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Kim S, Bhandari R, Brearley CA, Saiardi A. The inositol phosphate signalling network in physiology and disease. Trends Biochem Sci 2024:S0968-0004(24)00192-0. [PMID: 39317578 DOI: 10.1016/j.tibs.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/29/2024] [Accepted: 08/19/2024] [Indexed: 09/26/2024]
Abstract
Combinatorial substitution of phosphate groups on the inositol ring gives rise to a plethora of inositol phosphates (InsPs) and inositol pyrophosphates (PP-InsPs). These small molecules constitute an elaborate metabolic and signalling network that influences nearly every cellular function. This review delves into the knowledge accumulated over the past decades regarding the biochemical principles and significance of InsP metabolism. We focus on the biological actions of InsPs in mammals, with an emphasis on recent findings regarding specific target proteins. We further discuss the roles of InsP metabolism in contributing to physiological homeostasis and pathological conditions. A deeper understanding of InsPs and their metabolic pathways holds the potential to address unresolved questions and propel advances towards therapeutic applications.
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Affiliation(s)
- Seyun Kim
- Department of Biological Sciences, KAIST Stem Cell Center, KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics (CDFD), Inner Ring Road, Uppal, Hyderabad 500039, India.
| | - Charles A Brearley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
| | - Adolfo Saiardi
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK.
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2
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Su XB, Saiardi A. The role of inositol in the environmental organic phosphate cycle. Curr Opin Biotechnol 2024; 90:103196. [PMID: 39276615 DOI: 10.1016/j.copbio.2024.103196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/22/2024] [Accepted: 08/28/2024] [Indexed: 09/17/2024]
Abstract
Cellular synthesis of phytic acid sequesters phosphates in the sugar inositol. Phytic acid in soil represents the most abundant form of organic phosphates. The supplementation of phytase or phytase-producing organisms has been considered as a strategy to improve usable soil phosphates. However, the impacts on the environmental flow of inositol, which is generated along with phosphate by phytase, have not been examined. In this review, we discuss the origin and nature of inositol produced in soil and the several possible destinations of inositol released by phytase activities. We emphasise how an improved understanding of soil inositol flow could help to provide new solutions to the phosphate shortage problem in agriculture.
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Affiliation(s)
- Xue B Su
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Adolfo Saiardi
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK.
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Sowd GA, Stivison EA, Chapagain P, Hale AT, Poland JC, Rameh LE, Blind RD. IPMK regulates HDAC3 activity and histone H4 acetylation in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591660. [PMID: 38746349 PMCID: PMC11092501 DOI: 10.1101/2024.04.29.591660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Histone deacetylases (HDACs) repress transcription by catalyzing the removal of acetyl groups from histones. Class 1 HDACs are activated by inositol phosphate signaling molecules in vitro , but it is unclear if this regulation occurs in human cells. Inositol Polyphosphate Multikinase (IPMK) is required for production of inositol hexakisphosphate (IP6), pentakisphosphate (IP5) and certain tetrakisphosphate (IP4) species, all known activators of Class 1 HDACs in vitro . Here, we generated IPMK knockout (IKO) human U251 glioblastoma cells, which decreased cellular inositol phosphate levels and increased histone H4-acetylation by mass spectrometry. ChIP-seq showed IKO increased H4-acetylation at IKO-upregulated genes, but H4-acetylation was unchanged at IKO-downregulated genes, suggesting gene-specific responses to IPMK knockout. HDAC deacetylase enzyme activity was decreased in HDAC3 immunoprecipitates from IKO vs . wild-type cells, while deacetylase activity of other Class 1 HDACs had no detectable changes in activity. Wild-type IPMK expression in IKO cells fully rescued HDAC3 deacetylase activity, while kinase-dead IPMK expression had no effect. Further, the deficiency in HDAC3 activity in immunoprecipitates from IKO cells could be fully rescued by addition of synthesized IP4 (Ins(1,4,5,6)P4) to the enzyme assay, while control inositol had no effect. These data suggest that cellular IPMK-dependent inositol phosphates are required for full HDAC3 enzyme activity and proper histone H4-acetylation. Implications for targeting IPMK in HDAC3-dependent diseases are discussed.
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Escudeiro-Lopes S, Filimonenko VV, Jarolimová L, Hozák P. Lamin A/C and PI(4,5)P2-A Novel Complex in the Cell Nucleus. Cells 2024; 13:399. [PMID: 38474363 DOI: 10.3390/cells13050399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 03/14/2024] Open
Abstract
Lamins, the nuclear intermediate filaments, are important regulators of nuclear structural integrity as well as nuclear functional processes such as DNA transcription, replication and repair, and epigenetic regulations. A portion of phosphorylated lamin A/C localizes to the nuclear interior in interphase, forming a lamin A/C pool with specific properties and distinct functions. Nucleoplasmic lamin A/C molecular functions are mainly dependent on its binding partners; therefore, revealing new interactions could give us new clues on the lamin A/C mechanism of action. In the present study, we show that lamin A/C interacts with nuclear phosphoinositides (PIPs), and with nuclear myosin I (NM1). Both NM1 and nuclear PIPs have been previously reported as important regulators of gene expression and DNA damage/repair. Furthermore, phosphorylated lamin A/C forms a complex with NM1 in a phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2)-dependent manner in the nuclear interior. Taken together, our study reveals a previously unidentified interaction between phosphorylated lamin A/C, NM1, and PI(4,5)P2 and suggests new possible ways of nucleoplasmic lamin A/C regulation, function, and importance for the formation of functional nuclear microdomains.
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Affiliation(s)
- Sara Escudeiro-Lopes
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Vlada V Filimonenko
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
- Electron Microscopy Core Facility, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Lenka Jarolimová
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
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5
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Gu C, Li X, Zong G, Wang H, Shears SB. IP8: A quantitatively minor inositol pyrophosphate signaling molecule that punches above its weight. Adv Biol Regul 2024; 91:101002. [PMID: 38064879 DOI: 10.1016/j.jbior.2023.101002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 02/25/2024]
Abstract
The inositol pyrophosphates (PP-IPs) are specialized members of the wider inositol phosphate signaling family that possess functionally significant diphosphate groups. The PP-IPs exhibit remarkable functionally versatility throughout the eukaryotic kingdoms. However, a quantitatively minor PP-IP - 1,5 bisdiphosphoinositol tetrakisphosphate (1,5-IP8) - has received considerably less attention from the cell signalling community. The main purpose of this review is to summarize recently-published data which have now brought 1,5-IP8 into the spotlight, by expanding insight into the molecular mechanisms by which this polyphosphate regulates many fundamental biological processes.
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Affiliation(s)
- Chunfang Gu
- Inositol signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709 USA
| | - Xingyao Li
- Inositol signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709 USA
| | - Guangning Zong
- Inositol signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709 USA
| | - Huanchen Wang
- Inositol signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709 USA.
| | - Stephen B Shears
- Inositol signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709 USA.
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Su XB, Ko ALA, Saiardi A. Regulations of myo-inositol homeostasis: Mechanisms, implications, and perspectives. Adv Biol Regul 2023; 87:100921. [PMID: 36272917 DOI: 10.1016/j.jbior.2022.100921] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
Phosphorylation is the most common module of cellular signalling pathways. The dynamic nature of phosphorylation, which is conferred by the balancing acts of kinases and phosphatases, allows this modification to finely control crucial cellular events such as growth, differentiation, and cell cycle progression. Although most research to date has focussed on protein phosphorylation, non-protein phosphorylation substrates also play vital roles in signal transduction. The most well-established substrate of non-protein phosphorylation is inositol, whose phosphorylation generates many important signalling molecules such as the second messenger IP3, a key factor in calcium signalling. A fundamental question to our understanding of inositol phosphorylation is how the levels of cellular inositol are controlled. While the availability of protein phosphorylation substrates is known to be readily controlled at the levels of transcription, translation, and/or protein degradation, the regulatory mechanisms that control the uptake, synthesis, and removal of inositol are underexplored. Potentially, such mechanisms serve as an important layer of regulation of cellular signal transduction pathways. There are two ways in which mammalian cells acquire inositol. The historic use of radioactive 3H-myo-inositol revealed that inositol is promptly imported from the extracellular environment by three specific symporters SMIT1/2, and HMIT, coupling sodium or proton entry, respectively. Inositol can also be synthesized de novo from glucose-6P, thanks to the enzymatic activity of ISYNA1. Intriguingly, emerging evidence suggests that in mammalian cells, de novo myo-inositol synthesis occurs irrespective of inositol availability in the environment, prompting the question of whether the two sources of inositol go through independent metabolic pathways, thus serving distinct functions. Furthermore, the metabolic stability of myo-inositol, coupled with the uptake and endogenous synthesis, determines that there must be exit pathways to remove this extraordinary sugar from the cells to maintain its homeostasis. This essay aims to review our current knowledge of myo-inositol homeostatic metabolism, since they are critical to the signalling events played by its phosphorylated forms.
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Affiliation(s)
- Xue Bessie Su
- Medical Research Council, Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK
| | - An-Li Andrea Ko
- Medical Research Council, Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK
| | - Adolfo Saiardi
- Medical Research Council, Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK.
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Fabijanczuk KC, Chao HC, Fischer JL, McLuckey SA. Structural elucidation and isomeric differentiation/quantitation of monophosphorylated phosphoinositides using gas-phase ion/ion reactions and dissociation kinetics. Analyst 2022; 147:5000-5010. [PMID: 36254743 PMCID: PMC9651020 DOI: 10.1039/d2an00792d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Phosphoinositides, phosphorylated derivatives of phosphatidylinositols, are essential signaling phospholipids in all mammalian cellular membranes. With three known phosphorylated derivatives of phosphatidylinositols at the 3-, 4-, and 5-positions along the myo-inositol ring, various fatty acyl chain lengths, and varying degrees of unsaturation, numerous isomers can be present. It is challenging for shotgun-MS to accurately identify and characterize phosphoinositides and their isomers using the most readily available precursor ion types. To overcome this challenge, novel gas-phase ion/ion chemistry was used to expand the range of precursor ion-types for subsequent structural characterization of phosphoinositides using shot-gun tandem mass spectrometry. The degree of phosphorylation and fatty acyl sum composition are readily obtained by ion-trap CID of deprotonated phosphoinositides. Carbon-carbon double bond position of the fatty acyl chains can be localized via a charge inversion ion/ion reaction. Utilizing sequential ion/ion reactions and subsequent activation yields product ion information that is of limited utility for phosphorylation site localization. However, the kinetics of dissociation allowed for isomeric differentiation of the position of the phosphate group. Furthermore, employing the same kinetics method, relative quantitative information was gained for the isomeric species.
