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Yurinskaya VE, Vereninov AA. Cation-Chloride Cotransporters, Na/K Pump, and Channels in Cell Water/Ionic Balance Regulation Under Hyperosmolar Conditions: In Silico and Experimental Studies of Opposite RVI and AVD Responses of U937 Cells to Hyperosmolar Media. Front Cell Dev Biol 2022; 9:830563. [PMID: 35141234 PMCID: PMC8818862 DOI: 10.3389/fcell.2021.830563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/28/2021] [Indexed: 11/19/2022] Open
Abstract
Studying the transport of monovalent ions across the cell membrane in living cells is complicated by the strong interdependence of fluxes through parallel pathways and requires therefore computational analysis of the entire electrochemical system of the cell. Current paper shows how to calculate changes in the cell water balance and ion fluxes caused by changes in the membrane channels and transporters during a normal regulatory increase in cell volume in response to osmotic cell shrinkage (RVI) followed by a decrease in cell volume associated with apoptosis (AVD). Our recently developed software is used as a computational analysis tool and the established human lymphoid cells U937 are taken as an example of proliferating animal cells. It is found that, in contrast to countless statements in the literature that cell volume restoration requires the activation of certain ion channels and transporters, the cellular responses such as RVI and AVD can occur in an electrochemical system like U937 cells without any changes in the state of membrane channels or transporters. These responses depend on the types of chloride cotransporters in the membrane and differ in a hyperosmolar medium with additional sucrose and in a medium with additional NaCl. This finding is essential for the identification of the true changes in membrane channels and transporters responsible for RVI and AVD in living cells. It is determined which changes in membrane parameters predicted by computational analysis are consistent with experimental data obtained on living human lymphoid cells U937, Jurkat, and K562 and which are not. An essential part of the results is the developed software that allows researchers without programming experience to calculate the fluxes of monovalent ions via the main transmembrane pathways and electrochemical gradients that move ions across the membrane. The software is available for download. It is useful for studying the functional expression of the channels and transporters in living cells and understanding how the cell electrochemical system works.
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2
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Jobava R, Mao Y, Guan BJ, Hu D, Krokowski D, Chen CW, Shu XE, Chukwurah E, Wu J, Gao Z, Zagore LL, Merrick WC, Trifunovic A, Hsieh AC, Valadkhan S, Zhang Y, Qi X, Jankowsky E, Topisirovic I, Licatalosi DD, Qian SB, Hatzoglou M. Adaptive translational pausing is a hallmark of the cellular response to severe environmental stress. Mol Cell 2021; 81:4191-4208.e8. [PMID: 34686314 PMCID: PMC8559772 DOI: 10.1016/j.molcel.2021.09.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/27/2021] [Accepted: 09/28/2021] [Indexed: 12/12/2022]
Abstract
To survive, mammalian cells must adapt to environmental challenges. While the cellular response to mild stress has been widely studied, how cells respond to severe stress remains unclear. We show here that under severe hyperosmotic stress, cells enter a transient hibernation-like state in anticipation of recovery. We demonstrate this adaptive pausing response (APR) is a coordinated cellular response that limits ATP supply and consumption through mitochondrial fragmentation and widespread pausing of mRNA translation. This pausing is accomplished by ribosome stalling at translation initiation codons, which keeps mRNAs poised to resume translation upon recovery. We further show that recovery from severe stress involves ISR (integrated stress response) signaling that permits cell cycle progression, resumption of growth, and reversal of mitochondria fragmentation. Our findings indicate that cells can respond to severe stress via a hibernation-like mechanism that preserves vital elements of cellular function under harsh environmental conditions.
