Affiliation(s)
- Bhagavathi Ramamurthy
- Center for Biophysical Pathology, Newark, New Jersey.,Department of Biology, Delaware State University, Dover, Delaware
| | - Stanley Cohen
- Center for Biophysical Pathology, Newark, New Jersey.,Department of Pathology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | - Frederick D Coffman
- Center for Biophysical Pathology, Newark, New Jersey.,Department of Health Informatics and Department of Primary Care, Rutgers, The State University of New Jersey, Newark, New Jersey
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4
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Pham TX, Bae M, Lee Y, Park YK, Lee JY. Transcriptional and posttranscriptional repression of histone deacetylases by docosahexaenoic acid in macrophages. J Nutr Biochem 2018; 57:162-169. [PMID: 29734115 DOI: 10.1016/j.jnutbio.2018.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 01/13/2018] [Accepted: 03/01/2018] [Indexed: 01/12/2023]
Abstract
Histone deacetylation is one of the posttranslational modifications of histones by which eukaryotic cells alter gene transcription. Although fatty acids are the best known macronutrients that modulate gene expression in inflammatory pathways, it is unclear whether common fatty acids in diets can regulate the expression of histone deacetylases (HDACs) in macrophages. We determined the effects of fatty acids, including palmitic acid (PA), oleic acid (OA), linoleic acid, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), on the expression of HDAC isoforms in RAW 264.7 macrophages, mouse bone marrow-derived macrophages (BMDM) and human THP-1 cells. In RAW 264.7 macrophages, OA significantly increased mRNA levels of Hdac1, 2 and 3, and EPA induced Hdac2 expression compared with control. Marked repression of Hdac9 mRNA levels by EPA and DHA, with DHA being more potent, was observed in RAW 264.7 macrophages and BMDM. DHA also decreased HDAC3, 4 and 9 protein levels. EPA and DHA facilitated the proteasomal degradation of HDAC3 and 4 protein, while the transcriptional repression of HDAC9 by DHA may be mediated by the repression of myocyte enhancer factor 2 or by the activation of retinoid X receptor. Functionally, inhibition of HDAC activity or knockdown of Hdac9 in macrophages reduced lipopolysaccharide-induced inflammatory gene expression. Our results demonstrate that DHA represses the expression of HDAC3, 4 and 9 at the transcriptional or posttranscriptional levels in murine macrophages. This suggests that the anti-inflammatory effect of DHA may be mediated by the reduction of HDACs.
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Affiliation(s)
- Tho X Pham
- Department of Nutritional Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Minkyung Bae
- Department of Nutritional Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Yoojin Lee
- Department of Nutritional Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Young-Ki Park
- Department of Nutritional Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Ji-Young Lee
- Department of Nutritional Sciences, University of Connecticut, Storrs, CT 06269, USA; Department of Food and Nutrition, Kyung Hee University, Seoul, South Korea.
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5
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Reprogrammed lipid metabolism in bladder cancer with cisplatin resistance. Oncotarget 2018; 9:13231-13243. [PMID: 29568353 PMCID: PMC5862574 DOI: 10.18632/oncotarget.24229] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/06/2018] [Indexed: 02/04/2023] Open
Abstract
Due to its tendency to recur and acquire chemoresistance quickly, bladder cancer (BC) remains to be an elusive and difficult disease. Patients with recurrent and chemoresistant BC have an extremely poor prognosis. One possible approach that may provide insightful and valuable information regarding resistance mechanisms is looking into the lipid metabolism of BC cells. Metabolism of lipids is essential for cancer cells and is associated with the regulation of a variety of key cellular processes and functions. This study conducted a comparative lipidomic profiling of two isogenic human T24 bladder cancer cell lines, one of which is clinically characterized as cisplatin-sensitive (T24S) and the other as cisplatin-resistant (T24R). Immunohistochemistry analysis revealed that expression of cytosolic acetyl-CoA synthetase 2 (ACSS2) is positively correlated with aggressive BC. Ultra performance liquid chromatography-mass spectrometry (UPLC-MS) analysis profiled a total of 1,864 lipids and levels of differentially expressed lipids suspected of being associated with cisplatin resistance were determined. In addition, we found that ACSS2 inhibition greatly perturbed levels of metabolites, including CE(18:1), CE(22:6), TG(49:1), and TG(53:2). This study broadens our current knowledge on the links between cisplatin resistance and lipid metabolism in aggressive BC and suggests potential biomarkers for identifying higher-risk patients.
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6
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Silva ITG, Fernandes V, Souza C, Treptow W, Santos GM. Biophysical studies of cholesterol effects on chromatin. J Lipid Res 2017; 58:934-940. [PMID: 28331000 PMCID: PMC5408612 DOI: 10.1194/jlr.m074997] [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: 01/16/2017] [Revised: 03/20/2017] [Indexed: 11/20/2022] Open
Abstract
Changes in chromatin structure regulate gene expression and genome maintenance. Molecules that bind to the nucleosome, the complex of DNA and histone proteins, are key modulators of chromatin structure. Previous work indicated that cholesterol, a ubiquitous cellular lipid, may bind to chromatin in vivo, suggesting a potential function for lipids in modulating chromatin architecture. However, the molecular mechanisms of cholesterol’s action on chromatin structure have remained unclear. Here, we explored the biophysical impact of cholesterol on nucleosome and chromatin fibers reconstituted in vitro and characterized in silico the cholesterol binding to the nucleosome. Our findings support that cholesterol assists 10 and 30 nm chromatin formation and induces folding of long chromatin fibers as a result of direct interaction of the cholesterol to six nucleosomal binding sites.
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Affiliation(s)
- Isabel T G Silva
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília, Brazil
| | - Vinícius Fernandes
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília, Brazil.,Laboratório de Biologia Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Caio Souza
- Laboratório de Biologia Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Werner Treptow
- Laboratório de Biologia Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Guilherme M Santos
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília, Brazil
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7
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Nagpal A, Ndamukong I, Hassan A, Avramova Z, Baluška F. Subcellular localizations of Arabidopsis myotubularins MTM1 and MTM2 suggest possible functions in vesicular trafficking between ER and cis-Golgi. JOURNAL OF PLANT PHYSIOLOGY 2016; 200:45-52. [PMID: 27340857 DOI: 10.1016/j.jplph.2016.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/03/2016] [Accepted: 06/03/2016] [Indexed: 06/06/2023]
Abstract
The two Arabidopsis genes AtMTM1 and AtMTM2 encode highly similar phosphoinositide 3-phosphatases from the myotubularin family. Despite the high-level conservation of structure and biochemical activities, their physiological roles have significantly diverged. The nature of a membrane and the concentrations of their membrane-anchored substrates (PtdIns3P or PtdIns3,5P2) and/or products (PtdIns5P and PtdIns) are considered critical for determining the functional specificity of myotubularins. We have performed comprehensive analyses of the subcellular localization of AtMTM1 and AtMTM2 using a variety of specific constructs transiently expressed in Nicotiana benthamiana leaf epidermal cells under the control of 35S promoter. AtMTM1 co-localized preferentially with cis-Golgi membranes, while AtMTM2 associated predominantly with ER membranes. In a stark contrast with animal/human MTMs, neither AtMTM1 nor AtMTM2 co-localizes with early or late endosomes or with TGN/EE compartments, making them unlikely participants in the endosomal trafficking system. Localization of the AtMTM2 is sensitive to cold and osmotic stress challenges. In contrast to animal myotubularins, Arabidopsis myotubularins do not associate with endosomes. Our results suggest that Arabidopsis myotubularins play a role in the vesicular trafficking between ER exit sites and cis-Golgi elements. The significance of these results is discussed also in the context of stress biology and plant autophagy.
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Affiliation(s)
| | - Ivan Ndamukong
- School of Biological Sciences, UNL, Lincoln NE, 68588, United States
| | - Ammar Hassan
- IZMB, University of Bonn, Kirschalle 1, 53115 Bonn, Germany
| | - Zoya Avramova
- School of Biological Sciences, UNL, Lincoln NE, 68588, United States.
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8
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Jung JH, Lee MY, Choi DY, Lee JW, You S, Lee KY, Kim J, Kim KP. Phospholipids of tumor extracellular vesicles stratify gefitinib-resistant nonsmall cell lung cancer cells from gefitinib-sensitive cells. Proteomics 2015; 15:824-35. [PMID: 25404199 DOI: 10.1002/pmic.201400243] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 10/06/2014] [Accepted: 11/13/2014] [Indexed: 12/11/2022]
Abstract
Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) such as gefitinib are one of gold standard treatment options for nonsmall-cell lung cancer (NSCLC) patients, which eventually fail due to the acquired resistance and relapse because of the development of secondary activating mutations such as T790M in EGFR. Predicting chemo-responsiveness of cancer patients provides a major challenge in chemotherapy. The goal of the present study is to determine whether phospholipid signatures of tumor extracellular vesicles (EV) are associated with gefitinib-resistance of NSCLC. A sophisticated MS-based shotgun lipidomic assays were performed for in-depth analysis of the lipidomes of gefitinib-resistant (PC9R) and responsive (PC9) NSCLC cells and their shed EV from these cell lines (PC9EV or PC9REV). Lipid MALDI-MS analysis showed that EV phospholipid composition was significantly distinct in PC9R, compared to PC9 cells. Following statistical analyses has identified 35 (20 positive and 15 negative ion mode) differentially regulated lipids, which are significantly over- or underexpressed in PC9R EV, compared to PC9 EV (p value < 0.01, fold change > 1.5). Our phospholipid signatures suggest that EV associates with drug sensitivity, which is worthy of additional investigation to assess chemoresistance in patients with NSCLC treated with anti-EGFR TKIs.