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Affiliation(s)
| | - Hsi-Chun Chao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Joshua L Fischer
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
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Jiang T, Ling Z, Zhou Z, Chen X, Chen L, Liu S, Sun Y, Yang J, Yang B, Huang J, Huang L. Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs. J Anim Sci Biotechnol 2022; 13:112. [PMID: 36217153 PMCID: PMC9552403 DOI: 10.1186/s40104-022-00767-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Background A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits. However, the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs. Results Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq, and identified 557,273 merged peaks, which greatly expanded the pig regulatory element repository. We revealed tissue-specific regulatory elements which were associated with tissue-relevant biological functions. We identified both positive and negative significant correlations between the regulatory elements and gene transcripts, which showed distinct distributions in terms of their strength and distances from corresponding genes. We investigated the presence of transposable elements (TEs) in open chromatin regions across all tissues, these included identifications of porcine endogenous retroviruses (PERVs) exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable elements. Furthermore, we prioritized a potential causal variant for polyunsaturated fatty acid in the muscle. Conclusions Our data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions, as well as regulatory variants of loci associated with complex traits in pigs. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00767-3.
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Affiliation(s)
- Tao Jiang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ziqi Ling
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhimin Zhou
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaoyun Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Liqing Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Sha Liu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yingchun Sun
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jiawen Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Jianzhen Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
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Bellido AM, Souza Canadá ED, Permingeat HR, Echenique V. Genetic Transformation of Apomictic Grasses: Progress and Constraints. FRONTIERS IN PLANT SCIENCE 2021; 12:768393. [PMID: 34804102 PMCID: PMC8602796 DOI: 10.3389/fpls.2021.768393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/05/2021] [Indexed: 05/17/2023]
Abstract
The available methods for plant transformation and expansion beyond its limits remain especially critical for crop improvement. For grass species, this is even more critical, mainly due to drawbacks in in vitro regeneration. Despite the existence of many protocols in grasses to achieve genetic transformation through Agrobacterium or biolistic gene delivery, their efficiencies are genotype-dependent and still very low due to the recalcitrance of these species to in vitro regeneration. Many plant transformation facilities for cereals and other important crops may be found around the world in universities and enterprises, but this is not the case for apomictic species, many of which are C4 grasses. Moreover, apomixis (asexual reproduction by seeds) represents an additional constraint for breeding. However, the transformation of an apomictic clone is an attractive strategy, as the transgene is immediately fixed in a highly adapted genetic background, capable of large-scale clonal propagation. With the exception of some species like Brachiaria brizantha which is planted in approximately 100 M ha in Brazil, apomixis is almost non-present in economically important crops. However, as it is sometimes present in their wild relatives, the main goal is to transfer this trait to crops to fix heterosis. Until now this has been a difficult task, mainly because many aspects of apomixis are unknown. Over the last few years, many candidate genes have been identified and attempts have been made to characterize them functionally in Arabidopsis and rice. However, functional analysis in true apomictic species lags far behind, mainly due to the complexity of its genomes, of the trait itself, and the lack of efficient genetic transformation protocols. In this study, we review the current status of the in vitro culture and genetic transformation methods focusing on apomictic grasses, and the prospects for the application of new tools assayed in other related species, with two aims: to pave the way for discovering the molecular pathways involved in apomixis and to develop new capacities for breeding purposes because many of these grasses are important forage or biofuel resources.
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Affiliation(s)
- Andrés M. Bellido
- Departamento de Agronomía, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS – CCT – CONICET Bahía Blanca), Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | | | | | - Viviana Echenique
- Departamento de Agronomía, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS – CCT – CONICET Bahía Blanca), Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
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Rao MJ, Goodman JM. Seipin: harvesting fat and keeping adipocytes healthy. Trends Cell Biol 2021; 31:912-923. [PMID: 34215489 DOI: 10.1016/j.tcb.2021.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/29/2021] [Accepted: 06/03/2021] [Indexed: 01/17/2023]
Abstract
Seipin is a key protein in the assembly of cytoplasmic lipid droplets (cLDs) and their maintenance at endoplasmic reticulum (ER)-LD junctions; the absence of seipin results in generalized lipodystrophy. How seipin mediates LD dynamics and prevents lipodystrophy are not well understood. New evidence suggests that seipin attracts triglyceride monomers from the ER to sites of droplet formation. By contrast, seipin may not be directly involved in the assembly of nuclear LDs and may actually suppress their formation at a distance. Seipin promotes adipogenesis, but lipodystrophy may also involve postadipogenic effects. We hypothesize that among these are a cycle of runaway lipolysis and lipotoxicity caused by aberrant LDs, resulting in a depletion of fat stores and a failure of adipose and other cells to thrive.
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Affiliation(s)
- Monala Jayaprakash Rao
- Department of Pharmacology, University of Texas Southwestern Medical School, Dallas, TX 75390-9041, USA
| | - Joel M Goodman
- Department of Pharmacology, University of Texas Southwestern Medical School, Dallas, TX 75390-9041, USA.
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11
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Ithal D, Sukumaran SK, Bhattacharjee D, Vemula A, Nadella R, Mahadevan J, Sud R, Viswanath B, Purushottam M, Jain S. Exome hits demystified: The next frontier. Asian J Psychiatr 2021; 59:102640. [PMID: 33892377 DOI: 10.1016/j.ajp.2021.102640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/26/2021] [Indexed: 12/13/2022]
Abstract
Severe mental illnesses such as schizophrenia and bipolar disorder have complex inheritance patterns, involving both common and rare variants. Whole exome sequencing is a promising approach to find out the rare genetic variants. We had previously reported several rare variants in multiplex families with severe mental illnesses. The current article tries to summarise the biological processes and pattern of expression of genes harbouring the aforementioned variants, linking them to known clinical manifestations through a methodical narrative review. Of the 28 genes considered for this review from 7 families with multiple affected individuals, 6 genes are implicated in various neuropsychiatric manifestations including some variations in the brain morphology assessed by magnetic resonance imaging. Another 15 genes, though associated with neuropsychiatric manifestations, did not have established brain morphological changes whereas the remaining 7 genes did not have any previously recorded neuropsychiatric manifestations at all. Wnt/b-catenin signaling pathway was associated with 6 of these genes and PI3K/AKT, calcium signaling, ERK, RhoA and notch signaling pathways had at least 2 gene associations. We present a comprehensive review of biological and clinical knowledge about the genes previously reported in multiplex families with severe mental illness. A 'disease in dish approach' can be helpful to further explore the fundamental mechanisms.
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Affiliation(s)
- Dhruva Ithal
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Salil K Sukumaran
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Debanjan Bhattacharjee
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Alekhya Vemula
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Ravi Nadella
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Jayant Mahadevan
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Reeteka Sud
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Biju Viswanath
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Meera Purushottam
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India.
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
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12
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Laha D, Portela-Torres P, Desfougères Y, Saiardi A. Inositol phosphate kinases in the eukaryote landscape. Adv Biol Regul 2020; 79:100782. [PMID: 33422459 PMCID: PMC8024741 DOI: 10.1016/j.jbior.2020.100782] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 01/01/2023]
Abstract
Inositol phosphate encompasses a large multifaceted family of signalling molecules that originate from the combinatorial attachment of phosphate groups to the inositol ring. To date, four distinct inositol kinases have been identified, namely, IPK, ITPK, IPPK (IP5-2K), and PPIP5K. Although, ITPKs have recently been identified in archaea, eukaryotes have taken advantage of these enzymes to create a sophisticated signalling network based on inositol phosphates. However, it remains largely elusive what fundamental biochemical principles control the signalling cascade. Here, we present an evolutionary approach to understand the development of the 'inositol phosphate code' in eukaryotes. Distribution analyses of these four inositol kinase groups throughout the eukaryotic landscape reveal the loss of either ITPK, or of PPIP5K proteins in several species. Surprisingly, the loss of IPPK, an enzyme thought to catalyse the rate limiting step of IP6 (phytic acid) synthesis, was also recorded. Furthermore, this study highlights a noteworthy difference between animal (metazoan) and plant (archaeplastida) lineages. While metazoan appears to have a substantial amplification of IPK enzymes, archaeplastida genomes show a considerable increase in ITPK members. Differential evolution of IPK and ITPK between plant and animal lineage is likely reflective of converging functional adaptation of these two types of inositol kinases. Since, the IPK family comprises three sub-types IPMK, IP6K, and IP3-3K each with dedicated enzymatic specificity in metazoan, we propose that the amplified ITPK group in plant could be classified in sub-types with distinct enzymology.
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Affiliation(s)
- Debabrata Laha
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, WC1E6BT, London, UK
| | - Paloma Portela-Torres
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, WC1E6BT, London, UK
| | - Yann Desfougères
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, WC1E6BT, London, UK
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, WC1E6BT, London, UK.