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Affiliation(s)
- Raul Jobava
- Department of Biochemistry, CWRU, Cleveland, OH 44106, USA; Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Bo-Jhih Guan
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Di Hu
- Department of Physiology & Biophysics, CWRU, Cleveland, OH 44106, USA
| | - Dawid Krokowski
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA; Department of Molecular Biology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Lublin 20-033, Poland
| | - Chien-Wen Chen
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Xin Erica Shu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Evelyn Chukwurah
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Jing Wu
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Zhaofeng Gao
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA
| | - Leah L Zagore
- Department of Biochemistry, CWRU, Cleveland, OH 44106, USA; Center for RNA Science and Therapeutics, CWRU, Cleveland, OH 44106, USA
| | | | - Aleksandra Trifunovic
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Medical Faculty, University of Cologne, 50931 Cologne, Germany; Institute for Mitochondrial Diseases and Ageing, Medical Faculty and Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Andrew C Hsieh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Saba Valadkhan
- Department of Molecular Biology and Microbiology, CWRU, Cleveland, OH 44106, USA
| | - Youwei Zhang
- Department of Pharmacology, CWRU, Cleveland, OH 44106, USA
| | - Xin Qi
- Department of Physiology & Biophysics, CWRU, Cleveland, OH 44106, USA
| | - Eckhard Jankowsky
- Department of Biochemistry, CWRU, Cleveland, OH 44106, USA; Center for RNA Science and Therapeutics, CWRU, Cleveland, OH 44106, USA
| | - Ivan Topisirovic
- Gerald Bronfman Department of Oncology, Departments of Biochemistry and Experimental Medicine and Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC H3T 1E2, Canada
| | - Donny D Licatalosi
- Department of Biochemistry, CWRU, Cleveland, OH 44106, USA; Center for RNA Science and Therapeutics, CWRU, Cleveland, OH 44106, USA.
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, CWRU, Cleveland, OH 44106, USA.
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Rasmussen RN, Christensen KV, Holm R, Nielsen CU. Transcriptome analysis identifies activated signaling pathways and regulated ABC transporters and solute carriers after hyperosmotic stress in renal MDCK I cells. Genomics 2018; 111:1557-1565. [PMID: 30389539 DOI: 10.1016/j.ygeno.2018.10.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/22/2018] [Accepted: 10/29/2018] [Indexed: 12/01/2022]
Abstract
Hyperosmolality is found under physiological conditions in the kidneys, whereas hyperosmolality in other tissues may be associated with pathological conditions. In such tissues an association between inflammation and hyperosmolality has been suggested. During hyperosmotic stress, an important phenomenon is upregulation of solute carriers (SLCs). We hypothesize that hyperosmolality affects the expression of many SLCs as well as ABC transporters. Through RNA-sequencing and topological pathway analysis, the cell cycle, the cytokine-cytokine receptor interaction pathway, and the chemokine-signaling pathway were significantly activated in MDCK I cells after hyperosmotic treatment (Δ200 mOsm) with raffinose or NaCl. 9065, 8052 and 5018 genes were significantly regulated by raffinose, NaCl or urea supplementation (500 mOsm), respectively, compared to control (300 mOsm). Cytokines, that have not previously been associated with hyperosmolality, were identified. We further provide an overview of transport proteins that could be of relevance in tissues exposed to hyperosmolality. Especially Slc5a8 was found highly up-regulated.
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Affiliation(s)
- Rune Nørgaard Rasmussen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark..
| | | | - René Holm
- Drug Product Development, Janssens Research and Development, Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Carsten Uhd Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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4
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do Prado FD, Vera M, Hermida M, Bouza C, Pardo BG, Vilas R, Blanco A, Fernández C, Maroso F, Maes GE, Turan C, Volckaert FAM, Taggart JB, Carr A, Ogden R, Nielsen EE, Martínez P. Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot ( Scophthalmus maximus). Evol Appl 2018; 11:1322-1341. [PMID: 30151043 PMCID: PMC6099829 DOI: 10.1111/eva.12628] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/23/2018] [Indexed: 12/16/2022] Open
Abstract
Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which, in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 single nucleotide polymorphism discovered and genotyped by double-digest RAD sequencing. The species was structured into four main regions: Baltic Sea, Atlantic Ocean, Adriatic Sea, and Black Sea, with subtle differentiation apparent at the distribution margins of the Atlantic region. Genetic diversity and effective population size estimates were highest in the Atlantic populations, the area of greatest occurrence, while turbot from other regions showed lower levels, reflecting geographical isolation and reduced abundance. Divergent selection was detected within and between the Atlantic Ocean and Baltic Sea regions, and also when comparing these two regions with the Black Sea. Evidence of parallel evolution was detected between the two low salinity regions, the Baltic and Black seas. Correlation between genetic and environmental variation indicated that temperature and salinity were probably the main environmental drivers of selection. Mining around the four genomic regions consistently inferred to be under selection identified candidate genes related to osmoregulation, growth, and resistance to diseases. The new insights are useful for the management of turbot fisheries and aquaculture by providing the baseline for evaluating the consequences of turbot releases from restocking and farming.