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Affiliation(s)
- Jae Hun Jung
- Department of Applied Chemistry, College of Applied Science, Kyung Hee University, Yongin, Republic of Korea
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9
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Logothetis DE, Petrou VI, Zhang M, Mahajan R, Meng XY, Adney SK, Cui M, Baki L. Phosphoinositide control of membrane protein function: a frontier led by studies on ion channels. Annu Rev Physiol 2014; 77:81-104. [PMID: 25293526 DOI: 10.1146/annurev-physiol-021113-170358] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Anionic phospholipids are critical constituents of the inner leaflet of the plasma membrane, ensuring appropriate membrane topology of transmembrane proteins. Additionally, in eukaryotes, the negatively charged phosphoinositides serve as key signals not only through their hydrolysis products but also through direct control of transmembrane protein function. Direct phosphoinositide control of the activity of ion channels and transporters has been the most convincing case of the critical importance of phospholipid-protein interactions in the functional control of membrane proteins. Furthermore, second messengers, such as [Ca(2+)]i, or posttranslational modifications, such as phosphorylation, can directly or allosterically fine-tune phospholipid-protein interactions and modulate activity. Recent advances in structure determination of membrane proteins have allowed investigators to obtain complexes of ion channels with phosphoinositides and to use computational and experimental approaches to probe the dynamic mechanisms by which lipid-protein interactions control active and inactive protein states.
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Affiliation(s)
- Diomedes E Logothetis
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298-0551;
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10
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Martins IJ, Creegan R. Links between Insulin Resistance, Lipoprotein Metabolism and Amyloidosis in Alzheimer’s Disease. Health (London) 2014. [DOI: 10.4236/health.2014.612190] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Follo MY, Faenza I, Piazzi M, Blalock WL, Manzoli L, McCubrey JA, Cocco L. Nuclear PI-PLCβ1: an appraisal on targets and pathology. Adv Biol Regul 2013; 54:2-11. [PMID: 24296032 DOI: 10.1016/j.jbior.2013.11.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 11/08/2013] [Indexed: 11/16/2022]
Abstract
Lipid signalling molecules are essential components of the processes that allow one extracellular signal to be transferred inside the nucleus, where specific lipid second messengers elicit reactions capable of regulating gene transcription, DNA replication or repair and DNA cleavage, eventually resulting in cell growth, differentiation, apoptosis or many other cell functions. Nuclear inositides are independently regulated, suggesting that the nucleus constitutes a functionally distinct compartment of inositol lipids metabolism. Indeed, nuclear inositol lipids themselves can modulate nuclear processes, such as transcription and pre-mRNA splicing, growth, proliferation, cell cycle regulation and differentiation. Nuclear PI-PLCβ1 is a key molecule for nuclear inositide signalling, where it plays a role in cell cycle progression, proliferation and differentiation. Here we review the targets and possible involvement of nuclear PI-PLCβ1 in human physiology and pathology.
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Affiliation(s)
- Matilde Y Follo
- Department of Biomedical and Neuromotor Sciences, Cellular Signalling Laboratory, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy.
| | - Irene Faenza
- Department of Biomedical and Neuromotor Sciences, Cellular Signalling Laboratory, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Manuela Piazzi
- Department of Biomedical and Neuromotor Sciences, Cellular Signalling Laboratory, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - William L Blalock
- CNR - Consiglio Nazionale delle Ricerche, Istituto di Genetica Molecolare and SC Laboratorio di Biologia Cellulare Muscoloscheletrica, IOR, Bologna, Italy
| | - Lucia Manzoli
- Department of Biomedical and Neuromotor Sciences, Cellular Signalling Laboratory, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - James A McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Lucio Cocco
- Department of Biomedical and Neuromotor Sciences, Cellular Signalling Laboratory, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy.
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12
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Sharma RP. Blood chromatin as a biosensor of the epigenetic milieu: a tool for studies in living psychiatric patients. Epigenomics 2013; 4:551-9. [PMID: 23130836 DOI: 10.2217/epi.12.46] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
This article constructs an argument for using blood chromatin (contained in nucleated blood cells) as a protein biosensor to integrate the ambient epigenetic influences in the internal milieu. An analogy is made to blood glycated hemoglobin (HbA1c) in diabetes as an integrated proxy for glucose levels and body-wide protein glycation. Genome-wide chromatin can serve as an organizing principle that bridges the central and peripheral compartments by entraining commensurable gene networks. Chromatin deposition along these networks will be imposed by the totality of epigenetic influences, which incorporates significant contributions from biochemicals that readily traverse the blood-brain barrier. In a clinical trial, these influences would be dominated by pharmaceuticals designed to override pathophysiological signals. In practice, mRNA readouts would be limited to nonsynaptic gene networks whose critical nodes are occupied by a site-specific chromatin modification. Finally, chromatin measurements in peripheral tissue will retain the influences of a patient's lifestyle and unique genomic background.
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Affiliation(s)
- Rajiv P Sharma
- The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St, Chicago, IL 60612, USA.
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13
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Geeraerts A, Hsiu-Fang F, Zimmermann P, Engelborghs Y. The characterization of the nuclear dynamics of syntenin-2, a PIP2binding PDZ protein. Cytometry A 2013; 83:866-75. [DOI: 10.1002/cyto.a.22246] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 10/26/2012] [Accepted: 11/29/2012] [Indexed: 11/11/2022]
Affiliation(s)
| | - Fan Hsiu-Fang
- Department of Chemistry; Faculty of Science; University of Leuven; Leuven; Belgium
| | - Pascale Zimmermann
- Department of Human Genetics; Faculty of Medicine; University of Leuven; Leuven; Belgium
| | - Yves Engelborghs
- Department of Chemistry; Faculty of Science; University of Leuven; Leuven; Belgium
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14
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Signal transduction pathways involving phosphatidylinositol 4-phosphate and phosphatidylinositol 4,5-bisphosphate: Convergences and divergences among eukaryotic kingdoms. Prog Lipid Res 2013; 52:1-14. [DOI: 10.1016/j.plipres.2012.08.003] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/22/2012] [Accepted: 08/23/2012] [Indexed: 11/18/2022]
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15
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Jones DR, Foulger R, Keune WJ, Bultsma Y, Divecha N. PtdIns5P is an oxidative stress-induced second messenger that regulates PKB activation. FASEB J 2012; 27:1644-56. [PMID: 23241309 DOI: 10.1096/fj.12-218842] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Oxidative stress initiates signaling pathways, which protect from stress-induced cellular damage, initiate apoptosis, or drive cells into senescence or into tumorigenesis. Oxidative stress regulates the activity of the cell survival factor PKB, through the regulation of PtdIns(3,4,5)P₃ synthesis. Whether oxidative stress regulates other phosphoinositides to control PKB activation is not clear. Here we show that PtdIns5P is a redox-regulated second messenger. In response to hydrogen peroxide (H₂O₂), we measured an increase in PtdIns5P in cells derived from human osteosarcoma, U2OS (5-fold); breast tumors, MDA-MB-468 (2-fold); and fibrosarcoma, HT1080 (3-fold); and in p53-null murine embryonic fibroblasts (8-fold). In U2OS cells, the increase in H₂O₂-dependent PtdIns5P did not require mTOR, PDK1, PKB, ERK, and p38 signaling or PIKfyve, a lipid kinase that increases PtdIns5P in response to osmotic and oncogenic signaling. A reduction in H₂O₂-induced PtdIns5P levels by the overexpression of PIP4K revealed its role in PKB activation. Suppression of H₂O₂-induced PtdIns5P generation reduced PKB activation and, surprisingly, reduced cell sensitivity to growth inhibition by H₂O₂. These data suggest that inhibition of PIP4K signaling might be useful as a novel strategy to increase the susceptibility of tumor cells to therapeutics that function through increased oxidative stress.
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Affiliation(s)
- David R Jones
- Cancer Research UK Inositide Laboratory, The Paterson Institute for Cancer Research, University of Manchester, Manchester, UK
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16
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Unsaturated fatty acids repress expression of ATP binding cassette transporter A1 and G1 in RAW 264.7 macrophages. J Nutr Biochem 2012; 23:1271-6. [DOI: 10.1016/j.jnutbio.2011.07.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2011] [Revised: 05/28/2011] [Accepted: 07/13/2011] [Indexed: 12/28/2022]
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17
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Dieck CB, Wood A, Brglez I, Rojas-Pierce M, Boss WF. Increasing phosphatidylinositol (4,5) bisphosphate biosynthesis affects plant nuclear lipids and nuclear functions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 57:32-44. [PMID: 22677448 PMCID: PMC3601448 DOI: 10.1016/j.plaphy.2012.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 05/09/2012] [Indexed: 05/21/2023]
Abstract
In order to characterize the effects of increasing phosphatidylinositol(4,5)bisphosphate (PtdIns(4,5)P(2)) on nuclear function, we expressed the human phosphatidylinositol (4)-phosphate 5-kinase (HsPIP5K) 1α in Nicotiana tabacum (NT) cells. The HsPIP5K-expressing (HK) cells had altered nuclear lipids and nuclear functions. HK cell nuclei had 2-fold increased PIP5K activity and increased steady state PtdIns(4,5)P(2). HK nuclear lipid classes showed significant changes compared to NT (wild type) nuclear lipid classes including increased phosphatidylserine (PtdSer) and phosphatidylcholine (PtdCho) and decreased lysolipids. Lipids isolated from protoplast plasma membranes (PM) were also analyzed and compared with nuclear lipids. The lipid profiles revealed similarities and differences in the plasma membrane and nuclei from the NT and transgenic HK cell lines. A notable characteristic of nuclear lipids from both cell types is that PtdIns accounts for a higher mol% of total lipids compared to that of the protoplast PM lipids. The lipid molecular species composition of each lipid class was also analyzed for nuclei and protoplast PM samples. To determine whether expression of HsPIP5K1α affected plant nuclear functions, we compared DNA replication, histone 3 lysine 9 acetylation (H3K9ac) and phosphorylation of the retinoblastoma protein (pRb) in NT and HK cells. The HK cells had a measurable decrease in DNA replication, histone H3K9 acetylation and pRB phosphorylation.