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Ucuncu E, Rajamani K, Wilson MSC, Medina-Cano D, Altin N, David P, Barcia G, Lefort N, Banal C, Vasilache-Dangles MT, Pitelet G, Lorino E, Rabasse N, Bieth E, Zaki MS, Topcu M, Sonmez FM, Musaev D, Stanley V, Bole-Feysot C, Nitschké P, Munnich A, Bahi-Buisson N, Fossoud C, Giuliano F, Colleaux L, Burglen L, Gleeson JG, Boddaert N, Saiardi A, Cantagrel V. MINPP1 prevents intracellular accumulation of the chelator inositol hexakisphosphate and is mutated in Pontocerebellar Hypoplasia. Nat Commun 2020; 11:6087. [PMID: 33257696 PMCID: PMC7705663 DOI: 10.1038/s41467-020-19919-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Inositol polyphosphates are vital metabolic and secondary messengers, involved in diverse cellular functions. Therefore, tight regulation of inositol polyphosphate metabolism is essential for proper cell physiology. Here, we describe an early-onset neurodegenerative syndrome caused by loss-of-function mutations in the multiple inositol-polyphosphate phosphatase 1 gene (MINPP1). Patients are found to have a distinct type of Pontocerebellar Hypoplasia with typical basal ganglia involvement on neuroimaging. We find that patient-derived and genome edited MINPP1−/− induced stem cells exhibit an inefficient neuronal differentiation combined with an increased cell death. MINPP1 deficiency results in an intracellular imbalance of the inositol polyphosphate metabolism. This metabolic defect is characterized by an accumulation of highly phosphorylated inositols, mostly inositol hexakisphosphate (IP6), detected in HEK293 cells, fibroblasts, iPSCs and differentiating neurons lacking MINPP1. In mutant cells, higher IP6 level is expected to be associated with an increased chelation of intracellular cations, such as iron or calcium, resulting in decreased levels of available ions. These data suggest the involvement of IP6-mediated chelation on Pontocerebellar Hypoplasia disease pathology and thereby highlight the critical role of MINPP1 in the regulation of human brain development and homeostasis. Tight regulation of inositol polyphosphate metabolism is essential for proper cell physiology. Here, the authors describe an early-onset neurodegenerative syndrome caused by loss-of-function mutations in the MINPP1 gene, characterised by intracellular imbalance of inositol polyphosphate metabolism.
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Affiliation(s)
- Ekin Ucuncu
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Karthyayani Rajamani
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Miranda S C Wilson
- MRC Laboratory for Molecular Cell Biology, University College London, WC1E 6BT, London, UK
| | - Daniel Medina-Cano
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Nami Altin
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Pierre David
- Transgenesis Platform, Laboratoire d'Expérimentation Animale et Transgenèse (LEAT), Imagine Institute, Structure Fédérative de Recherche Necker INSERM US24/CNRS UMS3633, 75015, Paris, France
| | - Giulia Barcia
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France.,Département de Génétique Médicale, AP-HP, Hôpital Necker-Enfants Malades, F-75015, Paris, France
| | - Nathalie Lefort
- Université de Paris, iPSC Core Facility, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Céline Banal
- Université de Paris, iPSC Core Facility, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | | | - Gaële Pitelet
- Service de Neuropédiatrie, CHU Nice, 06200, Nice, France
| | - Elsa Lorino
- ESEAN, 44200 Nantes, Service de maladies chroniques de l'enfant, CHU Nantes, 44093, Nantes, France
| | - Nathalie Rabasse
- Service de pédiatrie, hôpital d'Antibes-Juan-les-Pins, 06600, Antibes-Juan-les-Pins, France
| | - Eric Bieth
- Service de Génétique Médicale, CHU Toulouse, 31059, Toulouse, France
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, 12311, Egypt
| | - Meral Topcu
- Department of Child Neurology, Faculty of Medicine, Hacettepe University, Ankara, 06100, Turkey
| | - Fatma Mujgan Sonmez
- Guven Hospital, Child Neurology Department, Ankara, Turkey.,Department of Child Neurology, Faculty of Medicine, Karadeniz Technical University, Trabzon, 61080, Turkey
| | - Damir Musaev
- Laboratory for Pediatric Brain Diseases, Rady Children's Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Valentina Stanley
- Laboratory for Pediatric Brain Diseases, Rady Children's Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Christine Bole-Feysot
- Université de Paris, Genomics Platform, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Patrick Nitschké
- Université de Paris, Bioinformatics Core Facility, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Arnold Munnich
- Université de Paris, Translational Genetics Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Nadia Bahi-Buisson
- Université de Paris, Genetics and Development of the Cerebral Cortex Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Catherine Fossoud
- Centre de Référence des Troubles des Apprentissages, Hôpitaux Pédiatriques de Nice CHU-Lenval, 06200, Nice, France
| | - Fabienne Giuliano
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nice, 06202, Nice, France
| | - Laurence Colleaux
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Lydie Burglen
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France.,Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Département de Génétique, AP-HP, Sorbonne Université, Hôpital Trousseau, 75012, Paris, France
| | - Joseph G Gleeson
- Laboratory for Pediatric Brain Diseases, Rady Children's Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nathalie Boddaert
- Département de radiologie pédiatrique, INSERM UMR 1163 and INSERM U1000, AP-HP, Hôpital Necker-Enfants Malades, F-75015, Paris, France
| | - Adolfo Saiardi
- MRC Laboratory for Molecular Cell Biology, University College London, WC1E 6BT, London, UK.
| | - Vincent Cantagrel
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France.
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Cridland C, Gillaspy G. Inositol Pyrophosphate Pathways and Mechanisms: What Can We Learn from Plants? Molecules 2020; 25:E2789. [PMID: 32560343 PMCID: PMC7356102 DOI: 10.3390/molecules25122789] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/11/2020] [Accepted: 06/13/2020] [Indexed: 11/25/2022] Open
Abstract
The ability of an organism to maintain homeostasis in changing conditions is crucial for growth and survival. Eukaryotes have developed complex signaling pathways to adapt to a readily changing environment, including the inositol phosphate (InsP) signaling pathway. In plants and humans the pyrophosphorylated inositol molecules, inositol pyrophosphates (PP-InsPs), have been implicated in phosphate and energy sensing. PP-InsPs are synthesized from the phosphorylation of InsP6, the most abundant InsP. The plant PP-InsP synthesis pathway is similar but distinct from that of the human, which may reflect differences in how molecules such as Ins(1,4,5)P3 and InsP6 function in plants vs. animals. In addition, PP-InsPs can potentially interact with several major signaling proteins in plants, suggesting PP-InsPs play unique signaling roles via binding to protein partners. In this review, we will compare the biosynthesis and role of PP-InsPs in animals and plants, focusing on three central themes: InsP6 synthesis pathways, synthesis and regulation of the PP-InsPs, and function of a specific protein domain called the Syg1, Pho1, Xpr1 (SPX ) domain in binding PP-InsPs and regulating inorganic phosphate (Pi) sensing. This review will provide novel insights into the biosynthetic pathway and bioactivity of these key signaling molecules in plant and human systems.
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Affiliation(s)
| | - Glenda Gillaspy
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA;
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15
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Structural analyses of inositol phosphate second messengers bound to signaling effector proteins. Adv Biol Regul 2019; 75:100667. [PMID: 31648945 DOI: 10.1016/j.jbior.2019.100667] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/17/2019] [Accepted: 09/30/2019] [Indexed: 01/02/2023]
Abstract
The higher-order inositol phosphate second messengers inositol tetrakisphosphate (IP4), inositol pentakisphosphate (IP5) and inositol hexakisphosphate (IP6) are important signaling molecules that regulate DNA-damage repair, cohesin dynamics, RNA-editing, retroviral assembly, nuclear transport, phosphorylation, acetylation, crotonylation, and ubiquitination. This functional diversity has made understanding how inositol polyphosphates regulate cellular processes challenging to dissect. However, some inositol phosphates have been unexpectedly found in X-ray crystal structures, occasionally revealing structural and mechanistic details of effector protein regulation before functional consequences have been described. This review highlights a sampling of crystal structures describing the interaction between inositol phosphates and protein effectors. This list includes the RNA editing enzyme "adenosine deaminase that acts on RNA 2" (ADAR2), the Pds5B regulator of cohesin dynamics, the class 1 histone deacetylases (HDACs) HDAC1 and HDAC3, and the PH domain of Bruton's tyrosine kinase (Btk). One of the most important enzymes responsible for higher-order inositol phosphate synthesis is inositol polyphosphate multikinase (IPMK), which plays dual roles in both inositol and phosphoinositide signaling. Structures of phosphoinositide lipid binding proteins have also revealed new aspects of protein effector regulation, as mediated by the nuclear receptors Steroidogenic Factor-1 (SF-1, NR5A2) and Liver Receptor Homolog-1 (LRH-1, NR5A2). Together, these studies underscore the structural diversity in binding interactions between effector proteins and inositol phosphate small signaling molecules, and further support that detailed structural studies can lead to new biological discovery.
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16
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Nakada-Tsukui K, Watanabe N, Maehama T, Nozaki T. Phosphatidylinositol Kinases and Phosphatases in Entamoeba histolytica. Front Cell Infect Microbiol 2019; 9:150. [PMID: 31245297 PMCID: PMC6563779 DOI: 10.3389/fcimb.2019.00150] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/23/2019] [Indexed: 12/11/2022] Open
Abstract
Phosphatidylinositol (PtdIns) metabolism is indispensable in eukaryotes. Phosphoinositides (PIs) are phosphorylated derivatives of PtdIns and consist of seven species generated by reversible phosphorylation of the inositol moieties at the positions 3, 4, and 5. Each of the seven PIs has a unique subcellular and membrane domain distribution. In the enteric protozoan parasite Entamoeba histolytica, it has been previously shown that the PIs phosphatidylinositol 3-phosphate (PtdIns3P), PtdIns(4,5)P2, and PtdIns(3,4,5)P3 are localized to phagosomes/phagocytic cups, plasma membrane, and phagocytic cups, respectively. The localization of these PIs in E. histolytica is similar to that in mammalian cells, suggesting that PIs have orthologous functions in E. histolytica. In contrast, the conservation of the enzymes that metabolize PIs in this organism has not been well-documented. In this review, we summarized the full repertoire of the PI kinases and PI phosphatases found in E. histolytica via a genome-wide survey of the current genomic information. E. histolytica appears to have 10 PI kinases and 23 PI phosphatases. It has a panel of evolutionarily conserved enzymes that generate all the seven PI species. However, class II PI 3-kinases, type II PI 4-kinases, type III PI 5-phosphatases, and PI 4P-specific phosphatases are not present. Additionally, regulatory subunits of class I PI 3-kinases and type III PI 4-kinases have not been identified. Instead, homologs of class I PI 3-kinases and PTEN, a PI 3-phosphatase, exist as multiple isoforms, which likely reflects that elaborate signaling cascades mediated by PtdIns(3,4,5)P3 are present in this organism. There are several enzymes that have the nuclear localization signal: one phosphatidylinositol phosphate (PIP) kinase, two PI 3-phosphatases, and one PI 5-phosphatase; this suggests that PI metabolism also has conserved roles related to nuclear functions in E. histolytica, as it does in model organisms.