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Affiliation(s)
- Fernanda Dotti do Prado
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
- CAPES FoundationMinistry of Education of BrazilBrasíliaBrazil
| | - Manuel Vera
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Miguel Hermida
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Carmen Bouza
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Belén G. Pardo
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Román Vilas
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Carlos Fernández
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Francesco Maroso
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Gregory E. Maes
- Laboratory of Biodiversity and Evolutionary GenomicsUniversity of LeuvenLeuvenBelgium
- Center for Human GeneticsUZ Leuven‐Genomics Core, KU LeuvenLeuvenBelgium
- Comparative Genomics CentreCollege of Science and EngineeringJames Cook UniversityTownsvilleQLDAustralia
| | - Cemal Turan
- Faculty of Marine Science and TechnologyIskenderun Technical UniversityIskenderunTurkey
| | - Filip A. M. Volckaert
- Laboratory of Biodiversity and Evolutionary GenomicsUniversity of LeuvenLeuvenBelgium
- Center for Human GeneticsUZ Leuven‐Genomics Core, KU LeuvenLeuvenBelgium
- Comparative Genomics CentreCollege of Science and EngineeringJames Cook UniversityTownsvilleQLDAustralia
| | | | | | - Rob Ogden
- Trace Wildlife Forensics NetworkRoyal Zoological Society of ScotlandEdinburghUK
| | - Einar Eg Nielsen
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | - Paulino Martínez
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
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Aboudehen K, Noureddine L, Cobo-Stark P, Avdulov S, Farahani S, Gearhart MD, Bichet DG, Pontoglio M, Patel V, Igarashi P. Hepatocyte Nuclear Factor-1 β Regulates Urinary Concentration and Response to Hypertonicity. J Am Soc Nephrol 2017; 28:2887-2900. [PMID: 28507058 DOI: 10.1681/asn.2016101095] [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: 10/14/2016] [Accepted: 04/16/2017] [Indexed: 12/18/2022] Open
Abstract
The transcription factor hepatocyte nuclear factor-1β (HNF-1β) is essential for normal kidney development and function. Inactivation of HNF-1β in mouse kidney tubules leads to early-onset cyst formation and postnatal lethality. Here, we used Pkhd1/Cre mice to delete HNF-1β specifically in renal collecting ducts (CDs). CD-specific HNF-1β mutant mice survived long term and developed slowly progressive cystic kidney disease, renal fibrosis, and hydronephrosis. Compared with wild-type littermates, HNF-1β mutant mice exhibited polyuria and polydipsia. Before the development of significant renal structural abnormalities, mutant mice exhibited low urine osmolality at baseline and after water restriction and administration of desmopressin. However, mutant and wild-type mice had similar plasma vasopressin and solute excretion levels. HNF-1β mutant kidneys showed increased expression of aquaporin-2 mRNA but mislocalized expression of aquaporin-2 protein in the cytoplasm of CD cells. Mutant kidneys also had decreased expression of the UT-A urea transporter and collectrin, which is involved in apical membrane vesicle trafficking. Treatment of HNF-1β mutant mIMCD3 cells with hypertonic NaCl inhibited the induction of osmoregulated genes, including Nr1h4, which encodes the transcription factor FXR that is required for maximal urinary concentration. Chromatin immunoprecipitation and sequencing experiments revealed HNF-1β binding to the Nr1h4 promoter in wild-type kidneys, and immunoblot analysis revealed downregulated expression of FXR in HNF-1β mutant kidneys. These findings reveal a novel role of HNF-1β in osmoregulation and identify multiple mechanisms, whereby mutations of HNF-1β produce defects in urinary concentration.