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Affiliation(s)
| | - Austin Wood
- Department of Biochemistry, North Carolina State University, Raleigh, NC
| | - Irena Brglez
- Department of Plant Biology, North Carolina State University, Raleigh, NC
| | | | - Wendy F. Boss
- Department of Plant Biology, North Carolina State University, Raleigh, NC
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18
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Cellular neurochemical characterization and subcellular localization of phospholipase C β1 in rat brain. Neuroscience 2012; 222:239-68. [PMID: 22735577 DOI: 10.1016/j.neuroscience.2012.06.039] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/15/2012] [Accepted: 06/15/2012] [Indexed: 11/21/2022]
Abstract
The present study describes a complete and detailed neuroanatomical distribution map of the phospholipase C beta1 (PLCβ1) isoform along the adult rat neuraxis, and defines the phenotype of cells expressing PLCβ1, along with its subcellular localization in cortical neurons as assessed by double-immunofluorescence staining and confocal laser scanning. Immunohistochemical labeling revealed a considerable morphological heterogeneity among PLCβ1-positive cells in the cortex, even though there was a marked predominance of pyramidal morphologies. As an exception to the general non-matching distribution of GFAP and PLCβ1, a high degree of co-expression was observed in radial glia-like processes of the spinal cord white matter. In the somatosensory cortex, the proportion of GABAergic neurons co-stained with PLCβ1 was similar (around 2/3) in layers I, II-III, IV and VI, and considerably lower in layer V (around 2/5). Double immunofluorescence against PLCβ1 and nuclear speckle markers SC-35 and NeuN/Fox3 in isolated nuclei from the rat cortex showed a high overlap of both markers with PLCβ1 within the nuclear matrix. In contrast, there was no apparent co-localization with markers of the nuclear envelope and lamina. Finally, to assess whether the subcellular expression pattern of PLCβ1 involved specifically one of the two splice variants of PLCβ1, we carried out Western blot experiments in cortical subcellular fractions. Notably, PLCβ1a/1b ratios were statistically higher in the cytoplasm than in the nuclear and plasma membrane fractions. These results provide a deeper knowledge of the cellular distribution of the PLCβ1 isoform in different cell subtypes of the rat brain, and of its presence in the neuronal nuclear compartment.
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19
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Ding Y, Ndamukong I, Zhao Y, Xia Y, Riethoven JJ, Jones DR, Divecha N, Avramova Z. Divergent functions of the myotubularin (MTM) homologs AtMTM1 and AtMTM2 in Arabidopsis thaliana: evolution of the plant MTM family. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:866-878. [PMID: 22324391 DOI: 10.1111/j.1365-313x.2012.04936.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Myotubularin and myotubularin-related proteins are evolutionarily conserved in eukaryotes. Defects in their function result in muscular dystrophy, neuronal diseases and leukemia in humans. In contrast to the animal lineage, where genes encoding both active and inactive myotubularins (phosphoinositide 3-phosphatases) have appeared and proliferated in the basal metazoan group, myotubularin genes are not found in the unicellular relatives of green plants. However, they are present in land plants encoding proteins highly similar to the active metazoan enzymes. Despite their remarkable structural conservation, plant and animal myotubularins have significantly diverged in their functions. While loss of myotubularin function causes severe disease phenotypes in humans it is not essential for the cellular homeostasis under normal conditions in Arabidopsis thaliana. Instead, myotubularin deficiency is associated with altered tolerance to dehydration stress. The two Arabidopsis genes AtMTM1 and AtMTM2 have originated from a segmental chromosomal duplication and encode catalytically active enzymes. However, only AtMTM1 is involved in elevating the cellular level of phosphatidylinositol 5-phosphate in response to dehydration stress, and the two myotubularins differentially affect the Arabidopsis dehydration stress-responding transcriptome. AtMTM1 and AtMTM2 display different localization patterns in the cell, consistent with the idea that they associate with different membranes to perform specific functions. A single amino acid mutation in AtMTM2 (L250W) results in a dramatic loss of subcellular localization. Mutations in this region are linked to disease conditions in humans.
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MESH Headings
- Amino Acid Substitution
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Chromosome Duplication
- Chromosomes, Plant/genetics
- Chromosomes, Plant/metabolism
- Dehydration/metabolism
- Enzyme Activation
- Evolution, Molecular
- Gene Expression Regulation, Plant
- Genes, Plant
- Mitochondrial Proteins/genetics
- Mitochondrial Proteins/metabolism
- Oligonucleotide Array Sequence Analysis/methods
- Phosphatidylinositol Phosphates/metabolism
- Phosphoric Monoester Hydrolases/genetics
- Phosphoric Monoester Hydrolases/metabolism
- Plant Cells/metabolism
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Protein Structure, Tertiary
- Protein Tyrosine Phosphatases, Non-Receptor/genetics
- Protein Tyrosine Phosphatases, Non-Receptor/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Soil
- Stress, Physiological
- Transcriptome
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Affiliation(s)
- Yong Ding
- School of Biological Sciences, University of Nebraska at Lincoln, Lincoln, NE 68588, USA
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20
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Nakano T, Hozumi Y, Iwazaki K, Okumoto K, Iseki K, Saito T, Kawata S, Wakabayashi I, Goto K. Altered expression of diacylglycerol kinase isozymes in regenerating liver. J Histochem Cytochem 2011; 60:130-8. [PMID: 22205637 DOI: 10.1369/0022155411429154] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The liver possesses the capacity to restore its function and mass after injury. Liver regeneration is controlled through complicated mechanisms, in which the phosphoinositide (PI) cycle is shown to be activated in hepatocytes. Using a rat partial hepatectomy (PH) model, the authors investigated the expression of the diacylglycerol kinase (DGK) family, a key enzyme in the PI cycle, which metabolizes a lipid second-messenger diacylglycerol (DG). RT-PCR analysis shows that DGKζ and DGKα are the major isozymes in the liver. Results showed that in the process of regeneration, the DGKζ protein, which is detected in the nucleus of a small population of hepatocytes in normal liver, is significantly increased in almost all hepatocytes. However, the mRNA levels remain largely unchanged. Double labeling with bromodeoxyuridine (BrdU), an S phase marker, reveals that DGKζ is expressed independently of DNA synthesis or cell proliferation. However, DGKα protein localizes to the cytoplasm in normal and regenerating livers, but immunoblot analysis reveals that the expected (80 kDa) and the lower (70 kDa) bands are detected in normal liver, whereas at day 10 after PH, the expected band is solely recognized, showing a different processing pattern of DGKα in liver regeneration. These results suggest that DGKζ and DGKα are involved, respectively, in the nucleus and the cytoplasm of hepatocytes in regenerating liver.
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Affiliation(s)
- Tomoyuki Nakano
- Department of Anatomy and Cell Biology, Yamagata University School of Medicine, Yamagata, Japan
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21
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Giatrellis S, Nounesis G. Nucleic acid-lipid membrane interactions studied by DSC. JOURNAL OF PHARMACY AND BIOALLIED SCIENCES 2011; 3:70-6. [PMID: 21430956 PMCID: PMC3053523 DOI: 10.4103/0975-7406.76470] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Revised: 10/19/2010] [Accepted: 10/19/2010] [Indexed: 11/04/2022] Open
Abstract
The interactions of nucleic acids with lipid membranes are of great importance for biological mechanisms as well as for biotechnological applications in gene delivery and drug carriers. The optimization of liposomal vectors for clinical use is absolutely dependent upon the formation mechanisms, the morphology, and the molecular organization of the lipoplexes, that is, the complexes of lipid membranes with DNA. Differential scanning calorimetry (DSC) has emerged as an efficient and relatively easy-to-operate experimental technique that can straightforwardly provide data related to the thermodynamics and the kinetics of the DNA-lipid complexation and especially to the lipid organization and phase transitions within the membrane. In this review, we summarize DSC studies considering nucleic acid-membrane systems, accentuating DSC capabilities, and data analysis. Published work involving cationic, anionic, and zwitterionic lipids as well as lipid mixtures interacting with RNA and DNA of different sizes and conformations are included. It is shown that despite limitations, issues such as DNA- or RNA-induced phase separation and microdomain lipid segregation, liposomal aggregation and fusion, alterations of the lipid long-range molecular order, as well as membrane-induced structural changes of the nucleic acids can be efficiently treated by systematic high-sensitivity DSC studies.
