1
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Wang M, Zhou J, Niu Q, Wang H. Mechanism of tacrolimus in the treatment of lupus nephritis. Front Pharmacol 2024; 15:1331800. [PMID: 38774214 PMCID: PMC11106426 DOI: 10.3389/fphar.2024.1331800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/19/2024] [Indexed: 05/24/2024] Open
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disorder, with more than half of the patients developing lupus nephritis (LN), which significantly contributes to chronic kidney disease (CKD) and end-stage renal disease (ESRD). The treatment of lupus nephritis has always been challenging. Tacrolimus (TAC), an effective immunosuppressant, has been increasingly used in the treatment of LN in recent years. This review aims to explore the mechanisms of action of tacrolimus in treating LN. Firstly, we briefly introduce the pharmacological properties of tacrolimus, including its role as a calcineurin (CaN) inhibitor, exerting immunosuppressive effects by inhibiting T cell activation and cytokine production. Subsequently, we focus on various other immunomodulatory mechanisms of tacrolimus in LN therapy, including its effects on T cells, B cells, and immune cells in kidney. Particularly, we emphasize tacrolimus' regulatory effect on inflammatory mediators and its importance in modulating the Th1/Th2 and Th17/Treg balance. Additionally, we review its effects on actin cytoskeleton, angiotensin II (Ang II)-specific vascular contraction, and P-glycoprotein activity, summarizing its impacts on non-immune mechanisms. Finally, we summarize the efficacy and safety of tacrolimus in clinical studies and trials. Although some studies have shown significant efficacy of tacrolimus in treating LN, its safety remains a challenge. We outline the potential adverse reactions of long-term tacrolimus use and provide suggestions on effectively monitoring and managing these adverse reactions in clinical practice. In general, tacrolimus, as a novel immunosuppressant, holds promising prospects for treating LN. Of course, further research is needed to better understand its therapeutic mechanisms and ensure its safety and efficacy in clinical practice.
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Affiliation(s)
| | | | | | - Hongyue Wang
- Department of Nephrology, The First Hospital of Jilin University, Changchun, China
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2
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Saini G, Parasa MK, Clayton KN, Fraseur JG, Bolton SC, Lin KP, Wereley ST, Kinzer-Ursem TL. Immobilization of azide-functionalized proteins to micro- and nanoparticles directly from cell lysate. Mikrochim Acta 2023; 191:46. [PMID: 38129631 PMCID: PMC10739308 DOI: 10.1007/s00604-023-06068-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/23/2023] [Indexed: 12/23/2023]
Abstract
Immobilization of proteins and enzymes on solid supports has been utilized in a variety of applications, from improved protein stability on supported catalysts in industrial processes to fabrication of biosensors, biochips, and microdevices. A critical requirement for these applications is facile yet stable covalent conjugation between the immobilized and fully active protein and the solid support to produce stable, highly bio-active conjugates. Here, we report functionalization of solid surfaces (gold nanoparticles and magnetic beads) with bio-active proteins using site-specific and biorthogonal labeling and azide-alkyne cycloaddition, a click chemistry. Specifically, we recombinantly express and selectively label calcium-dependent proteins, calmodulin and calcineurin, and cAMP-dependent protein kinase A (PKA) with N-terminal azide-tags for efficient conjugation to nanoparticles and magnetic beads. We successfully immobilized the proteins on to the solid supports directly from the cell lysate with click chemistry, forgoing the step of purification. This approach is optimized to yield low particle aggregation and high levels of protein activity post-conjugation. The entire process enables streamlined workflows for bioconjugation and highly active conjugated proteins.
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Affiliation(s)
- Gunjan Saini
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Mrugesh Krishna Parasa
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Katherine N Clayton
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Julia G Fraseur
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Scott C Bolton
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Kevin P Lin
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47906, USA
| | - Steven T Wereley
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Tamara L Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA.
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3
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Rodrigues YE, Tigaret CM, Marie H, O'Donnell C, Veltz R. A stochastic model of hippocampal synaptic plasticity with geometrical readout of enzyme dynamics. eLife 2023; 12:e80152. [PMID: 37589251 PMCID: PMC10435238 DOI: 10.7554/elife.80152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 03/22/2023] [Indexed: 08/18/2023] Open
Abstract
Discovering the rules of synaptic plasticity is an important step for understanding brain learning. Existing plasticity models are either (1) top-down and interpretable, but not flexible enough to account for experimental data, or (2) bottom-up and biologically realistic, but too intricate to interpret and hard to fit to data. To avoid the shortcomings of these approaches, we present a new plasticity rule based on a geometrical readout mechanism that flexibly maps synaptic enzyme dynamics to predict plasticity outcomes. We apply this readout to a multi-timescale model of hippocampal synaptic plasticity induction that includes electrical dynamics, calcium, CaMKII and calcineurin, and accurate representation of intrinsic noise sources. Using a single set of model parameters, we demonstrate the robustness of this plasticity rule by reproducing nine published ex vivo experiments covering various spike-timing and frequency-dependent plasticity induction protocols, animal ages, and experimental conditions. Our model also predicts that in vivo-like spike timing irregularity strongly shapes plasticity outcome. This geometrical readout modelling approach can be readily applied to other excitatory or inhibitory synapses to discover their synaptic plasticity rules.
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Affiliation(s)
- Yuri Elias Rodrigues
- Université Côte d’AzurNiceFrance
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), CNRSValbonneFrance
- Inria Center of University Côte d’Azur (Inria)Sophia AntipolisFrance
| | - Cezar M Tigaret
- Neuroscience and Mental Health Research Innovation Institute, Division of Psychological Medicine and Clinical Neurosciences,School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Hélène Marie
- Université Côte d’AzurNiceFrance
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), CNRSValbonneFrance
| | - Cian O'Donnell
- School of Computing, Engineering, and Intelligent Systems, Magee Campus, Ulster UniversityLondonderryUnited Kingdom
- School of Computer Science, Electrical and Electronic Engineering, and Engineering Mathematics, University of BristolBristolUnited Kingdom
| | - Romain Veltz
- Inria Center of University Côte d’Azur (Inria)Sophia AntipolisFrance
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4
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Williams RB, Alam Afsar MN, Tikunova S, Kou Y, Fang X, Somarathne RP, Gyawu RF, Knotts GM, Agee TA, Garcia SA, Losordo LD, Fitzkee NC, Kekenes-Huskey PM, Davis JP, Johnson CN. Human disease-associated calmodulin mutations alter calcineurin function through multiple mechanisms. Cell Calcium 2023; 113:102752. [PMID: 37245392 PMCID: PMC10330910 DOI: 10.1016/j.ceca.2023.102752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 04/29/2023] [Accepted: 05/03/2023] [Indexed: 05/30/2023]
Abstract
Calmodulin (CaM) is a ubiquitous, calcium-sensing protein that regulates a multitude of processes throughout the body. In response to changes in [Ca2+], CaM modifies, activates, and deactivates enzymes and ion channels, as well as many other cellular processes. The importance of CaM is highlighted by the conservation of an identical amino acid sequence in all mammals. Alterations to CaM amino acid sequence were once thought to be incompatible with life. During the last decade modifications to the CaM protein sequence have been observed in patients suffering from life-threatening heart disease (calmodulinopathy). Thus far, inadequate or untimely interaction between mutant CaM and several proteins (LTCC, RyR2, and CaMKII) have been identified as mechanisms underlying calmodulinopathy. Given the extensive number of CaM interactions in the body, there are likely many consequences for altering CaM protein sequence. Here, we demonstrate that disease-associated CaM mutations alter the sensitivity and activity of the Ca2+-CaM-enhanced serine/threonine phosphatase calcineurin (CaN). Biophysical characterization by circular dichroism, solution NMR spectroscopy, stopped-flow kinetic measurements, and MD simulations provide mechanistic insight into mutation dysfunction as well as highlight important aspects of CaM Ca2+ signal transduction. We find that individual CaM point mutations (N53I, F89L, D129G, and F141L) impair CaN function, however, the mechanisms are not the same. Specifically, individual point mutations can influence or modify the following properties: CaM binding, Ca2+ binding, and/or Ca2+kinetics. Moreover, structural aspects of the CaNCaM complex can be altered in manners that indicate changes to allosteric transmission of CaM binding to the enzyme active site. Given that loss of CaN function can be fatal, as well as evidence that CaN modifies ion channels already associated with calmodulinopathy, our results raise the possibility that altered CaN function contributes to calmodulinopathy.
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Affiliation(s)
- Ryan B Williams
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Md Nure Alam Afsar
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Svetlana Tikunova
- Department of Physiology and Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus OH 43210, U.S.A
| | - Yongjun Kou
- Department of Physiology and Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus OH 43210, U.S.A
| | - Xuan Fang
- Department of Cell and Molecular Physiology, Loyola University of Chicago, Maywood Illinois 60153, U.S.A
| | - Radha P Somarathne
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Rita F Gyawu
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Garrett M Knotts
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Taylor A Agee
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Sara A Garcia
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Luke D Losordo
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Peter M Kekenes-Huskey
- Department of Cell and Molecular Physiology, Loyola University of Chicago, Maywood Illinois 60153, U.S.A
| | - Jonathan P Davis
- Department of Physiology and Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus OH 43210, U.S.A.
| | - Christopher N Johnson
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A; Vanderbilt Center for Arrhythmia Research and Therapeutics, Nashville TN 37232, U.S.A.
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5
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Lim D, Tapella L, Dematteis G, Talmon M, Genazzani AA. Calcineurin Signalling in Astrocytes: From Pathology to Physiology and Control of Neuronal Functions. Neurochem Res 2023; 48:1077-1090. [PMID: 36083398 PMCID: PMC10030417 DOI: 10.1007/s11064-022-03744-4] [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: 07/31/2022] [Revised: 07/31/2022] [Accepted: 08/29/2022] [Indexed: 10/14/2022]
Abstract
Calcineurin (CaN), a Ca2+/calmodulin-activated serine/threonine phosphatase, acts as a Ca2+-sensitive switch regulating cellular functions through protein dephosphorylation and activation of gene transcription. In astrocytes, the principal homeostatic cells in the CNS, over-activation of CaN is known to drive pathological transcriptional remodelling, associated with neuroinflammation in diseases such as Alzheimer's disease, epilepsy and brain trauma. Recent reports suggest that, in physiological conditions, the activity of CaN in astrocytes is transcription-independent and is required for maintenance of basal protein synthesis rate and activation of astrocytic Na+/K+ pump thereby contributing to neuronal functions such as neuronal excitability and memory formation. In this contribution we overview the role of Ca2+ and CaN signalling in astroglial pathophysiology focusing on the emerging physiological role of CaN in astrocytes. We propose a model for the context-dependent switch of CaN activity from the post-transcriptional regulation of cell proteostasis in healthy astrocytes to the CaN-dependent transcriptional activation in neuroinflammation-associated diseases.
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Affiliation(s)
- Dmitry Lim
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale "Amedeo Avogadro", Via Bovio 6, 28100, Novara, Italy.
| | - Laura Tapella
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale "Amedeo Avogadro", Via Bovio 6, 28100, Novara, Italy
| | - Giulia Dematteis
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale "Amedeo Avogadro", Via Bovio 6, 28100, Novara, Italy
| | - Maria Talmon
- Department of Health Sciences, School of Medicine, Università del Piemonte Orientale "Amedeo Avogadro", Via Solaroli 17, 28100, Novara, Italy
| | - Armando A Genazzani
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale "Amedeo Avogadro", Via Bovio 6, 28100, Novara, Italy.
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6
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Funneling modulatory peptide design with generative models: Discovery and characterization of disruptors of calcineurin protein-protein interactions. PLoS Comput Biol 2023; 19:e1010874. [PMID: 36730443 PMCID: PMC9928118 DOI: 10.1371/journal.pcbi.1010874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/14/2023] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
Design of peptide binders is an attractive strategy for targeting "undruggable" protein-protein interfaces. Current design protocols rely on the extraction of an initial sequence from one known protein interactor of the target protein, followed by in-silico or in-vitro mutagenesis-based optimization of its binding affinity. Wet lab protocols can explore only a minor portion of the vast sequence space and cannot efficiently screen for other desirable properties such as high specificity and low toxicity, while in-silico design requires intensive computational resources and often relies on simplified binding models. Yet, for a multivalent protein target, dozens to hundreds of natural protein partners already exist in the cellular environment. Here, we describe a peptide design protocol that harnesses this diversity via a machine learning generative model. After identifying putative natural binding fragments by literature and homology search, a compositional Restricted Boltzmann Machine is trained and sampled to yield hundreds of diverse candidate peptides. The latter are further filtered via flexible molecular docking and an in-vitro microchip-based binding assay. We validate and test our protocol on calcineurin, a calcium-dependent protein phosphatase involved in various cellular pathways in health and disease. In a single screening round, we identified multiple 16-length peptides with up to six mutations from their closest natural sequence that successfully interfere with the binding of calcineurin to its substrates. In summary, integrating protein interaction and sequence databases, generative modeling, molecular docking and interaction assays enables the discovery of novel protein-protein interaction modulators.