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Affiliation(s)
- Karam Aboudehen
- Departments of Medicine and.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Lama Noureddine
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Patricia Cobo-Stark
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | | | | | - Micah D Gearhart
- Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota
| | - Daniel G Bichet
- Departments of Medicine and.,Molecular and Integrative Physiology, Université de Montréal, Montreal, Quebec, Canada; and
| | - Marco Pontoglio
- Department of Development, Reproduction and Cancer, Institut Cochin, Institut National de la Santé et de la Recherche Médicale U1016/Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Université Paris-Descartes, Paris, France
| | - Vishal Patel
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Peter Igarashi
- Departments of Medicine and .,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
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6
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Gao S, Cui X, Wang X, Burg MB, Dmitrieva NI. Cross-Sectional Positive Association of Serum Lipids and Blood Pressure With Serum Sodium Within the Normal Reference Range of 135-145 mmol/L. Arterioscler Thromb Vasc Biol 2016; 37:598-606. [PMID: 28062505 DOI: 10.1161/atvbaha.116.308413] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 12/08/2016] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Serum sodium concentration is maintained by osmoregulation within normal range of 135 to 145 mmol/L. Previous analysis of data from the ARIC study (Atherosclerosis Risk in Communities) showed association of serum sodium with the 10-year risk scores of coronary heart disease and stroke. Current study evaluated the association of within-normal-range serum sodium with cardiovascular risk factors. APPROACH AND RESULTS Only participants who did not take cholesterol or blood pressure medications and had sodium within normal 135 to 145 mmol/L range were included (n=8615), and the cohort was stratified based on race, sex, and smoking status. Multiple linear regression analysis of data from ARIC study was performed, with adjustment for age, blood glucose, insulin, glomerular filtration rate, body mass index, waist to hip ratio, and calorie intake. The analysis showed positive associations with sodium of total cholesterol, low-density lipoprotein cholesterol, and total cholesterol to high-density lipoprotein cholesterol ratio; apolipoprotein B; and systolic and diastolic blood pressure. Increases in lipids and blood pressure associated with 10 mmol/L increase in sodium are similar to the increases associated with 7 to 10 years of aging. Analysis of sodium measurements made 3 years apart demonstrated that it is stable within 2 to 3 mmol/L, explaining its association with long-term health outcomes. Furthermore, elevated sodium promoted lipid accumulation in cultured adipocytes, suggesting direct causative effects on lipid metabolism. CONCLUSIONS Serum sodium concentration is a cardiovascular risk factor even within the normal reference range. Thus, decreasing sodium to the lower end of the normal range by modification of water and salt intake is a personalizable strategy for decreasing cardiovascular risks.
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Affiliation(s)
- Shouguo Gao
- From the Bioinformatics and Systems Biology Core, Systems Biology Center (S.G., X.W.), Renal Cellular and Molecular Biology Section, Systems Biology Center (M.B.B., N.I.D.), and Laboratory of Cardiovascular and Regenerative Medicine, Center for Molecular Medicine (N.I.D.), National Heart, Lung and Blood Institute, Bethesda, MD; and Department of Biostatistics, University of Alabama at Birmingham (X.C.)
| | - Xiangqin Cui
- From the Bioinformatics and Systems Biology Core, Systems Biology Center (S.G., X.W.), Renal Cellular and Molecular Biology Section, Systems Biology Center (M.B.B., N.I.D.), and Laboratory of Cardiovascular and Regenerative Medicine, Center for Molecular Medicine (N.I.D.), National Heart, Lung and Blood Institute, Bethesda, MD; and Department of Biostatistics, University of Alabama at Birmingham (X.C.)