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Affiliation(s)
- Sarantis Giatrellis
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
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22
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Lee J, Park Y, Koo SI. ATP-binding cassette transporter A1 and HDL metabolism: effects of fatty acids. J Nutr Biochem 2011; 23:1-7. [PMID: 21684139 DOI: 10.1016/j.jnutbio.2011.03.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 03/14/2011] [Accepted: 03/18/2011] [Indexed: 01/08/2023]
Abstract
Ample evidence indicates that dietary fatty acids alter the plasma levels of high-density lipoprotein cholesterol (HDL-C). However, the mechanisms underlying the effects of fatty acids still remain elusive. Recent advances in our understanding of ATP-binding cassette transporter A1 (ABCA1) function and regulation have provided a valuable insight into the mechanisms by which fatty acids may affect plasma HDL-C levels. ABCA1 mediates the assembly of phospholipids and free cholesterol with apolipoprotein A-I, which is a critical step for HDL biogenesis. Studies have shown that unsaturated fatty acids, but not saturated fatty acids, repress the expression of ABCA1 in vitro. Although information on mechanisms for the fatty-acid-mediated regulation of ABCA1 expression is still limited and controversial, recent evidence suggests that unsaturated fatty acids inhibit the expression of ABCA1 at the transcriptional and posttranscriptional levels. The transcriptional repression of ABCA1 expression by unsaturated fatty acids is likely liver X receptor dependent. Evidence also suggests that histone deacetylation may play a role in the repression. Posttranscriptionally, unsaturated fatty acids may facilitate ABCA1 protein degradation, which may involve phosphorylation of ABCA1 by protein kinases. Further studies are warranted to better understand the role of dietary fatty acids in HDL metabolism and their effects on cardiovascular health.
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Affiliation(s)
- Jiyoung Lee
- Department of Nutritional Sciences, University of Connecticut, Storrs, Connecticut 06269, USA.
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23
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Aguissa-Touré AH, Wong RPC, Li G. The ING family tumor suppressors: from structure to function. Cell Mol Life Sci 2011; 68:45-54. [PMID: 20803232 PMCID: PMC11114739 DOI: 10.1007/s00018-010-0509-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 07/31/2010] [Accepted: 08/10/2010] [Indexed: 12/24/2022]
Abstract
The Inhibitor of Growth (ING) proteins belong to a well-conserved family which presents in diverse organisms with several structural and functional domains for each protein. The ING family members are found in association with many cellular processes. Thus, the ING family proteins are involved in regulation of gene transcription, DNA repair, tumorigenesis, apoptosis, cellular senescence and cell cycle arrest. The ING proteins have multiple domains that are potentially capable of binding to many partners. It is conceivable, therefore, that such proteins could function similarly within protein complexes. In this case, within this family, each function could be attributed to a specific domain. However, the role of ING domains is not definitively clear. In this review, we summarize recent advances in structure-function relationships in ING proteins. For each domain, we describe the known biological functions and the approaches utilized to identify the functions associated with ING proteins.
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Affiliation(s)
- Almass-Houd Aguissa-Touré
- Department of Dermatology and Skin Science, Jack Bell Research Centre, Vancouver Coastal Health Research Institute, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6 Canada
| | - Ronald P. C. Wong
- Department of Dermatology and Skin Science, Jack Bell Research Centre, Vancouver Coastal Health Research Institute, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6 Canada
| | - Gang Li
- Department of Dermatology and Skin Science, Jack Bell Research Centre, Vancouver Coastal Health Research Institute, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6 Canada
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24
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Bidlingmaier S, Wang Y, Liu Y, Zhang N, Liu B. Comprehensive analysis of yeast surface displayed cDNA library selection outputs by exon microarray to identify novel protein-ligand interactions. Mol Cell Proteomics 2010; 10:M110.005116. [PMID: 21127146 DOI: 10.1074/mcp.m110.005116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphatidylinositides are important signaling molecules that interact with a myriad of cellular proteins, many of which remain unidentified. We previously screened a yeast surface displayed human proteome library to identify protein fragments with affinity for the phosphatidylinositides, phosphatidylinositol-4,5-bisphosphate and phosphatidylinositol-3,4,5-trisphosphate. Much of the diversity in the screened selection outputs was represented by clones present at low frequencies, suggesting that a significant number of additional phosphatidylinositide-binding protein fragments might be present in the selection outputs. In the studies described in this report, we developed a novel cDNA library analysis method and comprehensively analyzed the polyclonal selection outputs from the phosphatidylinositol-4,5-bisphosphate and phosphatidylinositol-3,4,5-trisphosphate selections using a high-density exon microarray. In addition to the nine previously reported phosphatidylinositide-binding protein fragments, we identified 37 new phosphatidylinositide-binding candidates. Nine of 37 contain known phosphatidylinositide-binding domains, whereas the remaining 28 contain no known phosphatidylinositide-binding domain. We cloned and confirmed phosphatidylinositide binding by fluorescence-activated cell sorting for 17 of these novel candidate protein fragments. Our experiments suggest that phosphatidylinositide binding by these 17 novel protein fragments is dependent on both the inositol phosphate "headgroup" and the lipid "tail." This is in contrast with the PH domain containing fragments we tested, for which the inositol phosphate headgroup was sufficient for binding. The novel PtdIns-binding fragments come from a wide variety of proteins, including splicing factors, transcription factors, a kinase, and a polymerase. Intriguingly, 11 of the phosphatidylinositide-binding protein fragments are from nuclear proteins, including four containing homeobox domains. We found that phosphatidylinositides and double-stranded DNA oligonucleotides derived from homeobox domain target sequences compete for binding to homeobox domain-containing protein fragments, suggesting a possible mechanism for phospholipid-dependent transcriptional regulation. FACS enrichment of target-binding clones in yeast human cDNA display libraries coupled with comprehensive analysis of the selection output by DNA microarray analysis is an effective method for investigating common as well as rare protein interactions. In particular, this method is well suited for the study of small molecule/protein and drug/protein interactions.
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Affiliation(s)
- Scott Bidlingmaier
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA 94110, USA
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25
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Lewis AE, Sommer L, Arntzen MØ, Strahm Y, Morrice NA, Divecha N, D'Santos CS. Identification of nuclear phosphatidylinositol 4,5-bisphosphate-interacting proteins by neomycin extraction. Mol Cell Proteomics 2010; 10:M110.003376. [PMID: 21048195 DOI: 10.1074/mcp.m110.003376] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Considerable insight into phosphoinositide-regulated cytoplasmic functions has been gained by identifying phosphoinositide-effector proteins. Phosphoinositide-regulated nuclear functions however are fewer and less clear. To address this, we established a proteomic method based on neomycin extraction of intact nuclei to enrich for nuclear phosphoinositide-effector proteins. We identified 168 proteins harboring phosphoinositide-binding domains. Although the vast majority of these contained lysine/arginine-rich patches with the following motif, K/R-(X(n= 3-7)-K-X-K/R-K/R, we also identified a smaller subset of known phosphoinositide-binding proteins containing pleckstrin homology or plant homeodomain modules. Proteins with no prior history of phosphoinositide interaction were identified, some of which have functional roles in RNA splicing and processing and chromatin assembly. The remaining proteins represent potentially other novel nuclear phosphoinositide-effector proteins and as such strengthen our appreciation of phosphoinositide-regulated nuclear functions. DNA topology was exemplar among these: Biochemical assays validated our proteomic data supporting a direct interaction between phosphatidylinositol 4,5-bisphosphate and DNA Topoisomerase IIα. In addition, a subset of neomycin extracted proteins were further validated as phosphatidyl 4,5-bisphosphate-interacting proteins by quantitative lipid pull downs. In summary, data sets such as this serve as a resource for a global view of phosphoinositide-regulated nuclear functions.
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Affiliation(s)
- Aurélia E Lewis
- PROBE Proteomics Platform, Department of Biomedicine, University of Bergen, Bergen, Norway
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26
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Ndamukong I, Jones DR, Lapko H, Divecha N, Avramova Z. Phosphatidylinositol 5-phosphate links dehydration stress to the activity of ARABIDOPSIS TRITHORAX-LIKE factor ATX1. PLoS One 2010; 5:e13396. [PMID: 20967218 PMCID: PMC2954176 DOI: 10.1371/journal.pone.0013396] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 09/17/2010] [Indexed: 11/18/2022] Open
Abstract
Background Changes in gene expression enable organisms to respond to environmental stress. Levels of cellular lipid second messengers, such as the phosphoinositide PtdIns5P, change in response to a variety of stresses and can modulate the localization, conformation and activity of a number of intracellular proteins. The plant trithorax factor (ATX1) tri-methylates the lysine 4 residue of histone H3 (H3K4me3) at gene coding sequences, which positively correlates with gene transcription. Microarray analysis has identified a target gene (WRKY70) that is regulated by both ATX1 and by the exogenous addition of PtdIns5P in Arabidopsis. Interestingly, ATX1 contains a PtdIns5P interaction domain (PHD finger) and thus, phosphoinositide signaling, may link environmental stress to changes in gene transcription. Principal Findings Using the plant Arabidopsis as a model system, we demonstrate a link between PtdIns5P and the activity of the chromatin modifier ATX1 in response to dehydration stress. We show for the first time that dehydration leads to an increase in cellular PtdIns5P in Arabidopsis. The Arabidopsis homolog of myotubularin (AtMTM1) is capable of generating PtdIns5P and here, we show that AtMTM1 is essential for the induced increase in PtdIns5P upon dehydration. Furthermore, we demonstrate that the ATX1-dependent gene, WRKY70, is downregulated during dehydration and that lowered transcript levels are accompanied by a drastic reduction in H3K4me3 of its nucleosomes. We follow changes in WRKY70 nucleosomal K4 methylation as a model to study ATX1 activity at chromatin during dehydration stress. We found that during dehydration stress, the physical presence of ATX1 at the WRKY70 locus was diminished and that ATX1 depletion resulted from it being retained in the cytoplasm when PtdIns5P was elevated. The PHD of ATX1 and catalytically active AtMTM1 are required for the cytoplasmic localization of ATX1. Conclusions/Significance The novelty of the manuscript is in the discovery of a mechanistic link between a chromatin modifying activity (ATX1) and a lipid (PtdIns5P) synthesis in a signaling pathway that ultimately results in altered expression of ATX1 dependent genes downregulated in response to dehydration stress.