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Affiliation(s)
- Kumiko Nakada-Tsukui
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Natsuki Watanabe
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Tomohiko Maehama
- Division of Molecular and Cellular Biology, Graduate School of Medicine, Kobe University, Kobe, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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17
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Cumsky HJL, Costello CM, Zhang N, Butterfield R, Buras MR, Schmidt JE, Drenner K, Nelson SA, Ochoa SA, Baum CL, Pittelkow MR, DiCaudo DJ, Sekulic A, Mangold AR. The prognostic value of inositol polyphosphate 5-phosphatase in cutaneous squamous cell carcinoma. J Am Acad Dermatol 2019; 80:626-632.e1. [PMID: 30359624 PMCID: PMC10577667 DOI: 10.1016/j.jaad.2018.10.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 09/13/2018] [Accepted: 10/06/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND Inositol polyphosphate 5-phosphatase (INPP5A) has been shown to play a role in development and progression of cutaneous squamous cell carcinoma (cSCC). The goal of the current study was to explore the prognostic value of INPP5A expression in cSCC. METHODS A total of 189 cases of actinic keratosis and SCC in 174 patients were identified; clinical and outcome data were abstracted, histopathology was rereviewed, and immunohistochemical staining and interpretation was performed for INPP5A. RESULTS The majority of tumors (89.4%) had an INPP5A score of 2 or 3. No patients had complete loss of INPP5A. Tumors with an INPP5A score of 1 were more likely to be intermediate- to high-risk tumors (Brigham and Women's Hospital stage ≥T2a 85.0% vs 23.7% [P < .0001]) characterized by a larger diameter (2.4 cm vs 1.3 cm [P = .0004]), moderate-to-poor differentiation (86.7% vs 17.6% [P < .0001]), and perineural invasion (37.5% vs 5.3%, [P < .0001]). An INPP5A score of 1 was associated with a worse 3-year survival (a rate of 42.3% [hazard ratio, 2.81, P = .0006]) and a local metastasis rate of 48.0% (hazard ratio, 4.71; P < .0001). CONCLUSIONS Low INPP5A scores are predictive of aggressive tumors and may be a useful adjunct to guide clinical management of cSCC.
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Affiliation(s)
- Helen J L Cumsky
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona; Case Western Reserve University School of Medicine, Cleveland, Ohio
| | | | - Nan Zhang
- Department of Health Science Research, Mayo Clinic, Scottsdale, Arizona
| | | | - Matthew R Buras
- Department of Health Science Research, Mayo Clinic, Scottsdale, Arizona
| | | | - Kevin Drenner
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona
| | | | - Shari A Ochoa
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona
| | | | | | | | | | - Aaron R Mangold
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona.
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18
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PIP2 epigenetically represses rRNA genes transcription interacting with PHF8. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:266-275. [DOI: 10.1016/j.bbalip.2017.12.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/05/2017] [Accepted: 12/09/2017] [Indexed: 02/01/2023]
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19
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Zhang Q, van Wijk R, Shahbaz M, Roels W, Schooten BV, Vermeer JEM, Zarza X, Guardia A, Scuffi D, García-Mata C, Laha D, Williams P, Willems LAJ, Ligterink W, Hoffmann-Benning S, Gillaspy G, Schaaf G, Haring MA, Laxalt AM, Munnik T. Arabidopsis Phospholipase C3 is Involved in Lateral Root Initiation and ABA Responses in Seed Germination and Stomatal Closure. PLANT & CELL PHYSIOLOGY 2018; 59:469-486. [PMID: 29309666 DOI: 10.1093/pcp/pcx194] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 12/01/2017] [Indexed: 05/10/2023]
Abstract
Phospholipase C (PLC) is well known for its role in animal signaling, where it generates the second messengers, inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG), by hydrolyzing the minor phospholipid, phosphatidylinositol 4,5-bisphosphate (PIP2), upon receptor stimulation. In plants, PLC's role is still unclear, especially because the primary targets of both second messengers are lacking, i.e. the ligand-gated Ca2+ channel and protein kinase C, and because PIP2 levels are extremely low. Nonetheless, the Arabidopsis genome encodes nine PLCs. We used a reversed-genetic approach to explore PLC's function in Arabidopsis, and report here that PLC3 is required for proper root development, seed germination and stomatal opening. Two independent knock-down mutants, plc3-2 and plc3-3, were found to exhibit reduced lateral root densities by 10-20%. Mutant seeds germinated more slowly but were less sensitive to ABA to prevent germination. Guard cells of plc3 were also compromised in ABA-dependent stomatal closure. Promoter-β-glucuronidase (GUS) analyses confirmed PLC3 expression in guard cells and germinating seeds, and revealed that the majority is expressed in vascular tissue, most probably phloem companion cells, in roots, leaves and flowers. In vivo 32Pi labeling revealed that ABA stimulated the formation of PIP2 in germinating seeds and guard cell-enriched leaf peels, which was significantly reduced in plc3 mutants. Overexpression of PLC3 had no effect on root system architecture or seed germination, but increased the plant's tolerance to drought. Our results provide genetic evidence for PLC's involvement in plant development and ABA signaling, and confirm earlier observations that overexpression increases drought tolerance. Potential molecular mechanisms for the above observations are discussed.
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Affiliation(s)
- Qianqian Zhang
- Swammerdam Institute for Life Sciences, section Plant Physiology, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
- Swammerdam Institute for Life Sciences, section Plant Cell Biology, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Ringo van Wijk
- Swammerdam Institute for Life Sciences, section Plant Physiology, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
- Swammerdam Institute for Life Sciences, section Plant Cell Biology, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Muhammad Shahbaz
- Swammerdam Institute for Life Sciences, section Plant Physiology, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Wendy Roels
- Swammerdam Institute for Life Sciences, section Plant Physiology, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Bas van Schooten
- Swammerdam Institute for Life Sciences, section Plant Physiology, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Joop E M Vermeer
- Swammerdam Institute for Life Sciences, section Plant Physiology, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Xavier Zarza
- Swammerdam Institute for Life Sciences, section Plant Physiology, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
- Swammerdam Institute for Life Sciences, section Plant Cell Biology, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Aisha Guardia
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Denise Scuffi
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Carlos García-Mata
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Debabrata Laha
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, University of Bonn, Bonn, Germany
| | - Phoebe Williams
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Leo A J Willems
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Wilco Ligterink
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Susanne Hoffmann-Benning
- Departement of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Glenda Gillaspy
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Gabriel Schaaf
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, University of Bonn, Bonn, Germany
| | - Michel A Haring
- Swammerdam Institute for Life Sciences, section Plant Physiology, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Ana M Laxalt
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Teun Munnik
- Swammerdam Institute for Life Sciences, section Plant Physiology, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
- Swammerdam Institute for Life Sciences, section Plant Cell Biology, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
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20
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Belgaroui N, Lacombe B, Rouached H, Hanin M. Phytase overexpression in Arabidopsis improves plant growth under osmotic stress and in combination with phosphate deficiency. Sci Rep 2018; 8:1137. [PMID: 29348608 PMCID: PMC5773496 DOI: 10.1038/s41598-018-19493-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/07/2017] [Indexed: 12/28/2022] Open
Abstract
Engineering osmotolerant plants is a challenge for modern agriculture. An interaction between osmotic stress response and phosphate homeostasis has been reported in plants, but the identity of molecules involved in this interaction remains unknown. In this study we assessed the role of phytic acid (PA) in response to osmotic stress and/or phosphate deficiency in Arabidopsis thaliana. For this purpose, we used Arabidopsis lines (L7 and L9) expressing a bacterial beta-propeller phytase PHY-US417, and a mutant in inositol polyphosphate kinase 1 gene (ipk1-1), which were characterized by low PA content, 40% (L7 and L9) and 83% (ipk1-1) of the wild-type (WT) plants level. We show that the PHY-overexpressor lines have higher osmotolerance and lower sensitivity to abscisic acid than ipk1-1 and WT. Furthermore, PHY-overexpressors showed an increase by more than 50% in foliar ascorbic acid levels and antioxidant enzyme activities compared to ipk1-1 and WT plants. Finally, PHY-overexpressors are more tolerant to combined mannitol stresses and phosphate deficiency than WT plants. Overall, our results demonstrate that the modulation of PA improves plant growth under osmotic stress, likely via stimulation of enzymatic and non-enzymatic antioxidant systems, and that beside its regulatory role in phosphate homeostasis, PA may be also involved in fine tuning osmotic stress response in plants.
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Affiliation(s)
- Nibras Belgaroui
- Laboratoire de Biotechnologie et Amélioration des Plantes, Centre de Biotechnologie de Sfax, BP "1177", 3018, Sfax, Tunisia
| | - Benoit Lacombe
- BPMP, CNRS, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Hatem Rouached
- BPMP, CNRS, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France.
| | - Moez Hanin
- Laboratoire de Biotechnologie et Amélioration des Plantes, Centre de Biotechnologie de Sfax, BP "1177", 3018, Sfax, Tunisia. .,Unité de Génomique Fonctionnelle et Physiologie des Plantes, Institut Supérieur de Biotechnologie, Université de Sfax, BP "1175", 3038, Sfax, Tunisia.
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21
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Zhang T, Galdieri L, Hasek J, Vancura A. Yeast phospholipase C is required for stability of casein kinase I Yck2p and expression of hexose transporters. FEMS Microbiol Lett 2017; 364:4566517. [PMID: 29087456 DOI: 10.1093/femsle/fnx227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/25/2017] [Indexed: 11/12/2022] Open
Abstract
Phospholipase C (Plc1p) in Saccharomyces cerevisiae is required for normal degradation of repressor Mth1p and expression of the HXT genes encoding cell membrane transporters of glucose. Plc1p is also required for normal localization of glucose transporters to the cell membrane. Consequently, plc1Δ cells display histone hypoacetylation and transcriptional defects due to reduced uptake and metabolism of glucose to acetyl-CoA, a substrate for histone acetyltransferases. In the presence of glucose, Mth1p is phosphorylated by casein kinase I Yck1/2p, ubiquitinated by the SCFGrr1 complex and degraded by the proteasome. Here, we show that while Plc1p does not affect the function of the SCFGrr1 complex or the proteasome, it is required for normal protein level of Yck2p. Since stability of Yck1/2p is regulated by a glucose-dependent mechanism, PLC1 inactivation results in destabilization of Yck1/2p and defect in Mth1p degradation. Based on our results and published data, we propose a model in which plc1Δ mutation causes increased internalization of glucose transporters, decreased transport of glucose into the cells, and consequently decreased stability of Yck1/2p, increased stability of Mth1p and decreased expression of the HXT genes.