| | - Xujing Wang
- From the Bioinformatics and Systems Biology Core, Systems Biology Center (S.G., X.W.), Renal Cellular and Molecular Biology Section, Systems Biology Center (M.B.B., N.I.D.), and Laboratory of Cardiovascular and Regenerative Medicine, Center for Molecular Medicine (N.I.D.), National Heart, Lung and Blood Institute, Bethesda, MD; and Department of Biostatistics, University of Alabama at Birmingham (X.C.)
| | - Maurice B Burg
- From the Bioinformatics and Systems Biology Core, Systems Biology Center (S.G., X.W.), Renal Cellular and Molecular Biology Section, Systems Biology Center (M.B.B., N.I.D.), and Laboratory of Cardiovascular and Regenerative Medicine, Center for Molecular Medicine (N.I.D.), National Heart, Lung and Blood Institute, Bethesda, MD; and Department of Biostatistics, University of Alabama at Birmingham (X.C.)
| | - Natalia I Dmitrieva
- From the Bioinformatics and Systems Biology Core, Systems Biology Center (S.G., X.W.), Renal Cellular and Molecular Biology Section, Systems Biology Center (M.B.B., N.I.D.), and Laboratory of Cardiovascular and Regenerative Medicine, Center for Molecular Medicine (N.I.D.), National Heart, Lung and Blood Institute, Bethesda, MD; and Department of Biostatistics, University of Alabama at Birmingham (X.C.).
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7
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Dumond JF, Zhang X, Izumi Y, Ramkissoon K, Wang G, Gucek M, Wang X, Burg MB, Ferraris JD. Peptide affinity analysis of proteins that bind to an unstructured region containing the transactivating domain of the osmoprotective transcription factor NFAT5. Physiol Genomics 2016; 48:835-849. [PMID: 27764768 DOI: 10.1152/physiolgenomics.00100.2016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/03/2016] [Indexed: 11/22/2022] Open
Abstract
NFAT5 is a transcription factor originally identified because it is activated by hypertonicity and that activation increases expression of genes that protect against the adverse effects of the hypertonicity. However, its targets also include genes not obviously related to tonicity. The transactivating domain of NFAT5 is contained in its COOH-terminal region, which is predicted to be unstructured. Unstructured regions are common in transcription factors particularly in transactivating domains where they can bind co-regulatory proteins essential to their function. To identify potential binding partners of NFAT5 from either cytoplasmic or nuclear HEK293 cell extracts, we used peptide affinity chromatography followed by mass spectrometry. Peptide aptamer-baits consisted of overlapping 20 amino acid peptides within the predicted COOH-terminal unstructured region of NFAT5. We identify a total of 351 unique protein preys that associate with at least one COOH-terminal peptide bait from NFAT5 in either cytoplasmic or nuclear extracts from cells incubated at various tonicities (NaCl varied). In addition to finding many proteins already known to associate with NFAT5, we found many new ones whose function suggest novel aspects of NFAT5 regulation, interaction, and function. Relatively few of the proteins pulled down by peptide baits from NFAT5 are generally involved in transcription, and most, therefore, are likely to be specifically related to the regulation of NFAT5 or its function. The novel associated proteins are involved with cancer, effects of hypertonicity on chromatin, development, splicing of mRNA, transcription, and vesicle trafficking.