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7
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Ulengin-Talkish I, Cyert MS. A cellular atlas of calcineurin signaling. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119366. [PMID: 36191737 PMCID: PMC9948804 DOI: 10.1016/j.bbamcr.2022.119366] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Intracellular Ca2+ signals are temporally controlled and spatially restricted. Signaling occurs adjacent to sites of Ca2+ entry and/or release, where Ca2+-dependent effectors and their substrates co-localize to form signaling microdomains. Here we review signaling by calcineurin, the Ca2+/calmodulin regulated protein phosphatase and target of immunosuppressant drugs, Cyclosporin A and FK506. Although well known for its activation of the adaptive immune response via NFAT dephosphorylation, systematic mapping of human calcineurin substrates and regulators reveals unexpected roles for this versatile phosphatase throughout the cell. We discuss calcineurin function, with an emphasis on where signaling occurs and mechanisms that target calcineurin and its substrates to signaling microdomains, especially binding of cognate short linear peptide motifs (SLiMs). Calcineurin is ubiquitously expressed and regulates events at the plasma membrane, other intracellular membranes, mitochondria, the nuclear pore complex and centrosomes/cilia. Based on our expanding knowledge of localized CN actions, we describe a cellular atlas of Ca2+/calcineurin signaling.
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Affiliation(s)
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA 94035, United States.
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8
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Tandl D, Sponagel T, Alansary D, Fuck S, Smit T, Hehlgans S, Jakob B, Fournier C, Niemeyer BA, Rödel F, Roth B, Moroni A, Thiel G. X-ray irradiation triggers immune response in human T-lymphocytes via store-operated Ca2+ entry and NFAT activation. J Gen Physiol 2022; 154:213138. [PMID: 35416945 PMCID: PMC9011325 DOI: 10.1085/jgp.202112865] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 09/25/2021] [Accepted: 02/11/2022] [Indexed: 12/30/2022] Open
Abstract
Radiation therapy efficiently eliminates cancer cells and reduces tumor growth. To understand collateral agonistic and antagonistic effects of this treatment on the immune system, we examined the impact of x-ray irradiation on human T cells. We find that, in a major population of leukemic Jurkat T cells and peripheral blood mononuclear cells, clinically relevant radiation doses trigger delayed oscillations of the cytosolic Ca2+ concentration. They are generated by store-operated Ca2+ entry (SOCE) following x-ray–induced clustering of Orai1 and STIM1 and formation of a Ca2+ release–activated Ca2+ (CRAC) channel. A consequence of the x-ray–triggered Ca2+ signaling cascade is translocation of the transcription factor nuclear factor of activated T cells (NFAT) from the cytosol into the nucleus, where it elicits the expression of genes required for immune activation. The data imply activation of blood immune cells by ionizing irradiation, with consequences for toxicity and therapeutic effects of radiation therapy.
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Affiliation(s)
- Dominique Tandl
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Tim Sponagel
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Dalia Alansary
- Molecular Biophysics, University of Saarland, Center for Integrative Physiology and Molecular Medicine, Homburg/Saar, Germany
| | - Sebastian Fuck
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Timo Smit
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Stephanie Hehlgans
- Department of Radiotherapy and Oncology, Goethe-University, Frankfurt am Main, Germany
| | - Burkhard Jakob
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt, Germany
| | - Claudia Fournier
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt, Germany
| | - Barbara A Niemeyer
- Molecular Biophysics, University of Saarland, Center for Integrative Physiology and Molecular Medicine, Homburg/Saar, Germany
| | - Franz Rödel
- Department of Radiotherapy and Oncology, Goethe-University, Frankfurt am Main, Germany
| | - Bastian Roth
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Anna Moroni
- Department of Biosciences and CNR IBF-Mi, Università degli Studi di Milano, Milano, Italy
| | - Gerhard Thiel
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
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9
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Chaklader M, Rothermel BA. Calcineurin in the heart: New horizons for an old friend. Cell Signal 2021; 87:110134. [PMID: 34454008 PMCID: PMC8908812 DOI: 10.1016/j.cellsig.2021.110134] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/10/2021] [Accepted: 08/23/2021] [Indexed: 01/20/2023]
Abstract
Calcineurin, also known as PP2B or PPP3, is a member of the PPP family of protein phosphatases that also includes PP1 and PP2A. Together these three phosphatases carryout the majority of dephosphorylation events in the heart. Calcineurin is distinct in that it is activated by the binding of calcium/calmodulin (Ca2+/CaM) and therefore acts as a node for integrating Ca2+ signals with changes in phosphorylation, two fundamental intracellular signaling cascades. In the heart, calcineurin is primarily thought of in the context of pathological cardiac remodeling, acting through the Nuclear Factor of Activated T-cell (NFAT) family of transcription factors. However, calcineurin activity is also essential for normal heart development and homeostasis in the adult heart. Furthermore, it is clear that NFAT-driven changes in transcription are not the only relevant processes initiated by calcineurin in the setting of pathological remodeling. There is a growing appreciation for the diversity of calcineurin substrates that can impact cardiac function as well as the diversity of mechanisms for targeting calcineurin to specific sub-cellular domains in cardiomyocytes and other cardiac cell types. Here, we will review the basics of calcineurin structure, regulation, and function in the context of cardiac biology. Particular attention will be given to: the development of improved tools to identify and validate new calcineurin substrates; recent studies identifying new calcineurin isoforms with unique properties and targeting mechanisms; and the role of calcineurin in cardiac development and regeneration.
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Affiliation(s)
- Malay Chaklader
- Departments of Internal Medicine (Division of Cardiology) and Molecular Biology, University of Texas Southwestern Medical Centre, Dallas, TX, USA
| | - Beverly A Rothermel
- Departments of Internal Medicine (Division of Cardiology) and Molecular Biology, University of Texas Southwestern Medical Centre, Dallas, TX, USA.
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10
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Williams RB, Johnson CN. A Review of Calcineurin Biophysics with Implications for Cardiac Physiology. Int J Mol Sci 2021; 22:ijms222111565. [PMID: 34768996 PMCID: PMC8583826 DOI: 10.3390/ijms222111565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/20/2022] Open
Abstract
Calcineurin, also known as protein phosphatase 2B, is a heterodimeric serine threonine phosphatase involved in numerous signaling pathways. During the past 50 years, calcineurin has been the subject of extensive investigation. Many of its cellular and physiological functions have been described, and the underlying biophysical mechanisms are the subject of active investigation. With the abundance of techniques and experimental designs utilized to study calcineurin and its numerous substrates, it is difficult to reconcile the available information. There have been a plethora of reports describing the role of calcineurin in cardiac disease. However, a physiological role of calcineurin in healthy cardiomyocyte function requires clarification. Here, we review the seminal biophysical and structural details that are responsible for the molecular function and inhibition of calcineurin. We then focus on literature describing the roles of calcineurin in cardiomyocyte physiology and disease.
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Affiliation(s)
- Ryan B. Williams
- Department of Chemistry, Mississippi State University, Starkville, MS 39759, USA;
| | - Christopher N. Johnson
- Department of Chemistry, Mississippi State University, Starkville, MS 39759, USA;
- Center for Arrhythmia Research and Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Correspondence:
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11
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Church TW, Tewatia P, Hannan S, Antunes J, Eriksson O, Smart TG, Hellgren Kotaleski J, Gold MG. AKAP79 enables calcineurin to directly suppress protein kinase A activity. eLife 2021; 10:e68164. [PMID: 34612814 PMCID: PMC8560092 DOI: 10.7554/elife.68164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 10/04/2021] [Indexed: 12/28/2022] Open
Abstract
Interplay between the second messengers cAMP and Ca2+ is a hallmark of dynamic cellular processes. A common motif is the opposition of the Ca2+-sensitive phosphatase calcineurin and the major cAMP receptor, protein kinase A (PKA). Calcineurin dephosphorylates sites primed by PKA to bring about changes including synaptic long-term depression (LTD). AKAP79 supports signaling of this type by anchoring PKA and calcineurin in tandem. In this study, we discovered that AKAP79 increases the rate of calcineurin dephosphorylation of type II PKA regulatory subunits by an order of magnitude. Fluorescent PKA activity reporter assays, supported by kinetic modeling, show how AKAP79-enhanced calcineurin activity enables suppression of PKA without altering cAMP levels by increasing PKA catalytic subunit capture rate. Experiments with hippocampal neurons indicate that this mechanism contributes toward LTD. This non-canonical mode of PKA regulation may underlie many other cellular processes.
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Affiliation(s)
- Timothy W Church
- Department of Neuroscience, Physiology & Pharmacology, University College LondonLondonUnited Kingdom
| | - Parul Tewatia
- Science for Life Laboratory, School of Electrical Engineering and Computer Science, KTH Royal Institute of TechnologyStockholmSweden
- Department of Neuroscience, Karolinska InstituteStockholmSweden
| | - Saad Hannan
- Department of Neuroscience, Physiology & Pharmacology, University College LondonLondonUnited Kingdom
| | - João Antunes
- Science for Life Laboratory, School of Electrical Engineering and Computer Science, KTH Royal Institute of TechnologyStockholmSweden
| | - Olivia Eriksson
- Science for Life Laboratory, School of Electrical Engineering and Computer Science, KTH Royal Institute of TechnologyStockholmSweden
| | - Trevor G Smart
- Department of Neuroscience, Physiology & Pharmacology, University College LondonLondonUnited Kingdom
| | - Jeanette Hellgren Kotaleski
- Science for Life Laboratory, School of Electrical Engineering and Computer Science, KTH Royal Institute of TechnologyStockholmSweden
- Department of Neuroscience, Karolinska InstituteStockholmSweden
| | - Matthew G Gold
- Department of Neuroscience, Physiology & Pharmacology, University College LondonLondonUnited Kingdom
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12
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Phloretin Alleviates Arsenic Trioxide-Induced Apoptosis of H9c2 Cardiomyoblasts via Downregulation in Ca 2+/Calcineurin/NFATc Pathway and Inflammatory Cytokine Release. Cardiovasc Toxicol 2021; 21:642-654. [PMID: 34037972 DOI: 10.1007/s12012-021-09655-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/27/2021] [Indexed: 01/25/2023]
Abstract
Arsenic trioxide (ATO) is among the first-line chemotherapeutic drugs for treating acute promyelocytic leukemia patients, but its clinical use is hampered due to cardiotoxicity. The present investigation unveils the mechanism underlying ATO-induced oxidative stress that promotes calcineurin (a ubiquitous Ca2+/calmodulin-dependent serine/threonine phosphatase expressed only during sustained Ca2+ elevation) expression, inflammatory cytokine release and apoptosis in H9c2 cardiomyoblasts, and its possible modulation with phloretin (PHL, an antioxidant polyphenol present in apple peel). ATO caused Ca2+ overload resulting in elevated expression of calcineurin and its downstream transcriptional effector NFATc causing the release of cytokines such as IL-2, IL-6, MCP-1, IFN-γ, and TNF-α in H9c2 cardiomyoblast. There was a visible increase in the nuclear fraction of NF-κB and ROS-mediated apoptotic cell death. The expression levels of cardiac-specific genes (troponin, desmin, and caveolin-3) and genes of the apoptotic signaling pathway (BCL-2, BAX, IGF1, AKT, ERK1, -2, RAF1, and JNK) in response to ATO and PHL were studied. The putative binding mode and the potential ligand-target interactions of PHL with calcineurin using docking software (Autodock and iGEMDOCKv2) showed the high binding affinity of PHL to calcineurin. PHL co-treatment significantly reduced Ca2+ influx and normalized the expression of calcineurin, NFATc, NF-κB, and other cytokines. PHL co-treatment resulted in activation of BCL-2, IGF1, AKT, RAF1, ERK1, and ERK2 and inhibition of BAX and JNK. Overall, these results revealed that PHL has a protective effect against ATO-induced apoptosis and we propose calcineurin as a druggable target for the interaction of PHL in ATO cardiotoxicity in H9c2 cells.
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Persechini A, Armbruster H, Keightley A. Investigating the landscape of intracellular [Ca 2+] in live cells by rapid photoactivated cross-linking of calmodulin-protein interactions. Cell Calcium 2021; 98:102450. [PMID: 34375924 DOI: 10.1016/j.ceca.2021.102450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 11/30/2022]
Abstract
The Ca2+ sensor protein calmodulin interacts in a Ca2+-dependent manner with a large number of proteins that among them encompass a diverse assortment of functions and subcellular localizations. A method for monitoring calmodulin-protein interactions as they occur throughout a living cell would thus uniquely enable investigations of the intracellular landscape of [Ca2+] and its relationship to cell function. We have developed such a method based on capture of calmodulin-protein interactions by rapid photoactivated cross-linking (t1/2 ∼7s) in cells stably expressing a tandem affinity tagged calmodulin that have been metabolically labeled with a photoreactive methionine analog. Tagged adducts are stringently enriched, and captured calmodulin interactors are then identified and quantified based on tandem mass spectrometry data for their tryptic peptides. In this paper we show that the capture behaviors of interactors in cells are consistent with the presence of basal microdomains of elevated [Ca2+]. Ca2+ sensitivities for capture were determined, and these suggest that [Ca2+] levels are above ∼1 μM in these regions. Although the microdomains appear to affect capture of most proteins, capture of some is at an apparent Ca2+-dependent maximum, suggesting they are targeted to the domains. Removal of extracellular Ca2+ has both immediate (5 min) and delayed (30 min) effects on capture, implying that the microdomains are supported by a combination of Ca2+ influx across the cell membrane and Ca2+ derived from internal stores. The known properties of the presumptive microdomain targeted proteins suggestroles in a variety of Ca2+-dependent basal metabolism and in formation and maintenance of the domains.