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Affiliation(s)
- Tiantian Zhang
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Luciano Galdieri
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Jiri Hasek
- Laboratory of Cell Reproduction, Institute of Microbiology CAS, v.v.i., Videnska 1083, Prague 14220, Czech Republic
| | - Ales Vancura
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
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Patel AB, Mangold AR, Costello CM, Nagel TH, Smith ML, Hayden RE, Sekulic A. Frequent loss of inositol polyphosphate-5-phosphatase in oropharyngeal squamous cell carcinoma. J Eur Acad Dermatol Venereol 2017; 32:e36-e37. [PMID: 28696004 DOI: 10.1111/jdv.14462] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- A B Patel
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Phoenix, AZ, USA
| | - A R Mangold
- Department of Dermatology, Mayo Clinic, Scottsdale, AZ, USA
| | - C M Costello
- Department of Dermatology, Mayo Clinic, Scottsdale, AZ, USA.,University of Arizona College of Medicine - Tucson, Tucson, AZ, USA
| | - T H Nagel
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Phoenix, AZ, USA
| | - M L Smith
- Department of Pathology, Mayo Clinic, Phoenix, AZ, USA
| | - R E Hayden
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Phoenix, AZ, USA
| | - A Sekulic
- Department of Dermatology, Mayo Clinic, Scottsdale, AZ, USA
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Has Inositol Played Any Role in the Origin of Life? Life (Basel) 2017; 7:life7020024. [PMID: 28587245 PMCID: PMC5492146 DOI: 10.3390/life7020024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/26/2017] [Accepted: 06/02/2017] [Indexed: 12/11/2022] Open
Abstract
Phosphorus, as phosphate, plays a paramount role in biology. Since phosphate transfer reactions are an integral part of contemporary life, phosphate may have been incorporated into the initial molecules at the very beginning. To facilitate the studies into early phosphate utilization, we should look retrospectively to phosphate-rich molecules present in today’s cells. Overlooked by origin of life studies until now, inositol and the inositol phosphates, of which some species possess more phosphate groups that carbon atoms, represent ideal molecules to consider in this context. The current sophisticated association of inositol with phosphate, and the roles that some inositol phosphates play in regulating cellular phosphate homeostasis, intriguingly suggest that inositol might have played some role in the prebiotic process of phosphate exploitation. Inositol can be synthesized abiotically and, unlike glucose or ribose, is chemically stable. This stability makes inositol the ideal candidate for the earliest organophosphate molecules, as primitive inositol phosphates. I also present arguments suggesting roles for some inositol phosphates in early chemical evolution events. Finally, the possible prebiotic synthesis of inositol pyrophosphates could have generated high-energy molecules to be utilized in primitive trans-phosphorylating processes.
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24
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Hamann BL, Blind RD. Nuclear phosphoinositide regulation of chromatin. J Cell Physiol 2017; 233:107-123. [PMID: 28256711 DOI: 10.1002/jcp.25886] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/01/2017] [Indexed: 12/26/2022]
Abstract
Phospholipid signaling has clear connections to a wide array of cellular processes, particularly in gene expression and in controlling the chromatin biology of cells. However, most of the work elucidating how phospholipid signaling pathways contribute to cellular physiology have studied cytoplasmic membranes, while relatively little attention has been paid to the role of phospholipid signaling in the nucleus. Recent work from several labs has shown that nuclear phospholipid signaling can have important roles that are specific to this cellular compartment. This review focuses on the nuclear phospholipid functions and the activities of phospholipid signaling enzymes that regulate metazoan chromatin and gene expression. In particular, we highlight the roles that nuclear phosphoinositides play in several nuclear-driven physiological processes, such as differentiation, proliferation, and gene expression. Taken together, the recent discovery of several specifically nuclear phospholipid functions could have dramatic impact on our understanding of the fundamental mechanisms that enable tight control of cellular physiology.
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Affiliation(s)
- Bree L Hamann
- Division of Diabetes Endocrinology and Metabolism, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Raymond D Blind
- Division of Diabetes Endocrinology and Metabolism, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee.,Departments of Medicine, Biochemistry and Pharmacology, Division of Diabetes Endocrinology and Metabolism, The Vanderbilt Diabetes Research and Training Center and the Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
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Di Fino LM, D'Ambrosio JM, Tejos R, van Wijk R, Lamattina L, Munnik T, Pagnussat GC, Laxalt AM. Arabidopsis phosphatidylinositol-phospholipase C2 (PLC2) is required for female gametogenesis and embryo development. PLANTA 2017; 245:717-728. [PMID: 27999988 DOI: 10.1007/s00425-016-2634-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/02/2016] [Indexed: 05/20/2023]
Abstract
AtPLC2 is an essential gene in Arabidopsis, since it is required for female gametogenesis and embryo development. AtPLC2 might play a role in cell division during embryo-sac development and early embryogenesis. Phosphoinositide-specific phospholipase C (PI-PLC) plays an important role in signal transduction during plant development and in the response to various biotic- and abiotic stresses. The Arabidopsis PI-PLC gene family is composed of nine members, named PLC1 to PLC9. Here, we report that PLC2 is involved in female gametophyte development and early embryogenesis. Using two Arabidopsis allelic T-DNA insertion lines with different phenotypic penetrations, we observed both female gametophytic defects and aberrant embryos. For the plc2-1 mutant (Ws background), no homozygous plants could be recovered in the offspring from self-pollinated plants. Nonetheless, plc2-1 hemizygous mutants are affected in female gametogenesis, showing embryo sacs arrested at early developmental stages. Allelic hemizygous plc2-2 mutant plants (Col-0 background) present reduced seed set and embryos arrested at the pre-globular stage with abnormal patterns of cell division. A low proportion (0.8%) of plc2-2 homozygous mutants was found to escape lethality and showed morphological defects and disrupted megagametogenesis. PLC2-promoter activity was observed during early megagametogenesis, and after fertilization in the embryo proper. Immunolocalization studies in early stage embryos revealed that PLC2 is restricted to the plasma membrane. Altogether, these results establish a role for PLC2 in both reproductive- and embryo development, presumably by controlling mitosis and/or the formation of cell-division planes.
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Affiliation(s)
- Luciano M Di Fino
- Instituto de Investigaciones Biológicas IIB-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600, Mar del Plata, Argentina
| | - Juan Martín D'Ambrosio
- Instituto de Investigaciones Biológicas IIB-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600, Mar del Plata, Argentina
| | - Ricardo Tejos
- Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, 111093, Iquique, Chile
- Centro de Biología Molecular Vegetal, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, 7800003, Santiago, Chile
| | - Ringo van Wijk
- Swammerdam Institute for Life Sciences, Section Plant Cell Biology, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Lorenzo Lamattina
- Instituto de Investigaciones Biológicas IIB-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600, Mar del Plata, Argentina
| | - Teun Munnik
- Swammerdam Institute for Life Sciences, Section Plant Cell Biology, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Gabriela C Pagnussat
- Instituto de Investigaciones Biológicas IIB-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600, Mar del Plata, Argentina.
| | - Ana M Laxalt
- Instituto de Investigaciones Biológicas IIB-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600, Mar del Plata, Argentina.
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26
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Lu C, Yin J, Zhao F, Li F, Lu W. Metabolomics analysis of the effect of dissolved oxygen on spinosad production by Saccharopolyspora spinosa. Antonie van Leeuwenhoek 2017; 110:677-685. [DOI: 10.1007/s10482-017-0835-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 01/19/2017] [Indexed: 11/30/2022]
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27
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Wilson MSC, Saiardi A. Importance of Radioactive Labelling to Elucidate Inositol Polyphosphate Signalling. Top Curr Chem (Cham) 2017; 375:14. [PMID: 28101851 PMCID: PMC5396384 DOI: 10.1007/s41061-016-0099-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 12/21/2016] [Indexed: 01/09/2023]
Abstract
Inositol polyphosphates, in their water-soluble or lipid-bound forms, represent a large and multifaceted family of signalling molecules. Some inositol polyphosphates are well recognised as defining important signal transduction pathways, as in the case of the calcium release factor Ins(1,4,5)P3, generated by receptor activation-induced hydrolysis of the lipid PtdIns(4,5)P2 by phospholipase C. The birth of inositol polyphosphate research would not have occurred without the use of radioactive phosphate tracers that enabled the discovery of the “PI response”. Radioactive labels, mainly of phosphorus but also carbon and hydrogen (tritium), have been instrumental in the development of this research field and the establishment of the inositol polyphosphates as one of the most important networks of regulatory molecules present in eukaryotic cells. Advancements in microscopy and mass spectrometry and the development of colorimetric assays have facilitated inositol polyphosphate research, but have not eliminated the need for radioactive experimental approaches. In fact, such experiments have become easier with the cloning of the inositol polyphosphate kinases, enabling the systematic labelling of specific positions of the inositol ring with radioactive phosphate. This approach has been valuable for elucidating their metabolic pathways and identifying specific and novel functions for inositol polyphosphates. For example, the synthesis of radiolabelled inositol pyrophosphates has allowed the discovery of a new protein post-translational modification. Therefore, radioactive tracers have played and will continue to play an important role in dissecting the many complex aspects of inositol polyphosphate physiology. In this review we aim to highlight the historical importance of radioactivity in inositol polyphosphate research, as well as its modern usage.
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Affiliation(s)
- Miranda S C Wilson
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT, UK.
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28
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Inositol polyphosphate multikinase (IPMK) in transcriptional regulation and nuclear inositide metabolism. Biochem Soc Trans 2016; 44:279-85. [PMID: 26862216 DOI: 10.1042/bst20150225] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Inositol polyphosphate multikinase (IPMK, ipk2, Arg(82), ArgRIII) is an inositide kinase with unusually flexible substrate specificity and the capacity to partake in many functional protein-protein interactions (PPIs). By merging these two activities, IPMK is able to execute gene regulatory functions that are very unique and only now beginning to be recognized. In this short review, we present a brief history of IPMK, describe the structural biology of the enzyme and highlight a few recent discoveries that have shed more light on the role IPMK plays in inositide metabolism, nuclear signalling and transcriptional regulation.