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Affiliation(s)
- Jenna F Dumond
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, Maryland; and
| | - Xue Zhang
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, Maryland; and
| | - Yuichiro Izumi
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, Maryland; and.,Department of Nephrology, Kumamoto University Graduate School of Medical Sciences, Kumamoto, Japan
| | - Kevin Ramkissoon
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, Maryland; and
| | - Guanghui Wang
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, Maryland; and
| | - Marjan Gucek
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, Maryland; and
| | - Xujing Wang
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, Maryland; and
| | - Maurice B Burg
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, Maryland; and
| | - Joan D Ferraris
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, Maryland; and
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8
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DuMond JF, Ramkissoon K, Zhang X, Izumi Y, Wang X, Eguchi K, Gao S, Mukoyama M, Burg MB, Ferraris JD. Peptide affinity analysis of proteins that bind to an unstructured NH2-terminal region of the osmoprotective transcription factor NFAT5. Physiol Genomics 2016; 48:290-305. [PMID: 26757802 DOI: 10.1152/physiolgenomics.00110.2015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/09/2016] [Indexed: 11/22/2022] Open
Abstract
NFAT5 is an osmoregulated transcription factor that particularly increases expression of genes involved in protection against hypertonicity. Transcription factors often contain unstructured regions that bind co-regulatory proteins that are crucial for their function. The NH2-terminal region of NFAT5 contains regions predicted to be intrinsically disordered. We used peptide aptamer-based affinity chromatography coupled with mass spectrometry to identify protein preys pulled down by one or more overlapping 20 amino acid peptide baits within a predicted NH2-terminal unstructured region of NFAT5. We identify a total of 467 unique protein preys that associate with at least one NH2-terminal peptide bait from NFAT5 in either cytoplasmic or nuclear extracts from HEK293 cells treated with elevated, normal, or reduced NaCl concentrations. Different sets of proteins are pulled down from nuclear vs. cytoplasmic extracts. We used GeneCards to ascertain known functions of the protein preys. The protein preys include many that were previously known, but also many novel ones. Consideration of the novel ones suggests many aspects of NFAT5 regulation, interaction and function that were not previously appreciated, for example, hypertonicity inhibits NFAT5 by sumoylating it and the NFAT5 protein preys include components of the CHTOP complex that desumoylate proteins, an action that should contribute to activation of NFAT5.
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Affiliation(s)
- Jenna F DuMond
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda Maryland; and
| | - Kevin Ramkissoon
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda Maryland; and
| | - Xue Zhang
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda Maryland; and
| | - Yuichiro Izumi
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda Maryland; and Department of Nephrology, Kumamoto University Graduate School of Medical Sciences, Kumamoto, Japan
| | - Xujing Wang
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda Maryland; and
| | - Koji Eguchi
- Department of Nephrology, Kumamoto University Graduate School of Medical Sciences, Kumamoto, Japan
| | - Shouguo Gao
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda Maryland; and
| | - Masashi Mukoyama
- Department of Nephrology, Kumamoto University Graduate School of Medical Sciences, Kumamoto, Japan
| | - Maurice B Burg
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda Maryland; and
| | - Joan D Ferraris
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda Maryland; and
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9
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Abstract
High extracellular NaCl is known to change expression of numerous genes, many of which are regulated by the osmoprotective transcription factor nuclear factor of activated T cells-5 (NFAT5). In the present study we employed RNA-Seq to provide a comprehensive, unbiased account of genes regulated by high NaCl in mouse embryonic fibroblast cells (MEFs). To identify genes regulated by NFAT5 we compared wild-type MEFs (WT-MEFs) to MEFs in which mutation of the NFAT5 gene inhibits its transcriptional activity (Null-MEFs). In WT-MEFs adding NaCl to raise osmolality from 300 to 500 mosmol/kg for 24 h increases expression of 167 genes and reduces expression of 412. Raising osmolality through multiple passages (adapted cells) increases expression of 196 genes and reduces expression of 528. In Null-MEFs, after 24 h of high NaCl, expression of 217 genes increase and 428 decrease, while in adapted Null-MEFs 143 increase and 622 decrease. Fewer than 10% of genes are regulated in common between WT- and null-MEFs, indicating a profound difference in regulation of high-NaCl induced genes induced by NFAT5 compared with those induced in the absence of NFAT5. Based on our findings we suggest a mechanism for this phenomenon, which had previously been unexplained. The NFAT5 DNA-binding motif (osmotic response element) is overrepresented in the vicinity of genes that NFAT5 upregulates, but not genes that it downregulates. We used Gene Ontology and manual curation to determine the function of the genes targeted by NFAT5, revealing many novel consequences of NFAT5 transcriptional activity.
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Affiliation(s)
- Yuichiro Izumi
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Wenjing Yang
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Jun Zhu
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Maurice B Burg
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Joan D Ferraris
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
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