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Affiliation(s)
- Anthony Persechini
- Department of Cell and Molecular Biology and Biochemistry, School of Biological and Chemical Sciences, University of Missouri at Kansas City, 5007 Rockhill Road, Kansas City, MO, 64110, USA.
| | - Hailey Armbruster
- Department of Cell and Molecular Biology and Biochemistry, School of Biological and Chemical Sciences, University of Missouri at Kansas City, 5007 Rockhill Road, Kansas City, MO, 64110, USA
| | - Andrew Keightley
- Department of Cell and Molecular Biology and Biochemistry, School of Biological and Chemical Sciences, University of Missouri at Kansas City, 5007 Rockhill Road, Kansas City, MO, 64110, USA
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14
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Zhou M, Kamarshi V, Arvin AM, Oliver SL. Calcineurin phosphatase activity regulates Varicella-Zoster Virus induced cell-cell fusion. PLoS Pathog 2020; 16:e1009022. [PMID: 33216797 PMCID: PMC7717522 DOI: 10.1371/journal.ppat.1009022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 12/04/2020] [Accepted: 10/02/2020] [Indexed: 12/28/2022] Open
Abstract
Cell-cell fusion (abbreviated as cell fusion) is a characteristic pathology of medically important viruses, including varicella-zoster virus (VZV), the causative agent of chickenpox and shingles. Cell fusion is mediated by a complex of VZV glycoproteins, gB and gH-gL, and must be tightly regulated to enable skin pathogenesis based on studies with gB and gH hyperfusogenic VZV mutants. Although the function of gB and gH-gL in the regulation of cell fusion has been explored, whether host factors are directly involved in this regulation process is unknown. Here, we discovered host factors that modulated VZV gB/gH-gL mediated cell fusion via high-throughput screening of bioactive compounds with known cellular targets. Two structurally related non-antibiotic macrolides, tacrolimus and pimecrolimus, both significantly increased VZV gB/gH-gL mediated cell fusion. These compounds form a drug-protein complex with FKBP1A, which binds to calcineurin and specifically inhibits calcineurin phosphatase activity. Inhibition of calcineurin phosphatase activity also enhanced both herpes simplex virus-1 fusion complex and syncytin-1 mediated cell fusion, indicating a broad role of calcineurin in modulating this process. To characterize the role of calcineurin phosphatase activity in VZV gB/gH-gL mediated fusion, a series of biochemical, biological and infectivity assays was performed. Pimecrolimus-induced, enhanced cell fusion was significantly reduced by shRNA knockdown of FKBP1A, further supporting the role of calcineurin phosphatase activity in fusion regulation. Importantly, inhibition of calcineurin phosphatase activity during VZV infection caused exaggerated syncytia formation and suppressed virus propagation, which was consistent with the previously reported phenotypes of gB and gH hyperfusogenic VZV mutants. Seven host cell proteins that remained uniquely phosphorylated when calcineurin phosphatase activity was inhibited were identified as potential downstream factors involved in fusion regulation. These findings demonstrate that calcineurin is a critical host cell factor pivotal in the regulation of VZV induced cell fusion, which is essential for VZV pathogenesis.
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Affiliation(s)
- Momei Zhou
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Vivek Kamarshi
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ann M. Arvin
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Stefan L. Oliver
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
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15
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Hou YH, Hsu LH, Wang HF, Lai YH, Chen YL. Calcineurin Regulates Conidiation, Chlamydospore Formation and Virulence in Fusarium oxysporum f. sp. lycopersici. Front Microbiol 2020; 11:539702. [PMID: 33193126 PMCID: PMC7641966 DOI: 10.3389/fmicb.2020.539702] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 09/25/2020] [Indexed: 11/24/2022] Open
Abstract
Fusarium wilt of tomato caused by the ascomycetous fungus Fusarium oxysporum f. sp. lycopersici (Fol) is widespread in most tomato planting areas. Calcineurin is a heterodimeric calcium/calmodulin-dependent protein phosphatase comprised of catalytic (Cna1) and regulatory (Cnb1) subunits. Calcineurin has been studied extensively in human fungal pathogens, but less is known about its roles in plant fungal pathogens. It is known that calcineurin regulates fungal calcium signaling, growth, drug tolerance, and virulence. However, the roles of calcineurin in Fol have not yet been characterized. In this study, we deleted calcineurin CNA1 and CNB1 genes to characterize their roles in conidiation, chlamydospore formation and virulence in Fol. Our results revealed that both cna1 and cnb1 mutants show defects in calcineurin phosphatase activity, vegetative growth and conidiation as compared to the wild type. Furthermore, calcineurin mutants exhibited blunted and swollen hyphae as observed by scanning electron microscopy. Interestingly, we found that Fol calcineurin is critical for chlamydospore formation, a function of calcineurin previously undocumented in the fungal kingdom. According to transcriptome analysis, the expression of 323 and 414 genes was up- and down-regulated, respectively, in both cna1 and cnb1 mutants. Based on the pathogen infection assay, tomato plants inoculated with cna1 or cnb1 mutant have a dramatic reduction in disease severity, indicating that calcineurin has a vital role in Fol virulence. In conclusion, our findings suggest that Fol calcineurin is required, at least in part, for phosphatase activity, vegetative growth, conidiation, chlamydospore formation, and virulence.
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Affiliation(s)
- Yi-Hsuan Hou
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Li-Hang Hsu
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Hsuan-Fu Wang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Yu-Hsin Lai
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Ying-Lien Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
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Abstract
The serine/threonine phosphatase calcineurin acts as a crucial connection between calcium signaling the phosphorylation states of numerous important substrates. These substrates include, but are not limited to, transcription factors, receptors and channels, proteins associated with mitochondria, and proteins associated with microtubules. Calcineurin is activated by increases in intracellular calcium concentrations, a process that requires the calcium sensing protein calmodulin binding to an intrinsically disordered regulatory domain in the phosphatase. Despite having been studied for around four decades, the activation of calcineurin is not fully understood. This review largely focuses on what is known about the activation process and highlights aspects that are currently not understood. Video abstract.
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Affiliation(s)
- Trevor P Creamer
- Center for Structural Biology, Department of Molecular & Cellular Biochemistry, 741 S. Limestone Street, Lexington, KY, 40536-0509, USA.
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17
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Shoda W, Nomura N, Ando F, Tagashira H, Iwamoto T, Ohta A, Isobe K, Mori T, Susa K, Sohara E, Rai T, Uchida S. Sodium-calcium exchanger 1 is the key molecule for urinary potassium excretion against acute hyperkalemia. PLoS One 2020; 15:e0235360. [PMID: 32603346 PMCID: PMC7326190 DOI: 10.1371/journal.pone.0235360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 06/13/2020] [Indexed: 02/07/2023] Open
Abstract
The sodium (Na+)-chloride cotransporter (NCC) expressed in the distal convoluted tubule (DCT) is a key molecule regulating urinary Na+ and potassium (K+) excretion. We previously reported that high-K+ load rapidly dephosphorylated NCC and promoted urinary K+ excretion in mouse kidneys. This effect was inhibited by calcineurin (CaN) and calmodulin inhibitors. However, the detailed mechanism through which high-K+ signal results in CaN activation remains unknown. We used Flp-In NCC HEK293 cells and mice to evaluate NCC phosphorylation. We analyzed intracellular Ca2+ concentration ([Ca2+]in) using live cell Ca2+ imaging in HEK293 cells. We confirmed that high-K+-induced NCC dephosphorylation was not observed without CaN using Flp-In NCC HEK29 cells. Extracellular Ca2+ reduction with a Ca2+ chelator inhibited high-K+-induced increase in [Ca2+]in and NCC dephosphorylation. We focused on Na+/Ca2+ exchanger (NCX) 1, a bidirectional regulator of cytosolic Ca2+ expressed in DCT. We identified that NCX1 suppression with a specific inhibitor (SEA0400) or siRNA knockdown inhibited K+-induced increase in [Ca2+]in and NCC dephosphorylation. In a mouse study, SEA0400 treatment inhibited K+-induced NCC dephosphorylation. SEA0400 reduced urinary K+ excretion and induced hyperkalemia. Here, we identified NCX1 as a key molecule in urinary K+ excretion promoted by CaN activation and NCC dephosphorylation in response to K+ load.
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Affiliation(s)
- Wakana Shoda
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Naohiro Nomura
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
- * E-mail:
| | - Fumiaki Ando
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Hideaki Tagashira
- Department of pharmacology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Takahiro Iwamoto
- Department of pharmacology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Akihito Ohta
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Kiyoshi Isobe
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Takayasu Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Koichiro Susa
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Eisei Sohara
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Tatemitsu Rai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Shinichi Uchida
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
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18
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Roy J, Cyert MS. Identifying New Substrates and Functions for an Old Enzyme: Calcineurin. Cold Spring Harb Perspect Biol 2020; 12:a035436. [PMID: 31308145 PMCID: PMC7050593 DOI: 10.1101/cshperspect.a035436] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Biological processes are dynamically regulated by signaling networks composed of protein kinases and phosphatases. Calcineurin, or PP3, is a conserved phosphoserine/phosphothreonine-specific protein phosphatase and member of the PPP family of phosphatases. Calcineurin is unique, however, in its activation by Ca2+ and calmodulin. This ubiquitously expressed phosphatase controls Ca2+-dependent processes in all human tissues, but is best known for driving the adaptive immune response by dephosphorylating the nuclear factor of the activated T-cells (NFAT) family of transcription factors. Therefore, calcineurin inhibitors, FK506 (tacrolimus), and cyclosporin A serve as immunosuppressants. We describe some of the adverse effects associated with calcineurin inhibitors that result from inhibition of calcineurin in nonimmune tissues, illustrating the many functions of this enzyme that have yet to be elucidated. In fact, calcineurin has essential roles beyond the immune system, from yeast to humans, but since its discovery more than 30 years ago, only a small number of direct calcineurin substrates have been shown (∼75 proteins). This is because of limitations in current methods for identification of phosphatase substrates. Here we discuss recent insights into mechanisms of calcineurin activation and substrate recognition that have been critical in the development of novel approaches for identifying its targets systematically. Rather than comprehensively reviewing known functions of calcineurin, we highlight new approaches to substrate identification for this critical regulator that may reveal molecular mechanisms underlying toxicities caused by calcineurin inhibitor-based immunosuppression.
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Affiliation(s)
- Jagoree Roy
- Department of Biology, Stanford University, Stanford, California 94305-5020
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, California 94305-5020
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19
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Simplified calcium signaling cascade for synaptic plasticity. Neural Netw 2019; 123:38-51. [PMID: 31821949 DOI: 10.1016/j.neunet.2019.11.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 11/21/2019] [Accepted: 11/25/2019] [Indexed: 11/21/2022]
Abstract
We propose a model for synaptic plasticity based on a calcium signaling cascade. The model simplifies the full signaling pathways from a calcium influx to the phosphorylation (potentiation) and dephosphorylation (depression) of glutamate receptors that are gated by fictive C1 and C2 catalysts, respectively. This model is based on tangible chemical reactions, including fictive catalysts, for long-term plasticity rather than the conceptual theories commonplace in various models, such as preset thresholds of calcium concentration. Our simplified model successfully reproduced the experimental synaptic plasticity induced by different protocols such as (i) a synchronous pairing protocol and (ii) correlated presynaptic and postsynaptic action potentials (APs). Further, the ocular dominance plasticity (or the experimental verification of the celebrated Bienenstock-Cooper-Munro theory) was reproduced by two model synapses that compete by means of back-propagating APs (bAPs). The key to this competition is synapse-specific bAPs with reference to bAP-boosting on the physiological grounds.