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Lu HP, Pang WQ, Li WX, Tan YY, Wang Q, Zhao HJ, Shu QY. Tissue-specific expression, developmentally and spatially regulated alternative splicing, and protein subcellular localization of OsLpa rice. J Zhejiang Univ Sci B 2016; 17:100-9. [PMID: 26834011 DOI: 10.1631/jzus.b1500205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The OsLpa1 gene (LOC_Os57400) was identified to be involved in phytic acid (PA) metabolism because its knockout and missense mutants reduce PA content in rice grain. However, little is known about the molecular characteristics of OsLpa rice and of its homologues in other plants. In the present study, the spatial pattern of OsLpa1 expression was revealed using OsLpa1 promoter::GUS transgenic plants (GUS: β-glucuronidase); GUS histochemical assay showed that OsLpa1 was strongly expressed in stem, leaf, and root tissues, but in floral organ it is expressed mainly and strongly in filaments. In seeds, GUS staining was concentrated in the aleurone layers; a few blue spots were observed in the outer layers of embryo, but no staining was observed in the endosperm. Three OsLpa1 transcripts (OsLpa1.1, OsLpa1.2, OsLpa1.3) are produced due to alternative splicing; quantitative reverse-transcriptase polymerase chain reaction (RT-PCR) analysis revealed that the abundance of OsLpa1.3 was negligible compared with OsLpa1.1 and OsLpa all tissues. OsLpa1.2 is predominant in germinating seeds (about 5 times that of OsLpa1.1), but its abundance decreases quickly with the development of seedlings and plants, whereas the abundance of OsLpa1.1 rises and falls, reaching its highest level in 45-d-old plants, with abundance greater than that of OsLpa both leaves and roots. In seeds, the abundance of OsLpa1 continuously increases with seed growth, being 27.5 and 15 times greater in 28-DAF (day after flowering) seeds than in 7-DAF seeds for OsLpa1.1 and OsLpa1.2, respectively. Transient expression of chimeric genes with green fluorescence protein (GFP) in rice protoplasts demonstrated that all proteins encoded by the three OsLpa1 transcripts are localized to the chloroplast.
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Affiliation(s)
- Hai-ping Lu
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou 310029, China
| | - Wei-qin Pang
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou 310029, China
| | - Wen-xu Li
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou 310029, China
| | - Yuan-yuan Tan
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou 310029, China
| | - Qing Wang
- Wuxi Hupper Bioseed Technology Academy Ltd., Wuxi 214000, China
| | - Hai-jun Zhao
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou 310029, China
| | - Qing-yao Shu
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou 310029, China
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30
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Zhu Q, Ghoshal S, Rodrigues A, Gao S, Asterian A, Kamenecka TM, Barrow JC, Chakraborty A. Adipocyte-specific deletion of Ip6k1 reduces diet-induced obesity by enhancing AMPK-mediated thermogenesis. J Clin Invest 2016; 126:4273-4288. [PMID: 27701146 DOI: 10.1172/jci85510] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 08/29/2016] [Indexed: 12/15/2022] Open
Abstract
Enhancing energy expenditure (EE) is an attractive strategy to combat obesity and diabetes. Global deletion of Ip6k1 protects mice from diet-induced obesity (DIO) and insulin resistance, but the tissue-specific mechanism by which IP6K1 regulates body weight is unknown. Here, we have demonstrated that IP6K1 regulates fat accumulation by modulating AMPK-mediated adipocyte energy metabolism. Cold exposure led to downregulation of Ip6k1 in murine inguinal and retroperitoneal white adipose tissue (IWAT and RWAT) depots. Adipocyte-specific deletion of Ip6k1 (AdKO) enhanced thermogenic EE, which protected mice from high-fat diet-induced weight gain at ambient temperature (23°C), but not at thermoneutral temperature (30°C). AdKO-induced increases in thermogenesis also protected mice from cold-induced decreases in body temperature. UCP1, PGC1α, and other markers of browning and thermogenesis were elevated in IWAT and RWAT of AdKO mice. Cold-induced activation of sympathetic signaling was unaltered, whereas AMPK was enhanced, in AdKO IWAT. Moreover, beige adipocytes from AdKO IWAT displayed enhanced browning, which was diminished by AMPK depletion. Furthermore, we determined that IP6 and IP6K1 differentially regulate upstream kinase-mediated AMPK stimulatory phosphorylation in vitro. Finally, treating mildly obese mice with the IP6K inhibitor TNP enhanced thermogenesis and inhibited progression of DIO. Thus, IP6K1 regulates energy metabolism via a mechanism that could potentially be targeted in obesity.
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31
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Li C, Lev S, Saiardi A, Desmarini D, Sorrell TC, Djordjevic JT. Inositol Polyphosphate Kinases, Fungal Virulence and Drug Discovery. J Fungi (Basel) 2016; 2:jof2030024. [PMID: 29376941 PMCID: PMC5753137 DOI: 10.3390/jof2030024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/23/2016] [Accepted: 08/30/2016] [Indexed: 12/31/2022] Open
Abstract
Opportunistic fungi are a major cause of morbidity and mortality world-wide, particularly in immunocompromised individuals. Developing new treatments to combat invasive fungal disease is challenging given that fungal and mammalian host cells are eukaryotic, with similar organization and physiology. Even therapies targeting unique fungal cell features have limitations and drug resistance is emerging. New approaches to the development of antifungal drugs are therefore needed urgently. Cryptococcus neoformans, the commonest cause of fungal meningitis worldwide, is an accepted model for studying fungal pathogenicity and driving drug discovery. We recently characterized a phospholipase C (Plc1)-dependent pathway in C. neoformans comprising of sequentially-acting inositol polyphosphate kinases (IPK), which are involved in synthesizing inositol polyphosphates (IP). We also showed that the pathway is essential for fungal cellular function and pathogenicity. The IP products of the pathway are structurally diverse, each consisting of an inositol ring, with phosphate (P) and pyrophosphate (PP) groups covalently attached at different positions. This review focuses on (1) the characterization of the Plc1/IPK pathway in C. neoformans; (2) the identification of PP-IP₅ (IP₇) as the most crucial IP species for fungal fitness and virulence in a mouse model of fungal infection; and (3) why IPK enzymes represent suitable candidates for drug development.
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Affiliation(s)
- Cecilia Li
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia.
| | - Sophie Lev
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia.
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK.
| | - Desmarini Desmarini
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia.
| | - Tania C Sorrell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia.
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Westmead, NSW 2145, Australia.
- Westmead Hospital, Westmead, NSW 2145, Australia.
| | - Julianne T Djordjevic
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia.
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Westmead, NSW 2145, Australia.
- Westmead Hospital, Westmead, NSW 2145, Australia.
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32
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Profiling DNA damage-induced phosphorylation in budding yeast reveals diverse signaling networks. Proc Natl Acad Sci U S A 2016; 113:E3667-75. [PMID: 27298372 DOI: 10.1073/pnas.1602827113] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The DNA damage response (DDR) is regulated by a protein kinase signaling cascade that orchestrates DNA repair and other processes. Identifying the substrate effectors of these kinases is critical for understanding the underlying physiology and mechanism of the response. We have used quantitative mass spectrometry to profile DDR-dependent phosphorylation in budding yeast and genetically explored the dependency of these phosphorylation events on the DDR kinases MEC1, RAD53, CHK1, and DUN1. Based on these screens, a database containing many novel DDR-regulated phosphorylation events has been established. Phosphorylation of many of these proteins has been validated by quantitative peptide phospho-immunoprecipitation and examined for functional relevance to the DDR through large-scale analysis of sensitivity to DNA damage in yeast deletion strains. We reveal a link between DDR signaling and the metabolic pathways of inositol phosphate and phosphatidyl inositol synthesis, which are required for resistance to DNA damage. We also uncover links between the DDR and TOR signaling as well as translation regulation. Taken together, these data shed new light on the organization of DDR signaling in budding yeast.
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Scoumanne A, Molina-Ortiz P, Monteyne D, Perez-Morga D, Erneux C, Schurmans S. Specific expression and function of inositol 1,4,5-trisphosphate 3-kinase C (ITPKC) in wild type and knock-out mice. Adv Biol Regul 2016; 62:1-10. [PMID: 27036498 DOI: 10.1016/j.jbior.2016.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 03/16/2016] [Indexed: 12/16/2022]
Abstract
Inositol 1,4,5-trisphosphate 3-kinase C (ITPKC) is the last identified member of the inositol 1,4,5-trisphosphate 3-kinases family which phosphorylates inositol 1,4,5-trisphosphate into inositol 1,3,4,5-tetrakisphosphate. Although expression and function of the two other family members ITPKA and ITPKB are rather well characterized, similar information is lacking for ITPKC. Here, we first defined the expression of Itpkc mRNA and protein in mouse tissues and cells using in situ hybridization and new antibodies. Surprisingly, we found that cells positive for ITPKC in the studied tissues express either a multicilium (tracheal and bronchial epithelia, brain ependymal cells), microvilli forming a brush border (small and large intestine, and kidney proximal tubule cells) or a flagellum (spermatozoa), suggesting a role for ITPKC either in the development or the function of these specialized cellular structures. Given this surprising expression, we then analyzed ITPKC function in multiciliated tracheal epithelial cells and sperm cells using our Itpkc knock-out mouse model. Unfortunately, no significant difference was observed between control and mutant mice for any of the parameters tested, leaving the exact in vivo function of this third Ins(1,4,5)P3 3-kinase still open.