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Affiliation(s)
- Ivan Ndamukong
- School of Biological Sciences, University of Nebraska at Lincoln, Lincoln, Nebraska, United States of America
| | - David R. Jones
- Inositide Laboratory, Paterson Institute for Cancer Research, The University of Manchester, Manchester, United Kingdom
| | - Hanna Lapko
- School of Biological Sciences, University of Nebraska at Lincoln, Lincoln, Nebraska, United States of America
| | - Nullin Divecha
- Inositide Laboratory, Paterson Institute for Cancer Research, The University of Manchester, Manchester, United Kingdom
- * E-mail: (ZA); (ND)
| | - Zoya Avramova
- School of Biological Sciences, University of Nebraska at Lincoln, Lincoln, Nebraska, United States of America
- * E-mail: (ZA); (ND)
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27
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Wilson RJ, Tyas SR, Black CF, Dymond MK, Attard GS. Partitioning of ssRNA Molecules between Preformed Monolithic HII Liquid Crystalline Phases of Lipids and Supernatant Isotropic Phases. Biomacromolecules 2010; 11:3022-7. [DOI: 10.1021/bm1008469] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Richard J. Wilson
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Sarah R. Tyas
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Camilla F. Black
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Marcus K. Dymond
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - George S. Attard
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
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28
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Abstract
Phosphatidylinositol (PtdIns) and its phosphorylated derivatives represent less than 5% of total membrane phospholipids in cells. Despite their low abundance, they form a dynamic signalling system that is regulated in response to a variety of extra and intra-cellular cues (Curr Opin Genet Dev 14:196-202, 2004). Phosphoinositides and the enzymes that synthesize them are found in many different sub-cellular compartments including the nuclear matrix, heterochromatin, and sites of active RNA splicing, suggesting that phosphoinositides may regulate specific functions within the nuclear compartment (Nat Rev Mol Cell Biol 4:349-360, 2003; Curr Top Microbiol Immunol 282:177-206, 2004; Cell Mol Life Sci 61:1143-1156, 2004). The existence of distinct sub-cellular pools has led to the challenging task of understanding how the different pools are regulated and how changes in the mass of lipids within the nucleus can modulate nuclear specific pathways. Here we describe methods to determine how enzymatic activities that modulate nuclear phosphoinositides are changed in response to extracellular stimuli.
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Affiliation(s)
- Nullin Divecha
- CRUK Inositide Laboratory, Paterson Institute for Cancer Research, Manchester, UK.
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29
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Michanek A, Kristen N, Höök F, Nylander T, Sparr E. RNA and DNA interactions with zwitterionic and charged lipid membranes - a DSC and QCM-D study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1798:829-38. [PMID: 20036213 DOI: 10.1016/j.bbamem.2009.12.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 11/12/2009] [Accepted: 12/15/2009] [Indexed: 10/20/2022]
Abstract
The aim of the present study is to establish under which conditions tRNA associates with phospholipid bilayers, and to explore how this interaction influences the lipid bilayer. For this purpose we have studied the association of tRNA or DNA of different sizes and degrees of base pairing with a set of model membrane systems with varying charge densities, composed of zwitterionic phosphatidylcholines (PC) in mixtures with anionic phosphatidylserine (PS) or cationic dioctadecyl-dimethyl-ammoniumbromide (DODAB), and with fluid or solid acyl-chains (oleoyl, myristoyl and palmitoyl). To prove and quantify the attractive interaction between tRNA and model-lipid membrane we used quartz crystal microbalance with dissipation (QCM-D) monitoring to study the tRNA adsorption to deposit phospholipid bilayers from solutions containing monovalent (Na(+)) or divalent (Ca(2+)) cations. The influence of the adsorbed polynucleic acids on the lipid phase transitions and lipid segregation was studied by means of differential scanning calorimetry (DSC). The basic findings are: i) tRNA adsorbs to zwitterionic liquid-crystalline and gel-phase phospholipid bilayers. The interaction is weak and reversible, and cannot be explained only on the basis of electrostatic attraction. ii) The adsorbed amount of tRNA is higher for liquid-crystalline bilayers compared to gel-phase bilayers, while the presence of divalent cations show no significant effect on the tRNA adsorption. iii) The adsorption of tRNA can lead to segregation in the mixed 1,2-dimyristoyl-sn-glycerol-3-phosphatidylcholine (DMPC)-1,2-dimyristoyl-sn-glycero-3-phosphatidylserine (DMPS) and DMPC-DODAB bilayers, where tRNA is likely excluded from the anionic DMPS-rich domains in the first system, and associated with the cationic DODAB-rich domains in the second system. iv) The addition of shorter polynucleic acids influence the chain melting transition and induce segregation in a mixed DMPC-DMPS system, while larger polynucleic acids do not influence the melting transition in these system. The results in this study on tRNA-phospholipid interactions can have implications for understanding its biological function in, e.g., the cell nuclei, as well as in applications in biotechnology and medicine.
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Affiliation(s)
- Agnes Michanek
- Physical Chemistry 1, Lund University, P.O. Box 124, 22100 Lund, Sweden.
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30
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van den Bout I, Divecha N. PIP5K-driven PtdIns(4,5)P2 synthesis: regulation and cellular functions. J Cell Sci 2009; 122:3837-50. [DOI: 10.1242/jcs.056127] [Citation(s) in RCA: 230] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
It has long been known that phosphoinositides are present in cellular membranes, but only in the past four decades has our understanding of their importance for proper cell function advanced significantly. Key to determining the biological roles of phosphoinositides is understanding the enzymes involved in their metabolism. Although many such enzymes have now been identified, there is still much to learn about their cellular functions. Phosphatidylinositol 4-phosphate 5-kinases (PIP5Ks) are a group of kinases that catalyse the production of phosphatidylinositol (4,5)-bisphosphate [PtdIns(4,5)P2]. As well as being a substrate for the enzymes phospholipase C (PLC) and phosphatidylinositol 3-kinase (PI3K), PtdIns(4,5)P2 acts as a second messenger in its own right, influencing a variety of cellular processes. In this Commentary, we review how PIP5Ks are modulated to achieve regulated PtdIns(4,5)P2 production, and discuss the role of these proteins in different cellular processes.
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Affiliation(s)
- Iman van den Bout
- Inositide Laboratory, Paterson Institute for Cancer Research, Wilmslow Road, Manchester M20 4BX, UK
| | - Nullin Divecha
- Inositide Laboratory, Paterson Institute for Cancer Research, Wilmslow Road, Manchester M20 4BX, UK
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31
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Ding Y, Lapko H, Ndamukong I, Xia Y, Al-Abdallat A, Lalithambika S, Sadder M, Saleh A, Fromm M, Riethoven JJ, Lu G, Avramova Z. The Arabidopsis chromatin modifier ATX1, the myotubularin-like AtMTM and the response to drought. PLANT SIGNALING & BEHAVIOR 2009; 4:1049-58. [PMID: 19901554 PMCID: PMC2819512 DOI: 10.4161/psb.4.11.10103] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 09/15/2009] [Indexed: 05/19/2023]
Abstract
Plants respond to environmental stresses by altering transcription of genes involved in the response. The chromatin modifier ATX1 regulates expression of a large number of genes; consequently, factors that affect ATX1 activity would also influence expression from ATX1-regulated genes. Here, we demonstrate that dehydration is such a factor implicating ATX1 in the plant's response to drought. In addition, we report that a hitherto unknown Arabidopsis gene, At3g10550, encodes a phosphoinositide 3'-phosphatase related to the animal myotubularins (AtMTM1). Myotubularin activities in plants have not been described and herein, we identify an overlapping set of genes co-regulated by ATX1 and AtMTM under drought conditions. We propose that these shared genes represent the ultimate targets of partially overlapping branches of the pathways of the nuclear ATX1 and the cytoplasmic AtMTM1. Our analyses offer first genome-wide insights into the relationship of an epigenetic factor and a lipid phosphatase from the other end of a shared drought responding pathway in Arabidopsis.