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20
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Eriksson O, Jauhiainen A, Maad Sasane S, Kramer A, Nair AG, Sartorius C, Hellgren Kotaleski J. Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models. Bioinformatics 2019; 35:284-292. [PMID: 30010712 PMCID: PMC6330009 DOI: 10.1093/bioinformatics/bty607] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 07/10/2018] [Indexed: 11/14/2022] Open
Abstract
Motivation Dynamical models describing intracellular phenomena are increasing in size and complexity as more information is obtained from experiments. These models are often over-parameterized with respect to the quantitative data used for parameter estimation, resulting in uncertainty in the individual parameter estimates as well as in the predictions made from the model. Here we combine Bayesian analysis with global sensitivity analysis (GSA) in order to give better informed predictions; to point out weaker parts of the model that are important targets for further experiments, as well as to give guidance on parameters that are essential in distinguishing different qualitative output behaviours. Results We used approximate Bayesian computation (ABC) to estimate the model parameters from experimental data, as well as to quantify the uncertainty in this estimation (inverse uncertainty quantification), resulting in a posterior distribution for the parameters. This parameter uncertainty was next propagated to a corresponding uncertainty in the predictions (forward uncertainty propagation), and a GSA was performed on the predictions using the posterior distribution as the possible values for the parameters. This methodology was applied on a relatively large model relevant for synaptic plasticity, using experimental data from several sources. We could hereby point out those parameters that by themselves have the largest contribution to the uncertainty of the prediction as well as identify parameters important to separate between qualitatively different predictions. This approach is useful both for experimental design as well as model building. Availability and implementation Source code is freely available at https://github.com/alexjau/uqsa. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Olivia Eriksson
- Science for Life Laboratory, Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden.,Swedish e-Science Research Centre (SeRC), KTH Royal Institute of Technology, Stockholm, Sweden
| | - Alexandra Jauhiainen
- Biometrics, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | | | - Andrei Kramer
- Science for Life Laboratory, Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anu G Nair
- Science for Life Laboratory, Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Jeanette Hellgren Kotaleski
- Science for Life Laboratory, Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden.,Swedish e-Science Research Centre (SeRC), KTH Royal Institute of Technology, Stockholm, Sweden
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21
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Sun B, Vaughan D, Tikunova S, Creamer TP, Davis JP, Kekenes-Huskey PM. Calmodulin-Calcineurin Interaction beyond the Calmodulin-Binding Region Contributes to Calcineurin Activation. Biochemistry 2019; 58:4070-4085. [PMID: 31483613 DOI: 10.1021/acs.biochem.9b00626] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Calcineurin (CaN) is a calcium-dependent phosphatase involved in numerous signaling pathways. Its activation is in part driven by the binding of calmodulin (CaM) to a CaM recognition region (CaMBR) within CaN's regulatory domain (RD). However, secondary interactions between CaM and the CaN RD may be necessary to fully activate CaN. Specifically, it is established that the CaN RD folds upon CaM binding and a region C-terminal to CaMBR, the "distal helix", assumes an α-helix fold and contributes to activation [Dunlap, T. B., et al. (2013) Biochemistry 52, 8643-8651]. We hypothesized in that previous study that this distal helix can bind CaM in a region distinct from the canonical CaMBR. To test this hypothesis, we utilized molecular simulations, including replica-exchange molecular dynamics, protein-protein docking, and computational mutagenesis, to determine potential distal helix-binding sites on CaM's surface. We isolated a potential binding site on CaM (site D) that facilitates moderate-affinity interprotein interactions and predicted that mutation of site D residues K30 and G40 on CaM would weaken CaN distal helix binding. We experimentally confirmed that two variants (K30E and G40D) indicate weaker binding of a phosphate substrate p-nitrophenyl phosphate to the CaN catalytic site by a phosphatase assay. This weakened substrate affinity is consistent with competitive binding of the CaN autoinhibition domain to the catalytic site, which we suggest is due to the weakened distal helix-CaM interactions. This study therefore suggests a novel mechanism for CaM regulation of CaN that may extend to other CaM targets.
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Affiliation(s)
- Bin Sun
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40506 , United States
| | - Darin Vaughan
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40506 , United States
| | - Svetlana Tikunova
- Department of Physiology and Cell Biology , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Trevor P Creamer
- Center for Structural Biology and Department of Molecular & Cellular Biochemistry , University of Kentucky , Lexington , Kentucky 40536 , United States
| | - Jonathan P Davis
- Department of Physiology and Cell Biology , The Ohio State University , Columbus , Ohio 43210 , United States
| | - P M Kekenes-Huskey
- Department of Chemical and Materials Engineering , University of Kentucky , Lexington , Kentucky 40506 , United States.,Department of Cell and Molecular Physiology , Loyola University Chicago , Maywood , Illinois 60153 , United States
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22
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Lin W, Shi C, Wang W, Wu H, Yang C, Wang A, Shen X, Tian Y, Cao P, Yuan W. Osmolarity and calcium regulate connective tissue growth factor (CTGF/CCN2) expression in nucleus pulposus cells. Gene 2019; 704:15-24. [PMID: 30965128 DOI: 10.1016/j.gene.2019.04.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/26/2019] [Accepted: 04/05/2019] [Indexed: 10/27/2022]
Abstract
OBJECTIVE The objective of our study was to verify the hypothesis that the expression of connective tissue growth factor (CTGF/CCN2), a key molecule essential for the maintenance of nucleus pulposus (NP) matrix homeostasis, is regulated by osmolarity and intracellular calcium in NP cells. METHODS Gene and protein expression levels of CCN2 were assessed using quantitative real-time PCR and western blot. Transfections and dual luciferase assays were performed to measure the effect of hyperosmolarity, tonicity enhancer binding protein (TonEBP) and Ca2+-calcineurin (Cn)-NFAT signaling on CCN2 promoter activity. RESULTS Cultured in hyperosmotic media, there was a significant decrease in the levels of CCN2 promoter activity, gene and protein expression in NP cells. The JASPAR database was used to analyze the construction of human CCN2 promoter, we found conserved TonE and NFAT binding sites. We then investigated whether TonEBP controlled CCN2 expression. Forced expression of TonEBP in NP cells showed that TonEBP negatively regulated CCN2 promoter activity, while suppression of TonEBP induced CCN2 promoter activity and expression. We then examined if Ca2+-Cn-NFAT signaling participated in the regulation of CCN2 expression. Co-expression of CCN2 reporter with individual NFAT1-4 expression plasmids and/or calcineurin A/B constructs suggested this signaling pathway played a role in the regulation of CCN2expression in NP cells. CONCLUSIONS Results of these studies illustrated that the expression of CCN2 in NP cells was regulated by the NFAT family through a signaling pathway network involving both activator (Ca2+-Cn-NFAT signaling) and suppressor (Hyperosmolarity-TonEBP) molecules.
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Affiliation(s)
- Wenbo Lin
- Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
| | - Changgui Shi
- Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
| | - Weiheng Wang
- Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
| | - Huiqiao Wu
- Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
| | - Chen Yang
- Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - An Wang
- Department of Orthopaedics, Shanghai Armed Police Force Hospital, Shanghai 201103, China
| | - Xiaolong Shen
- Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Ye Tian
- Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Peng Cao
- Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
| | - Wen Yuan
- Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
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23
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Limpitikul WB, Greenstein JL, Yue DT, Dick IE, Winslow RL. A bilobal model of Ca 2+-dependent inactivation to probe the physiology of L-type Ca 2+ channels. J Gen Physiol 2018; 150:1688-1701. [PMID: 30470716 PMCID: PMC6279366 DOI: 10.1085/jgp.201812115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/01/2018] [Accepted: 10/26/2018] [Indexed: 12/20/2022] Open
Abstract
L-type calcium channels undergo Ca2+-dependent inactivation (CDI) in order to precisely control the entry of Ca2+ into cells such as cardiomyocytes. Limpitikul et al. develop a bilobal model of CDI and use it to understand the pathogenesis of arrhythmias associated with mutations in CaM. L-type calcium channels (LTCCs) are critical elements of normal cardiac function, playing a major role in orchestrating cardiac electrical activity and initiating downstream signaling processes. LTCCs thus use feedback mechanisms to precisely control calcium (Ca2+) entry into cells. Of these, Ca2+-dependent inactivation (CDI) is significant because it shapes cardiac action potential duration and is essential for normal cardiac rhythm. This important form of regulation is mediated by a resident Ca2+ sensor, calmodulin (CaM), which is comprised of two lobes that are each capable of responding to spatially distinct Ca2+ sources. Disruption of CaM-mediated CDI leads to severe forms of long-QT syndrome (LQTS) and life-threatening arrhythmias. Thus, a model capable of capturing the nuances of CaM-mediated CDI would facilitate increased understanding of cardiac (patho)physiology. However, one critical barrier to achieving a detailed kinetic model of CDI has been the lack of quantitative data characterizing CDI as a function of Ca2+. This data deficit stems from the experimental challenge of uncoupling the effect of channel gating on Ca2+ entry. To overcome this obstacle, we use photo-uncaging of Ca2+ to deliver a measurable Ca2+ input to CaM/LTCCs, while simultaneously recording CDI. Moreover, we use engineered CaMs with Ca2+ binding restricted to a single lobe, to isolate the kinetic response of each lobe. These high-resolution measurements enable us to build mathematical models for each lobe of CaM, which we use as building blocks for a full-scale bilobal model of CDI. Finally, we use this model to probe the pathogenesis of LQTS associated with mutations in CaM (calmodulinopathies). Each of these models accurately recapitulates the kinetics and steady-state properties of CDI in both physiological and pathological states, thus offering powerful new insights into the mechanistic alterations underlying cardiac arrhythmias.
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Affiliation(s)
- Worawan B Limpitikul
- Calcium Signals Laboratory, Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Joseph L Greenstein
- Institute for Computational Medicine, Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD
| | - David T Yue
- Calcium Signals Laboratory, Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ivy E Dick
- Calcium Signals Laboratory, Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD .,Department of Physiology, University of Maryland School of Medicine, Baltimore, MD
| | - Raimond L Winslow
- Institute for Computational Medicine, Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD
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Singh D, Bhalla US. Subunit exchange enhances information retention by CaMKII in dendritic spines. eLife 2018; 7:e41412. [PMID: 30418153 PMCID: PMC6286124 DOI: 10.7554/elife.41412] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 11/09/2018] [Indexed: 12/15/2022] Open
Abstract
Molecular bistables are strong candidates for long-term information storage, for example, in synaptic plasticity. Calcium/calmodulin-dependent protein Kinase II (CaMKII) is a highly expressed synaptic protein which has been proposed to form a molecular bistable switch capable of maintaining its state for years despite protein turnover and stochastic noise. It has recently been shown that CaMKII holoenzymes exchange subunits among themselves. Here, we used computational methods to analyze the effect of subunit exchange on the CaMKII pathway in the presence of diffusion in two different micro-environments, the post synaptic density (PSD) and spine cytosol. We show that CaMKII exhibits multiple timescales of activity due to subunit exchange. Further, subunit exchange enhances information retention by CaMKII both by improving the stability of its switching in the PSD, and by slowing the decay of its activity in the spine cytosol. The existence of diverse timescales in the synapse has important theoretical implications for memory storage in networks.
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Affiliation(s)
- Dilawar Singh
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBangaloreIndia
| | - Upinder Singh Bhalla
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBangaloreIndia
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25
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Schober R, Waldherr L, Schmidt T, Graziani A, Stilianu C, Legat L, Groschner K, Schindl R. STIM1 and Orai1 regulate Ca 2+ microdomains for activation of transcription. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1866:1079-1091. [PMID: 30408546 DOI: 10.1016/j.bbamcr.2018.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 02/07/2023]
Abstract
Since calcium (Ca2+) regulates a large variety of cellular signaling processes in a cell's life, precise control of Ca2+ concentrations within the cell is essential. This enables the transduction of information via Ca2+ changes in a time-dependent and spatially defined manner. Here, we review molecular and functional aspects of how the store-operated Ca2+ channel Orai1 creates spatiotemporal Ca2+ microdomains. The architecture of this channel is unique, with a long helical pore and a six-fold symmetry. Energetic barriers within the Ca2+ channel pathway limit permeation to allow an extensive local Ca2+ increase in close proximity to the channel. The precise timing of the Orai1 channel function is controlled by direct binding to STIM proteins upon Ca2+ depletion in the endoplasmic reticulum. These induced Ca2+ microdomains are tailored to, and sufficient for, triggering long-term activation processes, such as transcription factor activation and subsequent gene regulation. We describe the principles of spatiotemporal activation of the transcription factor NFAT and compare its signaling characteristics to those of the autophagy regulating transcription factors, MITF and TFEB.
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Affiliation(s)
- Romana Schober
- Institute for Biophysics, Johannes Kepler University Linz, A-4040 Linz, Austria.
| | - Linda Waldherr
- Gottfried Schatz Research Center, Medical University of Graz, A-8010 Graz, Austria
| | - Tony Schmidt
- Gottfried Schatz Research Center, Medical University of Graz, A-8010 Graz, Austria
| | - Annarita Graziani
- Gottfried Schatz Research Center, Medical University of Graz, A-8010 Graz, Austria
| | - Clemens Stilianu
- Gottfried Schatz Research Center, Medical University of Graz, A-8010 Graz, Austria
| | - Lorenz Legat
- Gottfried Schatz Research Center, Medical University of Graz, A-8010 Graz, Austria
| | - Klaus Groschner
- Gottfried Schatz Research Center, Medical University of Graz, A-8010 Graz, Austria
| | - Rainer Schindl
- Gottfried Schatz Research Center, Medical University of Graz, A-8010 Graz, Austria.
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26
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Gudlur A, Zeraik AE, Hirve N, Rajanikanth V, Bobkov AA, Ma G, Zheng S, Wang Y, Zhou Y, Komives EA, Hogan PG. Calcium sensing by the STIM1 ER-luminal domain. Nat Commun 2018; 9:4536. [PMID: 30382093 PMCID: PMC6208404 DOI: 10.1038/s41467-018-06816-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 09/26/2018] [Indexed: 12/22/2022] Open
Abstract
Stromal interaction molecule 1 (STIM1) monitors ER-luminal Ca2+ levels to maintain cellular Ca2+ balance and to support Ca2+ signalling. The prevailing view has been that STIM1 senses reduced ER Ca2+ through dissociation of bound Ca2+ from a single EF-hand site, which triggers a dramatic loss of secondary structure and dimerization of the STIM1 luminal domain. Here we find that the STIM1 luminal domain has 5-6 Ca2+-binding sites, that binding at these sites is energetically coupled to binding at the EF-hand site, and that Ca2+ dissociation controls a switch to a second structured conformation of the luminal domain rather than protein unfolding. Importantly, the other luminal-domain Ca2+-binding sites interact with the EF-hand site to control physiological activation of STIM1 in cells. These findings fundamentally revise our understanding of physiological Ca2+ sensing by STIM1, and highlight molecular mechanisms that govern the Ca2+ threshold for activation and the steep Ca2+ concentration dependence.