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Affiliation(s)
- Ariane Scoumanne
- Laboratoire de Génétique Fonctionnelle, GIGA-B34, Université de Liège, avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Patricia Molina-Ortiz
- Laboratoire de Génétique Fonctionnelle, GIGA-B34, Université de Liège, avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Daniel Monteyne
- Laboratoire de Parasitologie Moléculaire, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium
| | - David Perez-Morga
- Laboratoire de Parasitologie Moléculaire, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium; Center for Microscopy and Molecular Imaging (CMMI), Université Libre de Bruxelles (ULB), 8 rue Adrienne Bolland, B-6041 Gosselies, Belgium
| | - Christophe Erneux
- Institut de Recherches Interdisciplinaires en Biologie Humaine et Moléculaire (IRIBHM), Campus Erasme, Université Libre de Bruxelles, route de Lennik, 808, 1070 Bruxelles, Belgium
| | - Stéphane Schurmans
- Laboratoire de Génétique Fonctionnelle, GIGA-B34, Université de Liège, avenue de l'Hôpital 11, 4000 Liège, Belgium.
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Abstract
Eukaryotic cells have ubiquitously utilized the myo-inositol backbone to generate a diverse array of signalling molecules. This is achieved by arranging phosphate groups around the six-carbon inositol ring. There is virtually no biological process that does not take advantage of the uniquely variable architecture of phosphorylated inositol. In inositol biology, phosphates are able to form three distinct covalent bonds: phosphoester, phosphodiester and phosphoanhydride bonds, with each providing different properties. The phosphoester bond links phosphate groups to the inositol ring, the variable arrangement of which forms the basis of the signalling capacity of the inositol phosphates. Phosphate groups can also form the structural bridge between myo-inositol and diacylglycerol through the phosphodiester bond. The resulting lipid-bound inositol phosphates, or phosphoinositides, further expand the signalling potential of this family of molecules. Finally, inositol is also notable for its ability to host more phosphates than it has carbons. These unusual organic molecules are commonly referred to as the inositol pyrophosphates (PP-IPs), due to the presence of high-energy phosphoanhydride bonds (pyro- or diphospho-). PP-IPs themselves constitute a varied family of molecules with one or more pyrophosphate moiety/ies located around the inositol. Considering the relationship between phosphate and inositol, it is no surprise that members of the inositol phosphate family also regulate cellular phosphate homoeostasis. Notably, the PP-IPs play a fundamental role in controlling the metabolism of the ancient polymeric form of phosphate, inorganic polyphosphate (polyP). Here we explore the intimate links between phosphate, inositol phosphates and polyP, speculating on the evolution of these relationships.
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Erneux C, Ghosh S, Koenig S. Inositol(1,4,5)P3 3-kinase isoenzymes: Catalytic properties and importance of targeting to F-actin to understand function. Adv Biol Regul 2016; 60:135-143. [PMID: 26446452 DOI: 10.1016/j.jbior.2015.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 09/10/2015] [Accepted: 09/10/2015] [Indexed: 06/05/2023]
Abstract
Inositol(1,4,5)trisphosphate (Ins(1,4,5)P3) 3-kinases (Itpks) catalyze the phosphorylation of inositol(1,4,5)trisphosphate into inositol(1,3,4,5)tetrakisphosphate (Ins(1,3,4,5)P4). Three isoenzymes Itpka/b and c have been identified in human, rat and mouse. They share a catalytic domain relatively well conserved at the C-terminal end and a quite isoenzyme specific regulatory domain at the N-terminal end of the protein. Activity determined in cell homogenates with Ins(1,4,5)P3 and ATP as substrate is generally very low compared to Ins(1,4,5)P3 5-phosphatase, except in a few tissues such as brain, testis, thymus or intestine. Activity is very much Ca(2+) sensitive and increased in the presence of Ca(2+)/calmodulin (CaM) as compared to EGTA alone. When challenged after receptor activation, activity could be further activated several fold, e.g. in rat brain cortical slices stimulated by carbachol or in human astrocytoma cells stimulated by purinergic agonists. Two of the three isoenzymes show an unexpected cytoskeletal localization for Itpka/b or at the leading edge for Itpkb. This is explained by the presence of an F-actin binding site at the N-terminal part of the two isoenzymes. This interaction confers to Itpka the properties of an F-actin bundling protein with two major consequences: i) it can reorganize the cytoskeletal network, particularly in dendritic spines, and ii) can provide an opportunity for Ins(1,3,4,5)P4 to act very locally as second messenger.
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Affiliation(s)
- Christophe Erneux
- Interdisciplinary Research Institute (IRIBHM), Université Libre de Bruxelles, Campus Erasme, Bldg C, 808 Route de Lennik, 1070 Brussels, Belgium.
| | - Somadri Ghosh
- Interdisciplinary Research Institute (IRIBHM), Université Libre de Bruxelles, Campus Erasme, Bldg C, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Sandra Koenig
- Interdisciplinary Research Institute (IRIBHM), Université Libre de Bruxelles, Campus Erasme, Bldg C, 808 Route de Lennik, 1070 Brussels, Belgium
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Cheng YL, Andrew DJ. Extracellular Mipp1 Activity Confers Migratory Advantage to Epithelial Cells during Collective Migration. Cell Rep 2015; 13:2174-88. [PMID: 26628373 DOI: 10.1016/j.celrep.2015.10.071] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 10/12/2015] [Accepted: 10/24/2015] [Indexed: 12/13/2022] Open
Abstract
Multiple inositol polyphosphate phosphatase (Mipp), a highly conserved but poorly understood histidine phosphatase, dephosphorylates higher-order IPs (IP4-IP6) to IP3. To gain insight into the biological roles of these enzymes, we have characterized Drosophila mipp1. mipp1 is dynamically expressed in the embryonic trachea, specifically in the leading cells of migrating branches at late stages, where Mipp1 localizes to the plasma membrane and filopodia. FGF signaling activates mipp1 expression in these cells, where extensive filopodia form to drive migration and elongation by cell intercalation. We show that Mipp1 facilitates formation and/or stabilization of filopodia in leading cells through its extracellular activity. mipp1 loss decreases filopodia number, whereas mipp1 overexpression increases filopodia number in a phosphatase-activity-dependent manner. Importantly, expression of Mipp1 gives cells a migratory advantage for the lead position in elongating tracheal branches. Altogether, these findings suggest that extracellular pools of inositol polyphosphates affect cell behavior during development.
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Affiliation(s)
- Yim Ling Cheng
- Department of Cell Biology, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Deborah J Andrew
- Department of Cell Biology, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA.
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37
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Veiga N, Macho I, Gómez K, González G, Kremer C, Torres J. Potentiometric and spectroscopic study of the interaction of 3d transition metal ions with inositol hexakisphosphate. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.05.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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38
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Synthesis and in vitro anticancer activity evaluation of novel bioreversible phosphate inositol derivatives. Eur J Med Chem 2015; 93:172-81. [DOI: 10.1016/j.ejmech.2015.01.064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/29/2014] [Accepted: 01/31/2015] [Indexed: 01/13/2023]
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39
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Chen WB, Liu JB, Dou DL, Song FB, Li LY, Xi Z. Synthesis and screening of novel inositol phosphonate derivatives for anticancer functions in vitro. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2014.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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40
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The response to inositol: regulation of glycerolipid metabolism and stress response signaling in yeast. Chem Phys Lipids 2014; 180:23-43. [PMID: 24418527 DOI: 10.1016/j.chemphyslip.2013.12.013] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 12/26/2013] [Indexed: 12/13/2022]
Abstract
This article focuses on discoveries of the mechanisms governing the regulation of glycerolipid metabolism and stress response signaling in response to the phospholipid precursor, inositol. The regulation of glycerolipid lipid metabolism in yeast in response to inositol is highly complex, but increasingly well understood, and the roles of individual lipids in stress response are also increasingly well characterized. Discoveries that have emerged over several decades of genetic, molecular and biochemical analyses of metabolic, regulatory and signaling responses of yeast cells, both mutant and wild type, to the availability of the phospholipid precursor, inositol are discussed.
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41
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Veiga N, Torres J, Bazzicalupi C, Bianchi A, Kremer C. The copper(ii)–phytate–terpyridine ternary system: the first crystal structures showing the interaction of phytate with bivalent metal and ammonium cations. Chem Commun (Camb) 2014; 50:14971-4. [DOI: 10.1039/c4cc07226j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work reports the solution and crystallographic study of the Cu(ii)–phytate–terpyridine systems, showing for the first time the phytate binding mode toward a bivalent cation and protonated polyamine groups.
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Affiliation(s)
- Nicolás Veiga
- Departamento Estrella Campos
- Universidad de la República
- Montevideo, Uruguay
| | - Julia Torres
- Departamento Estrella Campos
- Universidad de la República
- Montevideo, Uruguay
| | - Carla Bazzicalupi
- Dipartimento di Chimica “Ugo Schiff”
- Universitá degli Studi di Firenze
- Firenze, Italy
| | - Antonio Bianchi
- Dipartimento di Chimica “Ugo Schiff”
- Universitá degli Studi di Firenze
- Firenze, Italy
| | - Carlos Kremer
- Departamento Estrella Campos
- Universidad de la República
- Montevideo, Uruguay
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42
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Mukherjee S, Rigaud S, Seok SC, Fu G, Prochenka A, Dworkin M, Gascoigne NRJ, Vieland VJ, Sauer K, Das J. In silico modeling of Itk activation kinetics in thymocytes suggests competing positive and negative IP4 mediated feedbacks increase robustness. PLoS One 2013; 8:e73937. [PMID: 24066087 PMCID: PMC3774804 DOI: 10.1371/journal.pone.0073937] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 07/25/2013] [Indexed: 12/29/2022] Open
Abstract
The inositol-phosphate messenger inositol(1,3,4,5)tetrakisphosphate (IP4) is essential for thymocyte positive selection by regulating plasma-membrane association of the protein tyrosine kinase Itk downstream of the T cell receptor (TCR). IP4 can act as a soluble analog of the phosphoinositide 3-kinase (PI3K) membrane lipid product phosphatidylinositol(3,4,5)trisphosphate (PIP3). PIP3 recruits signaling proteins such as Itk to cellular membranes by binding to PH and other domains. In thymocytes, low-dose IP4 binding to the Itk PH domain surprisingly promoted and high-dose IP4 inhibited PIP3 binding of Itk PH domains. However, the mechanisms that underlie the regulation of membrane recruitment of Itk by IP4 and PIP3 remain unclear. The distinct Itk PH domain ability to oligomerize is consistent with a cooperative-allosteric mode of IP4 action. However, other possibilities cannot be ruled out due to difficulties in quantitatively measuring the interactions between Itk, IP4 and PIP3, and in generating non-oligomerizing Itk PH domain mutants. This has hindered a full mechanistic understanding of how IP4 controls Itk function. By combining experimentally measured kinetics of PLCγ1 phosphorylation by Itk with in silico modeling of multiple Itk signaling circuits and a maximum entropy (MaxEnt) based computational approach, we show that those in silico models which are most robust against variations of protein and lipid expression levels and kinetic rates at the single cell level share a cooperative-allosteric mode of Itk regulation by IP4 involving oligomeric Itk PH domains at the plasma membrane. This identifies MaxEnt as an excellent tool for quantifying robustness for complex TCR signaling circuits and provides testable predictions to further elucidate a controversial mechanism of PIP3 signaling.