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Affiliation(s)
- Yong Ding
- UNL Center for Biotechnology and Plant Science Initiative; UNL; Lincoln, NE USA
| | - Hanna Lapko
- School of Biological Sciences; UNL; Lincoln, NE USA
| | | | - Yuannan Xia
- Genomics Core Research Facility; Center for Biotechnology UNL; Lincoln, NE USA
| | - Ayed Al-Abdallat
- UNL Center for Biotechnology and Plant Science Initiative; UNL; Lincoln, NE USA
- Faculty of Agriculture; University of Jordan; Amman, Jordan
| | | | - Monther Sadder
- School of Biological Sciences; UNL; Lincoln, NE USA
- Faculty of Agriculture; University of Jordan; Amman, Jordan
| | | | - Michael Fromm
- UNL Center for Biotechnology and Plant Science Initiative; UNL; Lincoln, NE USA
| | - Jean-Jack Riethoven
- Bioinformatics Core Research Facility; Center for Biotechnology UNL; Lincoln, NE USA
| | - Guoqing Lu
- Department of Biology; University of Nebraska at Omaha; Omaha, NE USA
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Alakoskela JM, Vitovic P, Kinnunen PKJ. Screening for the drug-phospholipid interaction: correlation to phospholipidosis. ChemMedChem 2009; 4:1224-51. [PMID: 19551800 DOI: 10.1002/cmdc.200900052] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Phospholipid bilayers represent a complex, anisotropic environment fundamentally different from bulk oil or octanol, for instance. Even "simple" drug association to phospholipid bilayers can only be fully understood if the slab-of-hydrocarbon approach is abandoned and the complex, anisotropic properties of lipid bilayers reflecting the chemical structures and organization of the constituent phospholipids are considered. The interactions of drugs with phospholipids are important in various processes, such as drug absorption, tissue distribution, and subcellular distribution. In addition, drug-lipid interactions may lead to changes in lipid-dependent protein activities, and further, to functional and morphological changes in cells, a prominent example being the phospholipidosis (PLD) induced by cationic amphiphilic drugs. Herein we briefly review drug-lipid interactions in general and the significance of these interactions in PLD in particular. We also focus on a potential causal connection between drug-induced PLD and steatohepatitis, which is induced by some cationic amphiphilic drugs.
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Affiliation(s)
- Juha-Matti Alakoskela
- Division of Biochemistry, Institute of Biomedicine, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland.
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Barlow CA, Laishram RS, Anderson RA. Nuclear phosphoinositides: a signaling enigma wrapped in a compartmental conundrum. Trends Cell Biol 2009; 20:25-35. [PMID: 19846310 DOI: 10.1016/j.tcb.2009.09.009] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 09/27/2009] [Accepted: 09/28/2009] [Indexed: 01/09/2023]
Abstract
While the presence of phosphoinositides in the nuclei of eukaryotes and the identity of the enzymes responsible for their metabolism have been known for some time, their functions in the nucleus are only now emerging. This is illustrated by the recent identification of effectors for nuclear phosphoinositides. Like the cytosolic phosphoinositide signaling pathway, nuclear phosphatidylinositol 4,5-bisphosphate (PI4,5P(2)) is at the center of the pathway and acts both as a messenger and as a precursor for many additional messengers. Here, recent advances in the understanding of nuclear phosphoinositide signaling and its functions are reviewed with an emphasis on PI4,5P(2) and its role in gene expression. The compartmentalization of nuclear phosphoinositide phosphates (PIP(n)) remains a mystery, but emerging evidence suggests that phosphoinositides occupy several functionally distinct compartments.
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Affiliation(s)
- Christy A Barlow
- University of Wisconsin-Madison, Department of Pharmacology, 1300 University Ave. University of Wisconsin Medical School, Madison, WI 53706, USA
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34
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Bassi C, Mello SS, Cardoso RS, Godoy PDV, Fachin AL, Junta CM, Sandrin-Garcia P, Carlotti CG, Falcão RP, Donadi EA, Passos GAS, Sakamoto-Hojo ET. Transcriptional changes in U343 MG-a glioblastoma cell line exposed to ionizing radiation. Hum Exp Toxicol 2009; 27:919-29. [PMID: 19273547 DOI: 10.1177/0960327108102045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Glioblastoma multiforme (GBM) is a highly invasive and radioresistant brain tumor. Aiming to study how glioma cells respond to gamma-rays in terms of biological processes involved in cellular responses, we performed experiments at cellular context and gene expression analysis in U343-MG-a GBM cells irradiated with 1 Gy and collected at 6 h post-irradiation. The survival rate was approximately 61% for 1 Gy and was completely reduced at 16 Gy. By performing the microarray technique, 859 cDNA clones were analyzed. The Significance Analysis of Microarray algorithm indicated 196 significant expressed genes (false discovery rate (FDR) = 0.42%): 67 down-regulated and 97 up-regulated genes, which belong to several classes: metabolism, adhesion/cytoskeleton, signal transduction, cell cycle/apoptosis, membrane transport, DNA repair/DNA damage signaling, transcription factor, intracellular signaling, and RNA processing. Differential expression patterns of five selected genes (HSPA9B, INPP5A, PIP5K1A, FANCG, and TPP2) observed by the microarray analysis were further confirmed by the quantitative real time RT-PCR method, which demonstrated an up-regulation status of those genes. These results indicate a broad spectrum of biological processes (which may reflect the radio-resistance of U343 cells) that were altered in irradiated glioma cells, so as to guarantee cell survival.
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Affiliation(s)
- Cl Bassi
- Department of Genetics, University of Sao Paulo, SP, Brazil
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35
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Frykholm K, Nordén B, Westerlund F. Mechanism of DNA strand exchange at liposome surfaces investigated using mismatched DNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:1606-1611. [PMID: 19123801 DOI: 10.1021/la8032513] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
DNA strand exchange is of great importance in vivo for genetic recombination and DNA repair. The detailed mechanism of strand exchange is not understood in full detail despite extensive studies. Simplistic model systems in which molecular parameters can be varied independently are therefore of interest to study. We chose the surface of a positively charged liposome as a scaffold, which we recently demonstrated to be able to catalyze the exchange of fully complementary DNA oligonucleotides. We here study how single base pair mismatches affect the rate of strand exchange on the liposome surface. Interestingly, the rate of the exchange does not simply follow the stability of the duplex in solution, as determined by melting temperatures, but also depends sensitively on the position of the mismatch. For duplexes with similar melting temperatures, the exchange is much faster for a mismatch close to the end than for a mismatch in the middle of the sequence. Our results suggest that the single strands are stabilized by the liposome surface; therefore, the duplex is fraying more and the DNA opens up in a zipperlike fashion on the surface, increasing the probability of strand exchange. We also show that the competition between greater stability (higher Tm in solution) and higher concentration is important for the final composition of the duplex when a large excess of single strands is added to a complementary double-stranded DNA. Finally, the similar exchange rate constants for fully base-paired duplexes on the liposome surface when adding fully matched single strands or single strands with a mismatched base indicate that the rate is governed largely by separation of the initial duplex and not by the formation of the product duplex.
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Affiliation(s)
- Karolin Frykholm
- Department of Chemical and Biological Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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Kayser-Bricker KJ, Jordan PA, Miller SJ. Catalyst-Dependent Syntheses of Phosphatidylinositol-5 Phosphate-DiC8 and its Enantiomer. Tetrahedron 2008; 64:7015-7020. [PMID: 19606206 PMCID: PMC2673006 DOI: 10.1016/j.tet.2008.03.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Peptide-based catalysts have been applied to the enantioselective syntheses of the title compounds, with this being the first report of the synthesis of an ent-PI5P analogue. The key steps in the synthesis involve asymmetric phosphorylation catalysis. Additional maneuvers were developed with a protecting groups scheme that enabled efficient, streamlined syntheses of these important mediators of biochemical events.
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Affiliation(s)
| | - Peter A. Jordan
- Department of Chemistry, Yale University, P. O. Box 208107, New Haven, CT 06520
| | - Scott J. Miller
- Department of Chemistry, Yale University, P. O. Box 208107, New Haven, CT 06520
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37
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Stallings JD, Zeng YX, Narvaez F, Rebecchi MJ. Phospholipase C-δ1 Expression Is Linked to Proliferation, DNA Synthesis, and Cyclin E Levels. J Biol Chem 2008; 283:13992-4001. [DOI: 10.1074/jbc.m800752200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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38
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Ho KK, Anderson AA, Rosivatz E, Lam EWF, Woscholski R, Mann DJ. Identification of Cyclin A2 as the Downstream Effector of the Nuclear Phosphatidylinositol 4,5-Bisphosphate Signaling Network. J Biol Chem 2008; 283:5477-85. [DOI: 10.1074/jbc.m706623200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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39
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Li D, Urs AN, Allegood J, Leon A, Merrill AH, Sewer MB. Cyclic AMP-stimulated interaction between steroidogenic factor 1 and diacylglycerol kinase theta facilitates induction of CYP17. Mol Cell Biol 2007; 27:6669-85. [PMID: 17664281 PMCID: PMC2099220 DOI: 10.1128/mcb.00355-07] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the human adrenal cortex, adrenocorticotropin (ACTH) activates CYP17 transcription by promoting the binding of the nuclear receptor steroidogenic factor 1 (SF1) (Ad4BP, NR5A1) to the promoter. We recently found that sphingosine is an antagonist for SF1 and inhibits cyclic AMP (cAMP)-dependent CYP17 gene transcription. The aim of the current study was to identify phospholipids that bind to SF1 and to characterize the mechanism by which ACTH/cAMP regulates the biosynthesis of this molecule(s). Using tandem mass spectrometry, we show that in H295R human adrenocortical cells, SF1 is bound to phosphatidic acid (PA). Activation of the ACTH/cAMP signal transduction cascade rapidly increases nuclear diacylglycerol kinase (DGK) activity and PA production. PA stimulates SF1-dependent transcription of CYP17 reporter plasmids, promotes coactivator recruitment, and induces the mRNA expression of CYP17 and several other steroidogenic genes. Inhibition of DGK activity attenuates the binding of SF1 to the CYP17 promoter, and silencing of DGK-theta expression inhibits cAMP-dependent CYP17 transcription. LXXLL motifs in DGK-theta mediate a direct interaction of SF1 with the kinase and may facilitate binding of PA to the receptor. We conclude that ACTH/cAMP stimulates PA production in the nucleus of H295R cells and that this increase in PA concentrations facilitates CYP17 induction.