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Affiliation(s)
- Aparna Gudlur
- Division of Signalling and Gene Expression, La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA
| | - Ana Eliza Zeraik
- Division of Signalling and Gene Expression, La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, CEP 13563-120, SP, Brazil
| | - Nupura Hirve
- Division of Signalling and Gene Expression, La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA
| | - V Rajanikanth
- Division of Signalling and Gene Expression, La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA
- H Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Andrey A Bobkov
- Protein Production and Analysis Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Guolin Ma
- Center for Translational Cancer Research, Institute of Biosciences & Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Sisi Zheng
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Youjun Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences & Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, 92037, USA
| | - Patrick G Hogan
- Division of Signalling and Gene Expression, La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA.
- Program in Immunology, University of California-San Diego, La Jolla, CA, 92037, USA.
- Moores Cancer Center, University of California-San Diego, La Jolla, CA, 92093, USA.
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Olivares-Florez S, Czolbe M, Riediger F, Seidlmayer L, Williams T, Nordbeck P, Strasen J, Glocker C, Jänsch M, Eder-Negrin P, Arias-Loza P, Mühlfelder M, Plačkić J, Heinze KG, Molkentin JD, Engelhardt S, Kockskämper J, Ritter O. Nuclear calcineurin is a sensor for detecting Ca2+ release from the nuclear envelope via IP3R. J Mol Med (Berl) 2018; 96:1239-1249. [DOI: 10.1007/s00109-018-1701-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 09/10/2018] [Accepted: 09/27/2018] [Indexed: 10/28/2022]
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Tarasova EO, Gaydukov AE, Balezina OP. Calcineurin and Its Role in Synaptic Transmission. BIOCHEMISTRY (MOSCOW) 2018; 83:674-689. [PMID: 30195324 DOI: 10.1134/s0006297918060056] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Calcineurin (CaN) is a serine/threonine phosphatase widely expressed in different cell types and structures including neurons and synapses. The most studied role of CaN is its involvement in the functioning of postsynaptic structures of central synapses. The role of CaN in the presynaptic structures of central and peripheral synapses is less understood, although it has generated a considerable interest and is a subject of a growing number of studies. The regulatory role of CaN in synaptic vesicle endocytosis in the synapse terminals is actively studied. In recent years, new targets of CaN have been identified and its role in the regulation of enzymes and neurotransmitter secretion in peripheral neuromuscular junctions has been revealed. CaN is the only phosphatase that requires calcium and calmodulin for activation. In this review, we present details of CaN molecular structure and give a detailed description of possible mechanisms of CaN activation involving calcium, enzymes, and endogenous and exogenous inhibitors. Known and newly discovered CaN targets at pre- and postsynaptic levels are described. CaN activity in synaptic structures is discussed in terms of functional involvement of this phosphatase in synaptic transmission and neurotransmitter release.
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Affiliation(s)
- E O Tarasova
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia
| | - A E Gaydukov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia. .,Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - O P Balezina
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia
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29
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Pharris MC, Patel NM, Kinzer-Ursem TL. Competitive Tuning Among Ca 2+/Calmodulin-Dependent Proteins: Analysis of in silico Model Robustness and Parameter Variability. Cell Mol Bioeng 2018; 11:353-365. [PMID: 31105797 DOI: 10.1007/s12195-018-0549-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Introduction Calcium/Calmodulin-dependent (Ca2+/CaM-dependent) regulation of protein signaling has long been recognized for its importance in a number of physiological contexts. Found in almost all eukaryotic cells, Ca2+/CaM-dependent signaling participates in muscle development, immune responses, cardiac myocyte function and regulation of neuronal connectivity. In excitatory neurons, dynamic changes in the strength of synaptic connections, known as synaptic plasticity, occur when calcium ions (Ca2+) flux through NMDA receptors and bind the Ca2+-sensor calmodulin (CaM). Ca2+/CaM, in turn, regulates downstream protein signaling in actin polymerization, receptor trafficking, and transcription factor activation.The activation of downstream Ca2+/CaM-dependent binding proteins (CBPs) is a function of the frequency of Ca2+ flux, such that each CBP is preferentially "tuned" to different Ca2+ input signals. We have recently reported that competition among CBPs for CaM binding is alone sufficient to recreate in silico the observed in vivo frequency-dependence of several CBPs. However, CBP activation may strongly depend on the identity and concentration of proteins that constitute the competitive pool; with important implications in the regulation of CBPs in both normal and disease states. Methods Here, we extend our previous deterministic model of competition among CBPs to include phosphodiesterases, AMPAR receptors that are important in synaptic plasticity, and enzymatic function of CBPs: cAMP regulation, kinase activity, and phosphatase activity. After rigorous parameterization and validation by global sensitivity analysis using Latin Hypercube Sampling (LHS) and Partial Rank Correlation Coefficients (PRCC), we explore how perturbing the competitive pool of CBPs influences downstream signaling events. In particular, we hypothesize that although perturbations may decrease activation of one CBP, increased activation of a separate, but enzymatically-related CBP could compensate for this loss, providing a homeostatic effect. Results and Conclusions First we compare dynamic model output of two models: a two-state model of Ca2+/CaM binding and a four-state model of Ca2+/CaM binding. We find that a four-state model of Ca2+/CaM binding best captures the dynamic nature of the rapid response of CaM and CBPs to Ca2+ flux in the system. Using global sensitivity analysis, we find that model output is robust to parameter variability. Indeed, although variations in the expression of the CaM buffer neurogranin (Ng) may cause a decrease in Ca2+/CaM-dependent kinase II (CaMKII) activation, overall AMPA receptor phosphorylation is preserved; ostensibly by a concomitant increase in adenylyl cyclase 8 (AC8)-mediated activation of protein kinase A (PKA). Indeed phosphorylation of AMPAR receptors by CaMKII and PKA is robust across a wide range of Ng concentrations, though increases in AMPAR phosphorylation is seen at low Ng levels approaching zero. Our results may explain recent counter-intuitive results in neurogranin knockout mice and provide further evidence that competitive tuning is an important mechanism in synaptic plasticity. These results may be readily translated to other Ca2+/CaM-dependent signaling systems in other cell types and can be used to suggest targeted experimental investigation to explain counter-intuitive or unexpected downstream signaling outcomes.Tamara Kinzer-Ursem is an Assistant Professor in the Weldon School of Biomedical Engineering. She received her B.S. in Bioengineering from the University of Toledo and her M.S. and Ph.D. degrees in Chemical Engineering from the University of Michigan, and her post-doctoral training in Molecular Neuroscience at the California Institute of Technology. Prior to joining Purdue she was the Head of R&D in Biochemistry at Maven Biotechnologies and Visiting Associate in Chemical Engineering at the California Institute of Technology.Research in the Kinzer-Ursem lab focuses on developing tools to advance quantitative descriptions of cellular processes and disease within three areas of expertise: 1) Using particle diffusivity measurements to quantify biomolecular processes. Particle diffusometry is being used as a sensitive biosensor to detect the presence of pathogens in environmental and patient samples. 2) Development of novel protein tagging technologies that are used to label proteins in vivo to enable quantitative description of protein function and elucidate disease mechanisms. 3) Computational modeling of signal transduction mechanisms to understand cellular processes. Using computational techniques, we have recently described "competitive tuning" as a mechanism that might be used to regulate information transfer through protein networks, with implications in cell behavior and drug target analysis.
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Affiliation(s)
- Matthew C Pharris
- Weldon School of Biomedical Engineering, Purdue University, 260 South Martin Jischke Drive, West Lafayette, IN 47907 USA
| | - Neal M Patel
- Weldon School of Biomedical Engineering, Purdue University, 260 South Martin Jischke Drive, West Lafayette, IN 47907 USA
| | - Tamara L Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, 260 South Martin Jischke Drive, West Lafayette, IN 47907 USA
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30
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Penny CJ, Gold MG. Mechanisms for localising calcineurin and CaMKII in dendritic spines. Cell Signal 2018; 49:46-58. [DOI: 10.1016/j.cellsig.2018.05.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 10/14/2022]
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31
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MicroRNA interactome analysis predicts post-transcriptional regulation of ADRB2 and PPP3R1 in the hypercholesterolemic myocardium. Sci Rep 2018; 8:10134. [PMID: 29973623 PMCID: PMC6031673 DOI: 10.1038/s41598-018-27740-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/07/2018] [Indexed: 02/06/2023] Open
Abstract
Little is known about the molecular mechanism including microRNAs (miRNA) in hypercholesterolemia-induced cardiac dysfunction. We aimed to explore novel hypercholesterolemia-induced pathway alterations in the heart by an unbiased approach based on miRNA omics, target prediction and validation. With miRNA microarray we identified forty-seven upregulated and ten downregulated miRNAs in hypercholesterolemic rat hearts compared to the normocholesterolemic group. Eleven mRNAs with at least 4 interacting upregulated miRNAs were selected by a network theoretical approach, out of which 3 mRNAs (beta-2 adrenergic receptor [Adrb2], calcineurin B type 1 [Ppp3r1] and calcium/calmodulin-dependent serine protein kinase [Cask]) were validated with qRT-PCR and Western blot. In hypercholesterolemic hearts, the expression of Adrb2 mRNA was significantly decreased. ADRB2 and PPP3R1 protein were significantly downregulated in hypercholesterolemic hearts. The direct interaction of Adrb2 with upregulated miRNAs was demonstrated by luciferase reporter assay. Gene ontology analysis revealed that the majority of the predicted mRNA changes may contribute to the hypercholesterolemia-induced cardiac dysfunction. In summary, the present unbiased target prediction approach based on global cardiac miRNA expression profiling revealed for the first time in the literature that both the mRNA and protein product of Adrb2 and PPP3R1 protein are decreased in the hypercholesterolemic heart.
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Nie B, Liu C, Bai X, Chen X, Wu S, Zhang S, Huang Z, Xie M, Xu T, Xin W, Zeng W, Ouyang H. AKAP150 involved in paclitaxel-induced neuropathic pain via inhibiting CN/NFAT2 pathway and downregulating IL-4. Brain Behav Immun 2018; 68:158-168. [PMID: 29056557 DOI: 10.1016/j.bbi.2017.10.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 10/03/2017] [Accepted: 10/17/2017] [Indexed: 12/31/2022] Open
Abstract
Antitubulin chemotherapeutics agents, such as paclitaxel, are effective chemotherapy drugs for cancer treatment. However, painful neuropathy is a major adverse effect limiting the wider application of chemotherapeutics. In this study, we found that A-kinase anchor protein 150 (AKAP150) was significantly upregulated after paclitaxel injection. Inhibition of AKAP150 via siRNA or AKAP150flox/flox in rodents alleviated the pain behavior induced by paclitaxel, and partly restored the decreased calcineurin (CN) phosphatase activity after paclitaxel treatment. Paclitaxel decreased the expression of anti-inflammatory cytokine interleukin-4 (IL-4), and intrathecal injections of IL-4 effectively alleviated paclitaxel-induced hypersensitivity and the frequency of dorsal root ganglion (DRG) neurons action potential. The decreased CN enzyme activity, resulted in reduced protein expression of nuclear factor of activated T cells 2 (NFAT2) in cell nuclei. Chromatin immunoprecipitation showed that, NFAT2 binds to the IL-4 gene promoter regulating the protein expression of IL-4. Overexpression of NFAT2 by intrathecal injection of the AAV5-NFAT2-GFP virus alleviated the pain behavior induced by paclitaxel via increasing the expression of IL-4. Knocked down AKAP150 by siRNA or AAV5-Cre-GFP partly restored the expression of IL-4 in DRG. Our results indicated that regulation of IL-4 via the CN/NFAT2 pathway mediated by AKAP150 could be a pivotal treatment target for paclitaxel-induced neuropathic pain and or other neuropsychiatric disorders.