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Affiliation(s)
- Sayak Mukherjee
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Stephanie Rigaud
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Sang-Cheol Seok
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Guo Fu
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Agnieszka Prochenka
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland
| | - Michael Dworkin
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Mathematics, The Ohio State University, Columbus, Ohio, United States of America
| | - Nicholas R. J. Gascoigne
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Veronica J. Vieland
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
- Department of Statistics, The Ohio State University, Columbus, Ohio, United States of America
| | - Karsten Sauer
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (KS); (JD)
| | - Jayajit Das
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
- Department of Physics, The Ohio State University, Columbus, Ohio, United States of America
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (KS); (JD)
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43
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Galdieri L, Chang J, Mehrotra S, Vancura A. Yeast phospholipase C is required for normal acetyl-CoA homeostasis and global histone acetylation. J Biol Chem 2013; 288:27986-98. [PMID: 23913687 DOI: 10.1074/jbc.m113.492348] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Phospholipase C (Plc1p) is required for the initial step of inositol polyphosphate (InsP) synthesis, and yeast cells with deletion of the PLC1 gene are completely devoid of any InsPs and display aberrations in transcriptional regulation. Here we show that Plc1p is required for a normal level of histone acetylation; plc1Δ cells that do not synthesize any InsPs display decreased acetylation of bulk histones and global hypoacetylation of chromatin histones. In accordance with the role of Plc1p in supporting histone acetylation, plc1Δ mutation is synthetically lethal with mutations in several subunits of SAGA and NuA4 histone acetyltransferase (HAT) complexes. Conversely, the growth rate, sensitivity to multiple stresses, and the transcriptional defects of plc1Δ cells are partially suppressed by deletion of histone deacetylase HDA1. The histone hypoacetylation in plc1Δ cells is due to the defect in degradation of repressor Mth1p, and consequently lower expression of HXT genes and reduced conversion of glucose to acetyl-CoA, a substrate for HATs. The histone acetylation and transcriptional defects can be partially suppressed and the overall fitness improved in plc1Δ cells by increasing the cellular concentration of acetyl-CoA. Together, our data indicate that Plc1p and InsPs are required for normal acetyl-CoA homeostasis, which, in turn, regulates global histone acetylation.
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Affiliation(s)
- Luciano Galdieri
- From the Department of Biological Sciences, St. John's University, Queens, New York 11439
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Abstract
The present review will explore the insights gained into inositol pyrophosphates in the 20 years since their discovery in 1993. These molecules are defined by the presence of the characteristic ‘high energy’ pyrophosphate moiety and can be found ubiquitously in eukaryotic cells. The enzymes that synthesize them are similarly well distributed and can be found encoded in any eukaryote genome. Rapid progress has been made in characterizing inositol pyrophosphate metabolism and they have been linked to a surprisingly diverse range of cellular functions. Two decades of work is now beginning to present a view of inositol pyrophosphates as fundamental, conserved and highly important agents in the regulation of cellular homoeostasis. In particular it is emerging that energy metabolism, and thus ATP production, is closely regulated by these molecules. Much of the early work on these molecules was performed in the yeast Saccharomyces cerevisiae and the social amoeba Dictyostelium discoideum, but the development of mouse knockouts for IP6K1 and IP6K2 [IP6K is IP6 (inositol hexakisphosphate) kinase] in the last 5 years has provided very welcome tools to better understand the physiological roles of inositol pyrophosphates. Another recent innovation has been the use of gel electrophoresis to detect and purify inositol pyrophosphates. Despite the advances that have been made, many aspects of inositol pyrophosphate biology remain far from clear. By evaluating the literature, the present review hopes to promote further research in this absorbing area of biology.
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45
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Li J, Ren LJ, Sun GN, Qu L, Huang H. Comparative metabolomics analysis of docosahexaenoic acid fermentation processes by Schizochytrium sp. under different oxygen availability conditions. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 17:269-81. [PMID: 23586678 DOI: 10.1089/omi.2012.0088] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The intracellular metabolic profile characterization of Schizochytrium sp. throughout docosahexaenoic acid fermentation was investigated using gas chromatography-mass spectrometry (GC-MS). Metabolite profiles originating from Schizochytrium sp. under normal and limited oxygen supply conditions were distinctive and distinguished by principal components analysis (PCA). A total of more than 60 intracellular metabolites were detected and quantified with the levels of some metabolites involved in central carbon metabolism varying throughout both processes. Both fermentation processes were differentiated into three main phases by principal components analysis. Potential biomarkers responsible for distinguishing the different fermentation phases were identified as glutamic acid, proline, glycine, alanine, and glucose. In addition, alanine, glutamic acid, glucose, inositol, ornithine, and galactose were found to make great contribution for dry cell weight and fatty acid composition during normal and limited oxygen supply fermentations. Furthermore, significantly higher levels of succinate and several amino acids in cells of limited oxygen supply fermentation revealed that they might play important roles in resisting oxygen deficiency and increasing DHA synthesis during the lipid accumulation. These findings provide novel insights into the metabolomic characteristics during docosahexaenoic acid fermentation processes by Schizochytrium sp.
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Affiliation(s)
- Juan Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology Nanjing, China
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46
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Barker CJ, Berggren PO. New Horizons in Cellular Regulation by Inositol Polyphosphates: Insights from the Pancreaticβ-Cell. Pharmacol Rev 2013; 65:641-69. [DOI: 10.1124/pr.112.006775] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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47
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Zhang WJ, Dewey RE, Boss W, Phillippy BQ, Qu R. Enhanced Agrobacterium-mediated transformation efficiencies in monocot cells is associated with attenuated defense responses. PLANT MOLECULAR BIOLOGY 2013; 81:273-286. [PMID: 23242917 DOI: 10.1007/s11103-012-9997-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 12/06/2012] [Indexed: 05/27/2023]
Abstract
Plant defense responses can lead to altered metabolism and even cell death at the sites of Agrobacterium infection, and thus lower transformation frequencies. In this report, we demonstrate that the utilization of culture conditions associated with an attenuation of defense responses in monocot plant cells led to highly improved Agrobacterium-mediated transformation efficiencies in perennial ryegrass (Lolium perenne L.). The removal of myo-inositol from the callus culture media in combination with a cold shock pretreatment and the addition of L-Gln prior to and during Agrobacterium-infection resulted in about 84 % of the treated calluses being stably transformed. The omission of myo-inositol from the callus culture media was associated with the failure of certain pathogenesis related genes to be induced after Agrobacterium infection. The addition of a cold shock and supplemental Gln appeared to have synergistic effects on infection and transformation efficiencies. Nearly 60 % of the stably transformed calluses regenerated into green plantlets. Calluses cultured on media lacking myo-inositol also displayed profound physiological and biochemical changes compared to ones cultured on standard growth media, such as reduced lignin within the cell walls, increased starch and inositol hexaphosphate accumulation, enhanced Agrobacterium binding to the cell surface, and less H(2)O(2) production after Agrobacterium infection. Furthermore, the cold treatment greatly reduced callus browning after infection. The simple modifications described in this report may have broad application for improving genetic transformation of recalcitrant monocot species.
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Affiliation(s)
- Wan-Jun Zhang
- Department of Grassland Science, China Agricultural University, Beijing 100193, China.
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48
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Lee JY, Kim YR, Park J, Kim S. Inositol polyphosphate multikinase signaling in the regulation of metabolism. Ann N Y Acad Sci 2013; 1271:68-74. [PMID: 23050966 PMCID: PMC3499638 DOI: 10.1111/j.1749-6632.2012.06725.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Inositol phosphates (IPs) act as signaling messengers to regulate various cellular processes such as growth. Inositol polyphosphate multikinase (IPMK) generates inositol tetrakis- and pentakisphosphates (IP4 and IP5), acting as a key enzyme for inositol polyphosphate biosynthesis. IPMK was initially discovered as an essential subunit of the arginine-sensing transcription complex in budding yeast. In mammals, IPMK is also known as a physiologically important phosphatidylinositol 3 kinase (PI3K) that forms phosphatidylinositol 3,4,5-trisphosphate (PIP3), which activates Akt/PKB and stimulates its signaling. Acting in a catalytically independent fashion, IPMK mediates the activation of mammalian target of rapamycin (mTOR) in response to essential amino acids. In addition, IPMK binds and modulates AMP-activated protein kinase (AMPK) signaling pathways, including those involved in hypothalamic control of food intake. These recent findings strongly suggest that IPMK is a versatile player in insulin-, nutrient-, and energy-mediated metabolism signaling networks. Agents that control IPMK functions may provide novel therapeutics in metabolic syndromes such as obesity and diabetes.
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Affiliation(s)
- Joo-Young Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
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49
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Wang X, Hirao H. ONIOM (DFT:MM) Study of the Catalytic Mechanism of myo-Inositol Monophosphatase: Essential Role of Water in Enzyme Catalysis in the Two-Metal Mechanism. J Phys Chem B 2013; 117:833-42. [DOI: 10.1021/jp312483n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xiaoqing Wang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore
637371
| | - Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore
637371
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50
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Vidyasagar A, Pathigoolla A, Sureshan KM. Chemoselective alcoholysis/acetolysis of trans-ketals over cis-ketals and its application in the total synthesis of the cellular second messenger, d-myo-inositol-1,4,5-trisphosphate. Org Biomol Chem 2013; 11:5443-53. [DOI: 10.1039/c3ob40789f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Adiyala Vidyasagar
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, India
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