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Affiliation(s)
- Donghui Li
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
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40
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Visnjic D, Banfic H. Nuclear phospholipid signaling: phosphatidylinositol-specific phospholipase C and phosphoinositide 3-kinase. Pflugers Arch 2007; 455:19-30. [PMID: 17558519 DOI: 10.1007/s00424-007-0288-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 05/08/2007] [Indexed: 10/23/2022]
Abstract
Over the last 20 years, numerous studies have demonstrated the existence of nuclear phosphoinositide signaling distinct from the one at the plasma membrane. The activation of phosphatidylinositol-specific phospholipase C (PI-PLC) and phosphoinositide 3-kinase (PI3K), the generation of diacylglycerol, and the accumulation of the 3-phosphorylated phosphoinositides have been documented in the nuclei of different cell types. In this review, we summarize some recent studies of the subnuclear localization, mechanisms of activation, and the possible physiological roles of the nuclear PI-PLC and PI-3 kinases in the regulation of cell cycle, survival, and differentiation.
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Affiliation(s)
- Dora Visnjic
- Department of Physiology and Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Salata 3, 10 000, Zagreb, Croatia
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41
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Liu DZ, Liang HJ, Chen CH, Lin SY, Zhong WB, Ho FM, Hou WC, Lo JL, Ho YS, Lin PJ, Hung LF, Liang YC. Switch activation of PI-PLC downstream signals in activated macrophages with wortmannin. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2007; 1773:869-79. [PMID: 17488650 DOI: 10.1016/j.bbamcr.2007.03.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 03/03/2007] [Accepted: 03/26/2007] [Indexed: 10/23/2022]
Abstract
Phosphatidylinositol (4,5)-bisphosphate (PtdIns(4,5)P(2)) has been known to serve as a substrate for phosphatidylinositol 3-kinase (PI(3)K) and phosphoinositide-specific phospholipase C (PI-PLC), which can produce PtdIns(3,4,5)P(3) and inositol 1,4,5-trisphosphate (Ins(1,4,5)P(3)) and diacylglycerol (DAG), respectively. In this study, we elucidated the role of PI-PLC during the LPS-activated mouse macrophages RAW264.7 treated with PI(3)K inhibitor wortmannin. First, wortmannin treatment enhanced Ins(1,4,5)P(3) production and iNOS expression in LPS-activated macrophages. Inhibition of PI(3)K by p85 siRNA also showed an enhancement of iNOS expression. On the other hand, overexpression of PI(3)K by ras-p110 expression plasmid significantly decreased iNOS expression in LPS-activated macrophages. In addition, overexpression of wild-type or dominant-negative Akt expression plasmid did not affect the iNOS expression in LPS-activated macrophages. Second, treatment of PI-PLC inhibitor U73122 reversed the enhancement of iNOS expression, the increase of phosphorylation level of ERK, JNK and p38, and the increase of AP-1-dependent gene expression in wortmannin-treated and LPS-activated macrophages. However, NF-kappaB activity determined by EMSA assay and reporter plasmid assay did not change during LPS-activated macrophages with or without wortmannin. We propose that the inhibition of PI(3)K by wortmannin in mouse macrophages enhances the PI-PLC downstream signals, and subsequently increases the LPS induction of iNOS expression independently of Akt pathway.
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Affiliation(s)
- Der-Zen Liu
- Graduate Institutes of Biomedical Materials, Taipei Medical University, Taipei, Taiwan
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42
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Huang W, Zhang H, Davrazou F, Kutateladze TG, Shi X, Gozani O, Prestwich GD. Stabilized phosphatidylinositol-5-phosphate analogues as ligands for the nuclear protein ING2: chemistry, biology, and molecular modeling. J Am Chem Soc 2007; 129:6498-506. [PMID: 17469822 PMCID: PMC2553394 DOI: 10.1021/ja070195b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The interaction of PtdIns(5)P with the tumor suppressor protein ING2 has been implicated in the regulation of chromatin modification. To enhance the stability of PtdIns(5)P for studies of the biological role in vivo, two phosphatase-resistant moieties were used to replace the labile 5-phosphate. The total asymmetric synthesis of the 5-methylenephosphonate (MP) and 5-phosphothionate (PT) analogues of PtdIns(5)P is described herein, and the resulting metabolically stabilized lipid analogues were evaluated in three ways. First, liposomes containing either the dioleoyl MP or PT analogues bound to recombinant ING2 similar to liposomes containing dipalmitoyl PtdIns(5)P, indicating that the replacement of the hydrolyzable 5-phosphate group does not compromise the binding. Second, the dioleoyl MP and PT PtdIns(5)P analogues were equivalent to dipalmitoyl PtdIns(5)P in augmenting cell death induced by a DNA double-strand break in HT1080 cells. Finally, molecular modeling and docking of the MP or PT analogues to the C-terminus PtdInsP-binding region of ING2 (consisting of a PHD finger and a polybasic region) revealed a number of complementary surface and electrostatic contacts between the lipids and ING2.
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Affiliation(s)
- Wei Huang
- Department of Medicinal Chemistry, The University of Utah, 419 Wakara Way, Suite 205, Salt Lake City, Utah 84108-1257 USA, Phone: +1-801-585-9051. Fax: +1-801-585-9053.
| | - Honglu Zhang
- Department of Medicinal Chemistry, The University of Utah, 419 Wakara Way, Suite 205, Salt Lake City, Utah 84108-1257 USA, Phone: +1-801-585-9051. Fax: +1-801-585-9053.
| | - Foteini Davrazou
- Department of Pharmacology, University of Colorado Health Sciences Center, Aurora, Colorado 80045-0511 USA
| | - Tatiana G. Kutateladze
- Department of Pharmacology, University of Colorado Health Sciences Center, Aurora, Colorado 80045-0511 USA
| | - Xiaobing Shi
- Department of Biological Sciences, Stanford University, Palo Alto, California 94305 USA
| | - Or Gozani
- Department of Biological Sciences, Stanford University, Palo Alto, California 94305 USA
| | - Glenn D. Prestwich
- Department of Medicinal Chemistry, The University of Utah, 419 Wakara Way, Suite 205, Salt Lake City, Utah 84108-1257 USA, Phone: +1-801-585-9051. Fax: +1-801-585-9053.
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43
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Bavelloni A, Faenza I, Cioffi G, Piazzi M, Parisi D, Matic I, Maraldi NM, Cocco L. Proteomic-based analysis of nuclear signaling: PLCbeta1 affects the expression of the splicing factor SRp20 in Friend erythroleukemia cells. Proteomics 2007; 6:5725-34. [PMID: 17022104 DOI: 10.1002/pmic.200600318] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
An extensive body of evidence links inositide-specific phospholipase C (PLC) to the nucleus and the main isoform located in the nucleus is PLCbeta(1). Constitutive overexpression of nuclear PLCbeta(1) has been previously shown to inhibit Friend erythroleukemia cells differentiation and to induce cell cycle progression targeting cyclin D3. The aim of this study was to identify new proteins regulated by PLCbeta(1) overexpression, given the role exerted by its signaling in the nucleus during cell growth and differentiation. To identify novel downstream effectors of nuclear PLCbeta(1)-dependent signaling in Friend erythroleukemia cells, we performed the high-resolution 2-DE-based proteomic analysis. Using a proteomic approach we found that SRp20, a member of the highly conserved SR family of splicing regulators, was down-regulated in cells overexpressing nuclear PLCbeta(1) as compared with wild-type cells. Reduction in SRp20 was confirmed by 2-D Western blotting. Moreover, we have shown that nuclear PLCbeta(1) is bound to the SRp20 splicing factor. Indeed, by immunoprecipitation and subcellular fractioning, we have demonstrated that endogenous PLCbeta(1) and SRp20 physically interact in the nucleus. Here we show the existence of a PLCbeta(1)-specific target, the splicing factor SRp20, whose expression is specifically down-regulated by the nuclear signaling evoked by PLCbeta(1).
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MESH Headings
- Animals
- Blotting, Western
- Cell Nucleus/metabolism
- Cells, Cultured
- Down-Regulation
- Electrophoresis, Gel, Two-Dimensional
- Fluorescein-5-isothiocyanate
- Fluorescent Antibody Technique, Direct
- Fluorescent Dyes
- Gene Expression Regulation, Neoplastic
- Isoelectric Focusing
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Leukemia, Erythroblastic, Acute/metabolism
- Leukemia, Erythroblastic, Acute/pathology
- Mice
- Microscopy, Fluorescence
- Peptide Mapping
- Phospholipase C beta
- Precipitin Tests
- Proteomics/methods
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/physiology
- Serine-Arginine Splicing Factors
- Signal Transduction
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Subcellular Fractions/metabolism
- Type C Phospholipases/genetics
- Type C Phospholipases/metabolism
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Affiliation(s)
- Alberto Bavelloni
- Laboratory of Cell Biology and Electron Microscopy, IOR, Bologna Italy
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44
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Cocco L, Follo MY, Faenza I, Bavelloni A, Billi AM, Martelli AM, Manzoli L. Nuclear inositide signaling: An appraisal of phospholipase C β1 behavior in myelodysplastic and leukemia cells. ACTA ACUST UNITED AC 2007; 47:2-9. [PMID: 17335878 DOI: 10.1016/j.advenzreg.2006.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Lucio Cocco
- Cellular Signalling Laboratory, Department of Anatomical Sciences, University of Bologna, via Irnerio 48, 40126 Bologna, Italy.