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Affiliation(s)
- Bilin Nie
- Department of Anesthesiology, Guangdong Women and Children Hospital, Guangzhou, China; Department of Anesthesiology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Cuicui Liu
- Department of Rehabilitation Medicine and Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaohui Bai
- Department of Rehabilitation Medicine and Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaodi Chen
- Department of Anesthesiology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Shaoyong Wu
- Department of Anesthesiology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Subo Zhang
- Department of Rehabilitation Medicine and Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhuxi Huang
- Department of Rehabilitation Medicine and Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Manxiu Xie
- Department of Anesthesiology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Ting Xu
- Zhongshan Medicine School, Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-sen University, Guangzhou, China.
| | - Wenjun Xin
- Zhongshan Medicine School, Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-sen University, Guangzhou, China
| | - Weian Zeng
- Department of Anesthesiology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Handong Ouyang
- Department of Anesthesiology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
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Romano DR, Pharris MC, Patel NM, Kinzer-Ursem TL. Competitive tuning: Competition's role in setting the frequency-dependence of Ca2+-dependent proteins. PLoS Comput Biol 2017; 13:e1005820. [PMID: 29107982 PMCID: PMC5690689 DOI: 10.1371/journal.pcbi.1005820] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 11/16/2017] [Accepted: 10/13/2017] [Indexed: 01/20/2023] Open
Abstract
A number of neurological disorders arise from perturbations in biochemical signaling and protein complex formation within neurons. Normally, proteins form networks that when activated produce persistent changes in a synapse’s molecular composition. In hippocampal neurons, calcium ion (Ca2+) flux through N-methyl-D-aspartate (NMDA) receptors activates Ca2+/calmodulin signal transduction networks that either increase or decrease the strength of the neuronal synapse, phenomena known as long-term potentiation (LTP) or long-term depression (LTD), respectively. The calcium-sensor calmodulin (CaM) acts as a common activator of the networks responsible for both LTP and LTD. This is possible, in part, because CaM binding proteins are “tuned” to different Ca2+ flux signals by their unique binding and activation dynamics. Computational modeling is used to describe the binding and activation dynamics of Ca2+/CaM signal transduction and can be used to guide focused experimental studies. Although CaM binds over 100 proteins, practical limitations cause many models to include only one or two CaM-activated proteins. In this work, we view Ca2+/CaM as a limiting resource in the signal transduction pathway owing to its low abundance relative to its binding partners. With this view, we investigate the effect of competitive binding on the dynamics of CaM binding partner activation. Using an explicit model of Ca2+, CaM, and seven highly-expressed hippocampal CaM binding proteins, we find that competition for CaM binding serves as a tuning mechanism: the presence of competitors shifts and sharpens the Ca2+ frequency-dependence of CaM binding proteins. Notably, we find that simulated competition may be sufficient to recreate the in vivo frequency dependence of the CaM-dependent phosphatase calcineurin. Additionally, competition alone (without feedback mechanisms or spatial parameters) could replicate counter-intuitive experimental observations of decreased activation of Ca2+/CaM-dependent protein kinase II in knockout models of neurogranin. We conclude that competitive tuning could be an important dynamic process underlying synaptic plasticity. Learning and memory formation are likely associated with dynamic fluctuations in the connective strength of neuronal synapses. These fluctuations, called synaptic plasticity, are regulated by calcium ion (Ca2+) influx through ion channels localized to the post-synaptic membrane. Within the post-synapse, the dominant Ca2+ sensor protein, calmodulin (CaM), may activate a variety of downstream binding partners, each contributing to synaptic plasticity outcomes. The conditions at which certain binding partners most strongly activate are increasingly studied using computational models. Nearly all computational studies describe these binding partners in combinations of only one or two CaM binding proteins. In contrast, we combine seven well-studied CaM binding partners into a single model wherein they simultaneously compete for access to CaM. Our dynamic model suggests that competition narrows the window of conditions for optimal activation of some binding partners, mimicking the Ca2+-frequency dependence of some proteins in vivo. Further characterization of CaM-dependent signaling dynamics in neuronal synapses may benefit our understanding of learning and memory formation. Furthermore, we propose that competitive binding may be another framework, alongside feedback and feed-forward loops, signaling motifs, and spatial localization, that can be applied to other signal transduction networks, particularly second messenger cascades, to explain the dynamical behavior of protein activation.
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Affiliation(s)
- Daniel R. Romano
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, United States of America
| | - Matthew C. Pharris
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, United States of America
| | - Neal M. Patel
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, United States of America
| | - Tamara L. Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, United States of America
- * E-mail:
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Bond R, Ly N, Cyert MS. The unique C terminus of the calcineurin isoform CNAβ1 confers non-canonical regulation of enzyme activity by Ca 2+ and calmodulin. J Biol Chem 2017; 292:16709-16721. [PMID: 28842480 PMCID: PMC5633132 DOI: 10.1074/jbc.m117.795146] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 08/17/2017] [Indexed: 11/06/2022] Open
Abstract
Calcineurin, the conserved Ca2+/calmodulin-regulated phosphatase and target of immunosuppressants, plays important roles in the circulatory, nervous, and immune systems. Calcineurin activity strictly depends on Ca2+ and Ca2+-bound calmodulin (Ca2+/CaM) to relieve autoinhibition of the catalytic subunit (CNA) by its C terminus. The C terminus contains two regulatory domains, the autoinhibitory domain (AID) and calmodulin-binding domain (CBD), which block the catalytic center and a conserved substrate-binding groove, respectively. However, this mechanism cannot apply to CNAβ1, an atypical CNA isoform generated by alternative 3'-end processing, whose divergent C terminus shares the CBD common to all isoforms, but lacks the AID. We present the first biochemical characterization of CNAβ1, which is ubiquitously expressed and conserved in vertebrates. We identify a distinct C-terminal autoinhibitory four-residue sequence in CNAβ1, 462LAVP465, which competitively inhibits substrate dephosphorylation. In vitro and cell-based assays revealed that the CNAβ1-containing holoenzyme, CNβ1, is autoinhibited at a single site by either of two inhibitory regions, CBD and LAVP, which block substrate access to the substrate-binding groove. We found that the autoinhibitory segment (AIS), located within the CBD, is progressively removed by Ca2+ and Ca2+/CaM, whereas LAVP remains engaged. This regulatory strategy conferred higher basal and Ca2+-dependent activity to CNβ1, decreasing its dependence on CaM, but also limited maximal enzyme activity through persistence of LAVP-mediated autoinhibiton during Ca2+/CaM stimulation. These regulatory properties may underlie observed differences between the biological activities of CNβ1 and canonical CNβ2. Our insights lay the groundwork for further studies of CNβ1, whose physiological substrates are currently unknown.
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Affiliation(s)
- Rachel Bond
- From the Department of Biology, Stanford University, Stanford, California 94305-5020
| | - Nina Ly
- From the Department of Biology, Stanford University, Stanford, California 94305-5020
| | - Martha S Cyert
- From the Department of Biology, Stanford University, Stanford, California 94305-5020
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35
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Yadav DK, Tata SR, Hunt J, Cook EC, Creamer TP, Fitzkee NC. 1H, 15N, and 13C chemical shift assignments of the regulatory domain of human calcineurin. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:215-219. [PMID: 28803387 PMCID: PMC5693698 DOI: 10.1007/s12104-017-9751-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 08/05/2017] [Indexed: 06/01/2023]
Abstract
Calcineurin (CaN) plays an important role in T-cell activation, cardiac system development and nervous system function. Previous studies have demonstrated that the regulatory domain (RD) of CaN binds calmodulin (CaM) towards the N-terminal end. Calcium-loaded CaM activates the serine/threonine phosphatase activity of CaN by binding to the RD, although the mechanistic details of this interaction remain unclear. It is thought that CaM binding at the RD displaces the auto-inhibitory domain (AID) from the active site of CaN, activating phosphatase activity. In the absence of calcium-loaded CaM, the RD is disordered, and binding of CaM induces folding in the RD. In order to provide mechanistic detail about the CaM-CaN interaction, we have undertaken an NMR study of the RD of CaN. Complete 13C, 15N and 1H assignments of the RD of CaN were obtained using solution NMR spectroscopy. The backbone of RD has been assigned using a combination of 13C-detected CON-IPAP experiments as well as traditional HNCO, HNCA, HNCOCA and HNCACB-based 3D NMR spectroscopy. A 15N-resolved TOCSY experiment has been used to assign Hα and Hβ chemical shifts.
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Affiliation(s)
- Dinesh K Yadav
- Department of Chemistry, Mississippi State University, Hand Lab 1115, 310 Presidents Circle, Mississippi State, MS, 39762, USA
| | - Sri Ramya Tata
- Department of Chemistry, Mississippi State University, Hand Lab 1115, 310 Presidents Circle, Mississippi State, MS, 39762, USA
| | - John Hunt
- Department of Chemistry, Mississippi State University, Hand Lab 1115, 310 Presidents Circle, Mississippi State, MS, 39762, USA
| | - Erik C Cook
- Department of Molecular and Cellular Biochemistry, Center for Structural Biology, University of Kentucky, Lexington, USA
| | - Trevor P Creamer
- Department of Molecular and Cellular Biochemistry, Center for Structural Biology, University of Kentucky, Lexington, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Hand Lab 1115, 310 Presidents Circle, Mississippi State, MS, 39762, USA.
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Yildirim V, Bertram R. Calcium Oscillation Frequency-Sensitive Gene Regulation and Homeostatic Compensation in Pancreatic β-Cells. Bull Math Biol 2017; 79:1295-1324. [PMID: 28497293 DOI: 10.1007/s11538-017-0286-1] [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] [Received: 01/25/2017] [Accepted: 04/27/2017] [Indexed: 02/03/2023]
Abstract
Pancreatic islet [Formula: see text]-cells are electrically excitable cells that secrete insulin in an oscillatory fashion when the blood glucose concentration is at a stimulatory level. Insulin oscillations are the result of cytosolic [Formula: see text] oscillations that accompany bursting electrical activity of [Formula: see text]-cells and are physiologically important. ATP-sensitive [Formula: see text] channels (K(ATP) channels) play the key role in setting the overall activity of the cell and in driving bursting, by coupling cell metabolism to the membrane potential. In humans, when there is a defect in K(ATP) channel function, [Formula: see text]-cells fail to respond appropriately to changes in the blood glucose level, and electrical and [Formula: see text] oscillations are lost. However, mice compensate for K(ATP) channel defects in islet [Formula: see text]-cells by employing alternative mechanisms to maintain electrical and [Formula: see text] oscillations. In a recent study, we showed that in mice islets in which K(ATP) channels are genetically knocked out another [Formula: see text] current, provided by inward-rectifying [Formula: see text] channels, is increased. With mathematical modeling, we demonstrated that a sufficient upregulation in these channels can account for the paradoxical electrical bursting and [Formula: see text] oscillations observed in these [Formula: see text]-cells. However, the question of determining the correct level of upregulation that is necessary for this compensation remained unanswered, and this question motivates the current study. [Formula: see text] is a well-known regulator of gene expression, and several examples have been shown of genes that are sensitive to the frequency of the [Formula: see text] signal. In this mathematical modeling study, we demonstrate that a [Formula: see text] oscillation frequency-sensitive gene transcription network can adjust the gene expression level of a compensating [Formula: see text] channel so as to rescue electrical bursting and [Formula: see text] oscillations in a model [Formula: see text]-cell in which the key K(ATP) current is removed. This is done without the prescription of a target [Formula: see text] level, but evolves naturally as a consequence of the feedback between the [Formula: see text]-dependent enzymes and the cell's electrical activity. More generally, the study indicates how [Formula: see text] can provide the link between gene expression and cellular electrical activity that promotes wild-type behavior in a cell following gene knockout.
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Affiliation(s)
- Vehpi Yildirim
- Department of Mathematics, Florida State University, Tallahassee, FL, 32306, USA
| | - Richard Bertram
- Department of Mathematics and Programs in Molecular Biophysics and Neuroscience, Florida State University, Tallahassee, FL, 32306, USA.
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Zhang X, Wang C, Zhao J, Xu J, Geng Y, Dai L, Huang Y, Fu SC, Dai K, Zhang X. miR-146a facilitates osteoarthritis by regulating cartilage homeostasis via targeting Camk2d and Ppp3r2. Cell Death Dis 2017; 8:e2734. [PMID: 28383548 PMCID: PMC5477577 DOI: 10.1038/cddis.2017.146] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/25/2017] [Accepted: 03/01/2017] [Indexed: 12/17/2022]
Abstract
Osteoarthritis (OA), characterized by insufficient extracellular matrix synthesis and cartilage degeneration, is known as an incurable disease because its pathogenesis is poorly elucidated. Thus far, limited information is available regarding the pathophysiological role of microRNAs (miRNAs) in OA. In this study, we investigated the specific function of miR-146a in OA pathophysiology using mouse OA models. We found that the articular cartilage degeneration of miR-146a knockout (KO) mice was alleviated compared with that of the wild-type (WT) mice in spontaneous and instability-induced OA models. We demonstrate that miR-146a aggravated pro-inflammatory cytokines induced suppressing the expression of cartilage matrix-associated genes. We further identified calcium/calmodulin-dependent protein kinase II delta (Camk2d) and protein phosphatase 3, regulatory subunit B, beta isoform (Ppp3r2, also known as calcineurin B, type II) were essential targets of miR-146a in regulating cartilage homeostasis. Moreover, we found that surgical-induced OA mice treated with a miR-146a inhibitor significantly alleviated the destruction of articular cartilage via targeting Camk2d and Ppp3r2. These results suggested that miR-146a has a crucial role in maintaining cartilage homeostasis. MiR-146a inhibition in chondrocytes can be a potential therapeutic strategy to ameliorate OA.