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45
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Trofimov VA, Dudko AA. Lipid spectrum in fractions of liver cell chromatin from mice after partial hepatectomy. Bull Exp Biol Med 2006; 141:77-80. [PMID: 16929970 DOI: 10.1007/s10517-006-0098-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The qualitative and quantitative differences in lipids composition were found in chromatin fractions differing by attachment to the nuclear matrix and transcriptional activity. During liver regeneration after partial hepatectomy Changes in the lipid spectrum of chromatin fractions in G1- and S-phases are associated with transcriptional activity and their primary involvement in replication.
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46
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Kaadige MR, Ayer DE. The polybasic region that follows the plant homeodomain zinc finger 1 of Pf1 is necessary and sufficient for specific phosphoinositide binding. J Biol Chem 2006; 281:28831-6. [PMID: 16893883 DOI: 10.1074/jbc.m605624200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The plant homeodomain (PHD) zinc finger is one of 14 known zinc-binding domains. PHD domains have been found in more than 400 eukaryotic proteins and are characterized by a Cys(4)-His-Cys(3) zinc-binding motif that spans 50-80 residues. The precise function of PHD domains is currently unknown; however, the PHD domains of the ING1 and ING2 tumor suppressors have been shown recently to bind phosphoinositides (PIs). We have recently identified a novel PHD-containing protein, Pf1, as a binding partner for the abundant and ubiquitous transcriptional corepressor mSin3A. Pf1 contains two PHD zinc fingers, PHD1 and PHD2, and functions to bridge mSin3A to the TLE1 corepressor. Here, we show that PHD1, but not PHD2, binds several monophosporylated PIs but most strongly to PI(3)P. Surprisingly, a polybasic region that follows the PHD1 is necessary for PI(3)P binding. Furthermore, this polybasic region binds specifically to PI(3)P when fused to maltose-binding protein, PHD2, or as an isolated peptide, demonstrating that it is sufficient for specific PI binding. By exchanging the polybasic regions between different PHD fingers we show that this region is a strong determinant of PI binding specificity. These findings establish the Pf1 polybasic region as a phosphoinositide-binding module and suggest that the PHD domains function down-stream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides.
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Affiliation(s)
- Mohan R Kaadige
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
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47
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Ling K, Schill NJ, Wagoner MP, Sun Y, Anderson RA. Movin' on up: the role of PtdIns(4,5)P2 in cell migration. Trends Cell Biol 2006; 16:276-84. [PMID: 16616849 DOI: 10.1016/j.tcb.2006.03.007] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Revised: 02/17/2006] [Accepted: 03/23/2006] [Indexed: 11/28/2022]
Abstract
Cell migration requires the coordination of many biochemical events, including cell-matrix contact turnover and cytoskeletal restructuring. Recent advances further implicate phosphatidylinositol(4,5)-bisphosphate [PtdIns(4,5)P(2)] in the control of these events. Many proteins that are crucial to the assembly of the migration machinery are regulated by PtdIns(4,5)P(2). Coordinated synthesis of PtdIns(4,5)P(2) at these sites is dependent on the precise targeting of the type I phosphatidylinositol phosphate kinases (PIPKs). Two PIPKI isoforms target to, and generate, PtdIns(4,5)P(2) at membrane ruffles and focal adhesions during cell migration. Here, we discuss our current understanding of PtdIns(4,5)P(2) in the regulation of cell responses to migratory stimuli and how the migrating cell controls PtdIns(4,5)P(2) availability.
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Affiliation(s)
- Kun Ling
- Program in Molecular and Cellular Pharmacology, University of Wisconsin-Madison, Department of Pharmacology, University of Wisconsin Medical School, 1300 University Ave, Madison, WI 53706, USA
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Goto K, Hozumi Y, Kondo H. Diacylglycerol, phosphatidic acid, and the converting enzyme, diacylglycerol kinase, in the nucleus. Biochim Biophys Acta Mol Cell Biol Lipids 2006; 1761:535-41. [PMID: 16731035 DOI: 10.1016/j.bbalip.2006.04.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Revised: 04/06/2006] [Accepted: 04/07/2006] [Indexed: 01/08/2023]
Abstract
There exists phosphoinositide (PI) cycle in the nucleus, which is operated differentially from the classical PI cycle at the plasma membrane. Evidence has been accumulated that nuclear PIs and the related enzymes are closely involved in a variety of nuclear processes, although the details remain to be elucidated. In this mini review, some components of PI cycle, i.e., diacylglycerol, phosphatidic acid, and the converting enzyme, diacylglycerol kinase, in the nucleus are discussed with focusing on the lipid metabolism, cell cycle regulation, and animal models.
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Affiliation(s)
- Kaoru Goto
- Department of Anatomy and Cell Biology, Yamagata University School of Medicine, Iida-Nishi 2-2-2, Yamagata 990-9585, Japan.
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Yagisawa H, Okada M, Naito Y, Sasaki K, Yamaga M, Fujii M. Coordinated intracellular translocation of phosphoinositide-specific phospholipase C-δ with the cell cycle. Biochim Biophys Acta Mol Cell Biol Lipids 2006; 1761:522-34. [PMID: 16580873 DOI: 10.1016/j.bbalip.2006.02.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Accepted: 02/16/2006] [Indexed: 11/18/2022]
Abstract
The delta family phosphoinositide (PI)-specific phospholipase C (PLC) are most fundamental forms of eukaryotic PI-PLCs. Despite the presence of lipid targeting domains such as the PH domain and C2 domain, the isoforms are also found in the cytoplasm and nucleus as well as at the plasma membrane. The isoforms have sequences or regions that can serve as a nuclear localization signal (NLS) and a nuclear export signal (NES). Their intracellular localization differs from one isoform to another, presumably due to the difference in the transport equilibrium balanced by the strength of the two signals of each isoform. Even for a particular isoform, its intracellular localization seems to vary during the cell cycle. As an example, PLCdelta(1), which is generally found at the plasma membrane and in the cytoplasm of quiescent cells, localizes to discrete nuclear structures in the G(1)/S boundary of the cell cycle. This may be at least partly due to an increase in intracellular Ca(2+), since Ca(2+) facilitates the formation of a nuclear transport complex comprised of PLCdelta(1) and importin beta1, a carrier molecule for the nuclear import. PLCdelta(1) as well as PLCdelta(4) may play a pivotal role in controlling the initiation of DNA synthesis in S phase. Spatio-temporal changes in the levels of PtdIns(4,5)P(2) seem to be another major determinant for the localization and regulation of the delta isoforms. High nuclear PtdIns(4,5)P(2) levels are associated with the G(1)/S phases. After entering M phase, PtdIns(4,5)P(2) synthesis at sites of cell division occurs and PLCs seem to localize to the cleavage furrow during cytokinesis. Coordinated translocation of PLCs with the cell cycle or with stress responses may result in changes in intra-nuclear environments and local membrane architectures that modulate proliferation and differentiation. In this review, recent findings regarding the molecular machineries and mechanisms of the nucleocytoplasmic shuttling as well as roles in the cell cycle progression of the delta isoforms of PLC will be discussed.
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Affiliation(s)
- Hitoshi Yagisawa
- Graduate School of Life Science, University of Hyogo, Harima Science Garden City, Hyogo 678-1297, Japan.
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Alvarez-Venegas R, Xia Y, Lu G, Avramova Z. Phosphoinositide 5-phosphate and phosphoinositide 4-phosphate trigger distinct specific responses of Arabidopsis genes: genome-wide expression analyses. PLANT SIGNALING & BEHAVIOR 2006; 1:140-51. [PMID: 19521494 PMCID: PMC2634585 DOI: 10.4161/psb.1.3.2997] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2006] [Accepted: 04/19/2006] [Indexed: 05/26/2023]
Abstract
Phosphoinositide phosphates, PtdInsP, are important components of the cell lipid pool that can function as messengers in diverse cellular processes. Lack of information on downstream targets, however, has impeded our understanding of the potential of lipid-signaling to influence gene activity. Our goals here were to identify genes that altered expression in the presence of two isomeric monophosphate lipid messengers (Phosphoinositide 5-Phosphate, PtdIns(5)P, and Phosphoinositide 4-Phosphate, PtdIns(4)P) and to establish whether the two lipids influence distinct or overlapping gene-sets. Our results indicated that PtdIns(5)P and PtdIns(4)P affected genes within shared gene-families but that each messenger influenced the expression of different members within the same family. These results suggested that PtdIns(5)P and PtdIns(4)P participate in separate pathways that, ultimately, may control gene expression. The pathways may have points of convergence but may also counteract each other's effects. A significant fraction ( approximately 40%) of the PtdIns(5)P-stimulated genes belong to various families of wall-modifying genes. Wall-modifying activities are recognized as factors affecting cell extension and plant growth. Elevated PtdIns(5)P concentration influenced stem growth and the effects were different from those triggered by PtdIns(4)P. The data allow insights into plants' response to two related PtdInsP at whole-plant/genome-wide levels and demonstrate that PtdIns(5)P-and PtdIns(4)P-involving mechanisms are distinct, selective and specific.
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Affiliation(s)
- Raul Alvarez-Venegas
- School of Biological Sciences, University of Nebraska Lincoln; Lincoln Nebraska USA
| | - Yuannan Xia
- Genomics Core Research Facility, Center for Biotechnology; University of Nebraska Lincoln; Lincoln Nebraska USA
| | - Guoqing Lu
- Department of Biology, University of Nebraska at Omaha; Omaha, Nebraska USA
| | - Zoya Avramova
- School of Biological Sciences, University of Nebraska Lincoln; Lincoln Nebraska USA
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