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Affiliation(s)
- Xudong Zhang
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chuandong Wang
- Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingyu Zhao
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiajia Xu
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yiyun Geng
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Liming Dai
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan Huang
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Sai-Chuen Fu
- Department of Orthopaedics and Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Hong kong, China
| | - Kerong Dai
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoling Zhang
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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38
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Parra V, Rothermel BA. Calcineurin signaling in the heart: The importance of time and place. J Mol Cell Cardiol 2017; 103:121-136. [PMID: 28007541 PMCID: PMC5778886 DOI: 10.1016/j.yjmcc.2016.12.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 12/12/2016] [Accepted: 12/16/2016] [Indexed: 12/20/2022]
Abstract
The calcium-activated protein phosphatase, calcineurin, lies at the intersection of protein phosphorylation and calcium signaling cascades, where it provides an essential nodal point for coordination between these two fundamental modes of intracellular communication. In excitatory cells, such as neurons and cardiomyocytes, that experience rapid and frequent changes in cytoplasmic calcium, calcineurin protein levels are exceptionally high, suggesting that these cells require high levels of calcineurin activity. Yet, it is widely recognized that excessive activation of calcineurin in the heart contributes to pathological hypertrophic remodeling and the progression to failure. How does a calcium activated enzyme function in the calcium-rich environment of the continuously contracting heart without pathological consequences? This review will discuss the wide range of calcineurin substrates relevant to cardiovascular health and the mechanisms calcineurin uses to find and act on appropriate substrates in the appropriate location while potentially avoiding others. Fundamental differences in calcineurin signaling in neonatal verses adult cardiomyocytes will be addressed as well as the importance of maintaining heterogeneity in calcineurin activity across the myocardium. Finally, we will discuss how circadian oscillations in calcineurin activity may facilitate integration with other essential but conflicting processes, allowing a healthy heart to reap the benefits of calcineurin signaling while avoiding the detrimental consequences of sustained calcineurin activity that can culminate in heart failure.
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Affiliation(s)
- Valentina Parra
- Advanced Centre for Chronic Disease (ACCDiS), Facultad Ciencias Quimicas y Farmaceuticas, Universidad de Chile, Santiago,Chile; Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Quimicas y Farmaceuticas, Universidad de Chie, Santiago, Chile
| | - Beverly A Rothermel
- Department of Internal Medicine (Cardiology Division), University of Texas Southwestern Medical Centre, Dallas, TX, USA; Department of Molecular Biology, University of Texas Southwestern Medical Centre, Dallas, TX, USA.
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Beck JR, Truong T, Stains CI. Temporal Analysis of PP2A Phosphatase Activity During Insulin Stimulation Using a Direct Activity Probe. ACS Chem Biol 2016; 11:3284-3288. [PMID: 27805358 DOI: 10.1021/acschembio.6b00697] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein serine/threonine phosphatases (PSPs) are ubiquitously expressed in mammalian cells. In particular, PP2A accounts for up to 1% of the total protein within cells. Despite clear evidence for the role of PP2A in cellular signaling, there is a lack of information concerning the magnitude and temporal dynamics of PP2A catalytic activity during insulin stimulation. Herein, we describe the development of a direct, fluorescent activity probe capable of reporting on global changes in PP2A enzymatic activity in unfractionated cell lysates. Utilizing this new probe, we profiled the magnitude as well as temporal dynamics of PP2A activity during insulin stimulation of liver hepatocytes. These results provide direct evidence for the rapid response of PP2A catalytic activity to extracellular stimulation, as well as insight into the complex regulation of phosphorylation levels by opposing kinase and phosphatase activities within the cell. This study provides a new tool for investigating the chemical biology of PSPs.
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Affiliation(s)
- Jon R. Beck
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Tiffany Truong
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Cliff I. Stains
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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40
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Dumitrescu AS, Evans MD, Grubb MS. Evaluating Tools for Live Imaging of Structural Plasticity at the Axon Initial Segment. Front Cell Neurosci 2016; 10:268. [PMID: 27932952 PMCID: PMC5120105 DOI: 10.3389/fncel.2016.00268] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/04/2016] [Indexed: 11/20/2022] Open
Abstract
The axon initial segment (AIS) is a specialized neuronal compartment involved in the maintenance of axo-dendritic polarity and in the generation of action potentials. It is also a site of significant structural plasticity—manipulations of neuronal activity in vitro and in vivo can produce changes in AIS position and/or size that are associated with alterations in intrinsic excitability. However, to date all activity-dependent AIS changes have been observed in experiments carried out on fixed samples, offering only a snapshot, population-wide view of this form of plasticity. To extend these findings by following morphological changes at the AIS of individual neurons requires reliable means of labeling the structure in live preparations. Here, we assessed five different immunofluorescence-based and genetically-encoded tools for live-labeling the AIS of dentate granule cells (DGCs) in dissociated hippocampal cultures. We found that an antibody targeting the extracellular domain of neurofascin provided accurate live label of AIS structure at baseline, but could not follow rapid activity-dependent changes in AIS length. Three different fusion constructs of GFP with full-length AIS proteins also proved unsuitable: while neurofascin-186-GFP and NaVβ4-GFP did not localize to the AIS in our experimental conditions, overexpressing 270kDa-AnkyrinG-GFP produced abnormally elongated AISs in mature neurons. In contrast, a genetically-encoded construct consisting of a voltage-gated sodium channel intracellular domain fused to yellow fluorescent protein (YFP-NaVII–III) fulfilled all of our criteria for successful live AIS label: this construct specifically localized to the AIS, accurately revealed plastic changes at the structure within hours, and, crucially, did not alter normal cell firing properties. We therefore recommend this probe for future studies of live AIS plasticity in vitro and in vivo.
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Affiliation(s)
- Adna S Dumitrescu
- Centre for Developmental Neurobiology, King's College London London, UK
| | - Mark D Evans
- Centre for Developmental Neurobiology, King's College London London, UK
| | - Matthew S Grubb
- Centre for Developmental Neurobiology, King's College London London, UK
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41
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Naoki H, Nishiyama M, Togashi K, Igarashi Y, Hong K, Ishii S. Multi-phasic bi-directional chemotactic responses of the growth cone. Sci Rep 2016; 6:36256. [PMID: 27808115 PMCID: PMC5093620 DOI: 10.1038/srep36256] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 10/12/2016] [Indexed: 11/23/2022] Open
Abstract
The nerve growth cone is bi-directionally attracted and repelled by the same cue molecules depending on the situations, while other non-neural chemotactic cells usually show uni-directional attraction or repulsion toward their specific cue molecules. However, how the growth cone differs from other non-neural cells remains unclear. Toward this question, we developed a theory for describing chemotactic response based on a mathematical model of intracellular signaling of activator and inhibitor. Our theory was first able to clarify the conditions of attraction and repulsion, which are determined by balance between activator and inhibitor, and the conditions of uni- and bi-directional responses, which are determined by dose-response profiles of activator and inhibitor to the guidance cue. With biologically realistic sigmoidal dose-responses, our model predicted tri-phasic turning response depending on intracellular Ca2+ level, which was then experimentally confirmed by growth cone turning assays and Ca2+ imaging. Furthermore, we took a reverse-engineering analysis to identify balanced regulation between CaMKII (activator) and PP1 (inhibitor) and then the model performance was validated by reproducing turning assays with inhibitions of CaMKII and PP1. Thus, our study implies that the balance between activator and inhibitor underlies the multi-phasic bi-directional turning response of the growth cone.
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Affiliation(s)
- Honda Naoki
- Graduate School of Medicine, Kyoto University, Sakyo, Kyoto, Japan.,Imaging Platform for Spatio-temporal Information, Kyoto University, Sakyo, Kyoto, Japan
| | - Makoto Nishiyama
- Department of Biochemistry, New York University School of Medicine, New York, USA.,Kasah Technology Inc. New York, New York, USA
| | - Kazunobu Togashi
- Department of Biochemistry, New York University School of Medicine, New York, USA
| | | | - Kyonsoo Hong
- Department of Biochemistry, New York University School of Medicine, New York, USA.,Kasah Technology Inc. New York, New York, USA
| | - Shin Ishii
- Imaging Platform for Spatio-temporal Information, Kyoto University, Sakyo, Kyoto, Japan.,Graduate School of Informatics, Kyoto University, Sakyo, Kyoto, Japan
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Nair AG, Bhalla US, Hellgren Kotaleski J. Role of DARPP-32 and ARPP-21 in the Emergence of Temporal Constraints on Striatal Calcium and Dopamine Integration. PLoS Comput Biol 2016; 12:e1005080. [PMID: 27584878 PMCID: PMC5008828 DOI: 10.1371/journal.pcbi.1005080] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/22/2016] [Indexed: 01/06/2023] Open
Abstract
In reward learning, the integration of NMDA-dependent calcium and dopamine by striatal projection neurons leads to potentiation of corticostriatal synapses through CaMKII/PP1 signaling. In order to elicit the CaMKII/PP1-dependent response, the calcium and dopamine inputs should arrive in temporal proximity and must follow a specific (dopamine after calcium) order. However, little is known about the cellular mechanism which enforces these temporal constraints on the signal integration. In this computational study, we propose that these temporal requirements emerge as a result of the coordinated signaling via two striatal phosphoproteins, DARPP-32 and ARPP-21. Specifically, DARPP-32-mediated signaling could implement an input-interval dependent gating function, via transient PP1 inhibition, thus enforcing the requirement for temporal proximity. Furthermore, ARPP-21 signaling could impose the additional input-order requirement of calcium and dopamine, due to its Ca2+/calmodulin sequestering property when dopamine arrives first. This highlights the possible role of phosphoproteins in the temporal aspects of striatal signal transduction. A response towards an environmental stimulus could be reinforced if it elicits a reward. On the subcellular level, the environmental stimulus and the reward signal lead to a transient increase in striatal calcium- and dopamine-signaling, respectively. The integration of calcium and dopamine signals, which is important for reward-learning, could elicit a downstream response only if they are close in time and arrive in correct order (first calcium and then dopamine). This study proposes that the requirement for the input signals to be temporally close and in correct order could emerge due to the coordinated signaling via two striatal phosphoproteins, DARPP-32 and ARPP-21. The DARPP-32 signaling implements an input-interval dependent gating function and ARPP-21 implements an input-order dependent threshold-like function. Thus, a molecular mechanism has been presented here which could explain the emergence of important temporal aspects of subcellular signal integration in reward-learning.
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Affiliation(s)
- Anu G. Nair
- Science for Life Laboratory, School of Computer Science and Communication, KTH Royal Institute of Technology, Stockholm, Sweden
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
- Manipal University, Manipal, India
| | - Upinder S. Bhalla
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Jeanette Hellgren Kotaleski
- Science for Life Laboratory, School of Computer Science and Communication, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Neuroscience, Karolinska Institutet, Solna, Sweden
- * E-mail:
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43
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Stochastic Induction of Long-Term Potentiation and Long-Term Depression. Sci Rep 2016; 6:30899. [PMID: 27485552 PMCID: PMC4971485 DOI: 10.1038/srep30899] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/10/2016] [Indexed: 01/23/2023] Open
Abstract
Long-term depression (LTD) and long-term potentiation (LTP) of granule-Purkinje cell synapses are persistent synaptic alterations induced by high and low rises of the intracellular calcium ion concentration ([Ca2+]), respectively. The occurrence of LTD involves the activation of a positive feedback loop formed by protein kinase C, phospholipase A2, and the extracellular signal-regulated protein kinase pathway, and its expression comprises the reduction of the population of synaptic AMPA receptors. Recently, a stochastic computational model of these signalling processes demonstrated that, in single synapses, LTD is probabilistic and bistable. Here, we expanded this model to simulate LTP, which requires protein phosphatases and the increase in the population of synaptic AMPA receptors. Our results indicated that, in single synapses, while LTD is bistable, LTP is gradual. Ca2+ induced both processes stochastically. The magnitudes of the Ca2+ signals and the states of the signalling network regulated the likelihood of LTP and LTD and defined dynamic macroscopic Ca2+ thresholds for the synaptic modifications in populations of synapses according to an inverse Bienenstock, Cooper and Munro (BCM) rule or a sigmoidal function. In conclusion, our model presents a unifying mechanism that explains the macroscopic properties of LTP and LTD from their dynamics in single synapses.
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Modelling intracellular competition for calcium: kinetic and thermodynamic control of different molecular modes of signal decoding. Sci Rep 2016; 6:23730. [PMID: 27033299 PMCID: PMC4817061 DOI: 10.1038/srep23730] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/14/2016] [Indexed: 02/06/2023] Open
Abstract
Frequently, a common chemical entity triggers opposite cellular processes, which implies that the components of signalling networks must detect signals not only through their chemical natures, but also through their dynamic properties. To gain insights on the mechanisms of discrimination of the dynamic properties of cellular signals, we developed a computational stochastic model and investigated how three calcium ion (Ca2+)-dependent enzymes (adenylyl cyclase (AC), phosphodiesterase 1 (PDE1), and calcineurin (CaN)) differentially detect Ca2+ transients in a hippocampal dendritic spine. The balance among AC, PDE1 and CaN might determine the occurrence of opposite Ca2+-induced forms of synaptic plasticity, long-term potentiation (LTP) and long-term depression (LTD). CaN is essential for LTD. AC and PDE1 regulate, indirectly, protein kinase A, which counteracts CaN during LTP. Stimulations of AC, PDE1 and CaN with artificial and physiological Ca2+ signals demonstrated that AC and CaN have Ca2+ requirements modulated dynamically by different properties of the signals used to stimulate them, because their interactions with Ca2+ often occur under kinetic control. Contrarily, PDE1 responds to the immediate amplitude of different Ca2+ transients and usually with the same Ca2+ requirements observed under steady state. Therefore, AC, PDE1 and CaN decode different dynamic properties of Ca2+ signals.
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Chay A, Zamparo I, Koschinski A, Zaccolo M, Blackwell KT. Control of βAR- and N-methyl-D-aspartate (NMDA) Receptor-Dependent cAMP Dynamics in Hippocampal Neurons. PLoS Comput Biol 2016; 12:e1004735. [PMID: 26901880 PMCID: PMC4763502 DOI: 10.1371/journal.pcbi.1004735] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 01/05/2016] [Indexed: 11/18/2022] Open
Abstract
Norepinephrine, a neuromodulator that activates β-adrenergic receptors (βARs), facilitates learning and memory as well as the induction of synaptic plasticity in the hippocampus. Several forms of long-term potentiation (LTP) at the Schaffer collateral CA1 synapse require stimulation of both βARs and N-methyl-D-aspartate receptors (NMDARs). To understand the mechanisms mediating the interactions between βAR and NMDAR signaling pathways, we combined FRET imaging of cAMP in hippocampal neuron cultures with spatial mechanistic modeling of signaling pathways in the CA1 pyramidal neuron. Previous work implied that cAMP is synergistically produced in the presence of the βAR agonist isoproterenol and intracellular calcium. In contrast, we show that when application of isoproterenol precedes application of NMDA by several minutes, as is typical of βAR-facilitated LTP experiments, the average amplitude of the cAMP response to NMDA is attenuated compared with the response to NMDA alone. Models simulations suggest that, although the negative feedback loop formed by cAMP, cAMP-dependent protein kinase (PKA), and type 4 phosphodiesterase may be involved in attenuating the cAMP response to NMDA, it is insufficient to explain the range of experimental observations. Instead, attenuation of the cAMP response requires mechanisms upstream of adenylyl cyclase. Our model demonstrates that Gs-to-Gi switching due to PKA phosphorylation of βARs as well as Gi inhibition of type 1 adenylyl cyclase may underlie the experimental observations. This suggests that signaling by β-adrenergic receptors depends on temporal pattern of stimulation, and that switching may represent a novel mechanism for recruiting kinases involved in synaptic plasticity and memory. Noradrenaline is a stress related molecule that facilitates learning and memory when released in the hippocampus. The facilitation of memory is related to modulation of synaptic plasticity, but the mechanisms underlying this modulation are not well understood. We utilize a combination of live cell imaging and computational modeling to discover how noradrenergic receptor stimulation interacts with other molecules, such as calcium, required for synaptic plasticity and memory storage. Though prior work has shown that noradrenergic receptors and calcium interact synergistically to elevate intracellular second messengers when combined simultaneously, our results demonstrate that prior stimulation of noradrenergic receptors inhibits the elevation of intracellular second messengers. Our results further demonstrate that the inhibition may be caused by the noradrenergic receptor switching signaling pathways, thereby recruiting a different set of memory kinases. This switching represents a novel mechanism for recruiting molecules involved in synaptic plasticity and memory.
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Affiliation(s)
- Andrew Chay
- Molecular Neuroscience Department, Krasnow Institute, George Mason University, Fairfax, Virginia, United States of America
| | | | - Andreas Koschinski
- Department of Physiology, Anatomy and Genetics, Oxford University, Oxford, United Kingdom
| | - Manuela Zaccolo
- Department of Physiology, Anatomy and Genetics, Oxford University, Oxford, United Kingdom
| | - Kim T. Blackwell
- Molecular Neuroscience Department, Krasnow Institute, George Mason University, Fairfax, Virginia, United States of America
- * E-mail:
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Cooperative autoinhibition and multi-level activation mechanisms of calcineurin. Cell Res 2016; 26:336-49. [PMID: 26794871 DOI: 10.1038/cr.2016.14] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/12/2015] [Accepted: 11/27/2015] [Indexed: 11/08/2022] Open
Abstract
The Ca(2+)/calmodulin-dependent protein phosphatase calcineurin (CN), a heterodimer composed of a catalytic subunit A and an essential regulatory subunit B, plays critical functions in various cellular processes such as cardiac hypertrophy and T cell activation. It is the target of the most widely used immunosuppressants for transplantation, tacrolimus (FK506) and cyclosporin A. However, the structure of a large part of the CNA regulatory region remains to be determined, and there has been considerable debate concerning the regulation of CN activity. Here, we report the crystal structure of full-length CN (β isoform), which revealed a novel autoinhibitory segment (AIS) in addition to the well-known autoinhibitory domain (AID). The AIS nestles in a hydrophobic intersubunit groove, which overlaps the recognition site for substrates and immunosuppressant-immunophilin complexes. Indeed, disruption of this AIS interaction results in partial stimulation of CN activity. More importantly, our biochemical studies demonstrate that calmodulin does not remove AID from the active site, but only regulates the orientation of AID with respect to the catalytic core, causing incomplete activation of CN. Our findings challenge the current model for CN activation, and provide a better understanding of molecular mechanisms of CN activity regulation.
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Kulkarni C, Lo M, Fraseur JG, Tirrell DA, Kinzer-Ursem TL. Bioorthogonal Chemoenzymatic Functionalization of Calmodulin for Bioconjugation Applications. Bioconjug Chem 2015; 26:2153-60. [PMID: 26431265 DOI: 10.1021/acs.bioconjchem.5b00449] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Calmodulin (CaM) is a widely studied Ca(2+)-binding protein that is highly conserved across species and involved in many biological processes, including vesicle release, cell proliferation, and apoptosis. To facilitate biophysical studies of CaM, researchers have tagged and mutated CaM at various sites, enabling its conjugation to fluorophores, microarrays, and other reactive partners. However, previous attempts to add a reactive label to CaM for downstream studies have generally employed nonselective labeling methods or resulted in diminished CaM function. Here we report the first engineered CaM protein that undergoes site-specific and bioorthogonal labeling while retaining wild-type activity levels. By employing a chemoenzymatic labeling approach, we achieved selective and quantitative labeling of the engineered CaM protein with an N-terminal 12-azidododecanoic acid tag; notably, addition of the tag did not interfere with the ability of CaM to bind Ca(2+) or a partner protein. The specificity of our chemoenzymatic labeling approach also allowed for selective conjugation of CaM to reactive partners in bacterial cell lysates, without intermediate purification of the engineered protein. Additionally, we prepared CaM-affinity resins that were highly effective in purifying a representative CaM-binding protein, demonstrating that the engineered CaM remains active even after surface capture. Beyond studies of CaM and CaM-binding proteins, the protein engineering and surface capture methods described here should be translatable to other proteins and other bioconjugation applications.
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Affiliation(s)
- Chethana Kulkarni
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Blvd., Pasadena, California 91125, United States
| | - Megan Lo
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Blvd., Pasadena, California 91125, United States
| | - Julia G Fraseur
- Weldon School of Biomedical Engineering, Purdue University , 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Blvd., Pasadena, California 91125, United States
| | - Tamara L Kinzer-Ursem
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Blvd., Pasadena, California 91125, United States.,Weldon School of Biomedical Engineering, Purdue University , 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
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48
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Bazzazi H, Sang L, Dick IE, Joshi-Mukherjee R, Yang W, Yue DT. Novel fluorescence resonance energy transfer-based reporter reveals differential calcineurin activation in neonatal and adult cardiomyocytes. J Physiol 2015; 593:3865-84. [PMID: 26096996 PMCID: PMC4575574 DOI: 10.1113/jp270510] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/16/2015] [Indexed: 12/26/2022] Open
Abstract
Novel fluorescence resonance energy transfer-based genetically encoded reporters of calcineurin are constructed by fusing the two subunits of calcineurin with P2A-based linkers retaining the expected native conformation of calcineurin. Calcineurin reporters display robust responses to calcium transients in HEK293 cells. The sensor responses are correlated with NFATc1 translocation dynamics in HEK293 cells. The sensors are uniformly distributed in neonatal myocytes and respond efficiently to single electrically evoked calcium transients and show cumulative activation at frequencies of 0.5 and 1 Hz. In adult myocytes, the calcineurin sensors appear to be localized to the cardiac z-lines, and respond to cumulative calcium transients at frequencies of 0.5 and 1 Hz. The phosphatase calcineurin is a central component of many calcium signalling pathways, relaying calcium signals from the plasma membrane to the nucleus. It has critical functions in a multitude of systems, including immune, cardiac and neuronal. Given the widespread importance of calcineurin in both normal and pathological conditions, new tools that elucidate the spatiotemporal dynamics of calcineurin activity would be invaluable. Here we develop two separate genetically encoded fluorescence resonance energy transfer (FRET)-based sensors of calcineurin activation, DuoCaN and UniCaN. Both sensors showcase a large dynamic range and rapid response kinetics, differing primarily in the linker structure between the FRET pairs. Both sensors were calibrated in HEK293 cells and their responses correlated well with NFAT translocation to the nucleus, validating the biological relevance of the sensor readout. The sensors were subsequently expressed in neonatal rat ventricular myocytes and acutely isolated adult guinea pig ventricular myocytes. Both sensors demonstrated robust responses in myocytes and revealed kinetic differences in calcineurin activation during changes in pacing rate for neonatal versus adult myocytes. Finally, mathematical modelling combined with quantitative FRET measurements provided novel insights into the kinetics and integration of calcineurin activation in response to myocyte Ca transients. In all, DuoCaN and UniCaN stand as valuable new tools for understanding the role of calcineurin in normal and pathological signalling.
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Affiliation(s)
- Hojjat Bazzazi
- Departments of Biomedical Engineering and Neuroscience, Centre for Cell Dynamics, Johns Hopkins University School of MedicineBaltimore, MD, USA
| | - Lingjie Sang
- Departments of Biomedical Engineering and Neuroscience, Centre for Cell Dynamics, Johns Hopkins University School of MedicineBaltimore, MD, USA
| | - Ivy E Dick
- Departments of Biomedical Engineering and Neuroscience, Centre for Cell Dynamics, Johns Hopkins University School of MedicineBaltimore, MD, USA
| | - Rosy Joshi-Mukherjee
- Departments of Biomedical Engineering and Neuroscience, Centre for Cell Dynamics, Johns Hopkins University School of MedicineBaltimore, MD, USA
| | - Wanjun Yang
- Departments of Biomedical Engineering and Neuroscience, Centre for Cell Dynamics, Johns Hopkins University School of MedicineBaltimore, MD, USA
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Marshall CB, Nishikawa T, Osawa M, Stathopulos PB, Ikura M. Calmodulin and STIM proteins: Two major calcium sensors in the cytoplasm and endoplasmic reticulum. Biochem Biophys Res Commun 2015; 460:5-21. [PMID: 25998729 DOI: 10.1016/j.bbrc.2015.01.106] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 01/22/2015] [Indexed: 01/22/2023]
Abstract
The calcium (Ca(2+)) ion is a universal signalling messenger which plays vital physiological roles in all eukaryotes. To decode highly regulated intracellular Ca(2+) signals, cells have evolved a number of sensor proteins that are ideally adapted to respond to a specific range of Ca(2+) levels. Among many such proteins, calmodulin (CaM) is a multi-functional cytoplasmic Ca(2+) sensor with a remarkable ability to interact with and regulate a plethora of structurally diverse target proteins. CaM achieves this 'multi-talented' functionality through two EF-hand domains, each with an independent capacity to bind targets, and an adaptable flexible linker. By contrast, stromal interaction molecule-1 and -2 (STIMs) have evolved for a specific role in endoplasmic reticulum (ER) Ca(2+) sensing using EF-hand machinery analogous to CaM; however, whereas CaM structurally adjusts to dissimilar binding partners, STIMs use the EF-hand machinery to self-regulate the stability of the Ca(2+) sensing domain. The molecular mechanisms underlying the Ca(2+)-dependent signal transduction by CaM and STIMs have revealed a remarkable repertoire of actions and underscore the flexibility of nature in molecular evolution and adaption to discrete Ca(2+) levels. Recent genomic sequencing efforts have uncovered a number of disease-associated mutations in both CaM and STIM1. This article aims to highlight the most recent key structural and functional findings in the CaM and STIM fields, and discusses how these two Ca(2+) sensor proteins execute their biological functions.
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Affiliation(s)
- Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Tadateru Nishikawa
- Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo, 113-0033, Japan
| | - Peter B Stathopulos
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada.
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, M5G 1L7, Canada.
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Shou J, Jing J, Xie J, You L, Jing Z, Yao J, Han W, Pan H. Nuclear factor of activated T cells in cancer development and treatment. Cancer Lett 2015; 361:174-84. [PMID: 25766658 DOI: 10.1016/j.canlet.2015.03.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/04/2015] [Accepted: 03/04/2015] [Indexed: 01/03/2023]
Abstract
Since nuclear factor of activated T cells (NFAT) was first identified as a transcription factor in T cells, various NFAT isoforms have been discovered and investigated. Accumulating studies have suggested that NFATs are involved in many aspects of cancer, including carcinogenesis, cancer cell proliferation, metastasis, drug resistance and tumor microenvironment. Different NFAT isoforms have distinct functions in different cancers. The exact function of NFAT in cancer or the tumor microenvironment is context dependent. In this review, we summarize our current knowledge of NFAT regulation and function in cancer development and treatment. NFATs have emerged as a potential target for cancer prevention and therapy.
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Affiliation(s)
- Jiawei Shou
- Department of Medical Oncology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jing Jing
- Department of Medical Oncology, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jiansheng Xie
- Laboratory of Cancer Biology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liangkun You
- Department of Medical Oncology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhao Jing
- Department of Medical Oncology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Junlin Yao
- Department of Medical Oncology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Weidong Han
- Department of Medical Oncology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Laboratory of Cancer Biology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Hongming Pan
- Department of Medical Oncology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Laboratory of Cancer Biology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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