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Hildebrandt ER, Sarkar A, Ravishankar R, Kim JH, Schmidt WK. Evaluating protein prenylation of human and viral CaaX sequences using a humanized yeast system. Dis Model Mech 2024; 17:dmm050516. [PMID: 38818856 PMCID: PMC11152559 DOI: 10.1242/dmm.050516] [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: 09/19/2023] [Accepted: 04/23/2024] [Indexed: 06/01/2024] Open
Abstract
Prenylated proteins are prevalent in eukaryotic biology (∼1-2% of proteins) and are associated with human disease, including cancer, premature aging and infections. Prenylated proteins with a C-terminal CaaX sequence are targeted by CaaX-type prenyltransferases and proteases. To aid investigations of these enzymes and their targets, we developed Saccharomyces cerevisiae strains that express these human enzymes instead of their yeast counterparts. These strains were developed in part to explore human prenyltransferase specificity because of findings that yeast FTase has expanded specificity for sequences deviating from the CaaX consensus (i.e. atypical sequence and length). The humanized yeast strains displayed robust prenyltransferase activity against CaaX sequences derived from human and pathogen proteins containing typical and atypical CaaX sequences. The system also recapitulated prenylation of heterologously expressed human proteins (i.e. HRas and DNAJA2). These results reveal that substrate specificity is conserved for yeast and human farnesyltransferases but is less conserved for type I geranylgeranyltransferases. These yeast systems can be easily adapted for investigating the prenylomes of other organisms and are valuable new tools for helping define the human prenylome, which includes physiologically important proteins for which the CaaX modification status is unknown.
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Affiliation(s)
- Emily R. Hildebrandt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Anushka Sarkar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Rajani Ravishankar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - June H. Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Walter K. Schmidt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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2
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Martín JF, Liras P. Targeting of Specialized Metabolites Biosynthetic Enzymes to Membranes and Vesicles by Posttranslational Palmitoylation: A Mechanism of Non-Conventional Traffic and Secretion of Fungal Metabolites. Int J Mol Sci 2024; 25:1224. [PMID: 38279221 PMCID: PMC10816013 DOI: 10.3390/ijms25021224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/30/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024] Open
Abstract
In nature, the formation of specialized (secondary) metabolites is associated with the late stages of fungal development. Enzymes involved in the biosynthesis of secondary metabolites in fungi are located in distinct subcellular compartments including the cytosol, peroxisomes, endosomes, endoplasmic reticulum, different types of vesicles, the plasma membrane and the cell wall space. The enzymes traffic between these subcellular compartments and the secretion through the plasma membrane are still unclear in the biosynthetic processes of most of these metabolites. Recent reports indicate that some of these enzymes initially located in the cytosol are later modified by posttranslational acylation and these modifications may target them to membrane vesicle systems. Many posttranslational modifications play key roles in the enzymatic function of different proteins in the cell. These modifications are very important in the modulation of regulatory proteins, in targeting of proteins, intracellular traffic and metabolites secretion. Particularly interesting are the protein modifications by palmitoylation, prenylation and miristoylation. Palmitoylation is a thiol group-acylation (S-acylation) of proteins by palmitic acid (C16) that is attached to the SH group of a conserved cysteine in proteins. Palmitoylation serves to target acylated proteins to the cytosolic surface of cell membranes, e.g., to the smooth endoplasmic reticulum, whereas the so-called toxisomes are formed in trichothecene biosynthesis. Palmitoylation of the initial enzymes involved in the biosynthesis of melanin serves to target them to endosomes and later to the conidia, whereas other non-palmitoylated laccases are secreted directly by the conventional secretory pathway to the cell wall space where they perform the last step(s) of melanin biosynthesis. Six other enzymes involved in the biosynthesis of endocrosin, gliotoxin and fumitremorgin believed to be cytosolic are also targeted to vesicles, although it is unclear if they are palmitoylated. Bioinformatic analysis suggests that palmitoylation may be frequent in the modification and targeting of polyketide synthetases and non-ribosomal peptide synthetases. The endosomes may integrate other small vesicles with different cargo proteins, forming multivesicular bodies that finally fuse with the plasma membrane during secretion. Another important effect of palmitoylation is that it regulates calcium metabolism by posttranslational modification of the phosphatase calcineurin. Mutants defective in the Akr1 palmitoyl transferase in several fungi are affected in calcium transport and homeostasis, thus impacting on the biosynthesis of calcium-regulated specialized metabolites. The palmitoylation of secondary metabolites biosynthetic enzymes and their temporal distribution respond to the conidiation signaling mechanism. In summary, this posttranslational modification drives the spatial traffic of the biosynthetic enzymes between the subcellular organelles and the plasma membrane. This article reviews the molecular mechanism of palmitoylation and the known fungal palmitoyl transferases. This novel information opens new ways to improve the biosynthesis of the bioactive metabolites and to increase its secretion in fungi.
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Affiliation(s)
- Juan F. Martín
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, 24071 León, Spain;
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3
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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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Dong L, Xiang J, Guo J, Chen G, Di G. Can static electric fields increase the activity of nitric oxide synthase and induce oxidative stress and damage of spleen? ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:4093-4100. [PMID: 34398376 DOI: 10.1007/s11356-021-15853-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
With the rapid development of ultra-high-voltage (UHV) direct-current (DC) transmissions, the impact of static electric fields (SEF) in the vicinity of overhead UHV DC transmission lines on health has aroused much public concern. This study explored the effects of 56.3kV/m SEF on the spleen of mice. Results showed that SEF exposure of 21days significantly increased malonic dialdehyde content, superoxide dismutase activity, calcineurin activity, nitric oxide synthase (NOS) activity, and the mRNA expression levels of tumor necrosis factor-α (TNF-α) and nuclear factor-κB (NF-κB) in the spleen and caused the separation of nucleus and nuclear membrane, the disappearance of mitochondrial membrane, and the deficiency of mitochondrial cristae in splenic lymphocytes. By analysis and discussion, it was deduced that SEF could induce oxidative stress of the spleen by increasing the activity of NOS. Oxidative stress could further cause ultrastructural changes of splenic lymphocytes. Moreover, oxidative stress could cause the increase of the mRNA expression levels of TNF-α and NF-κB, which contributed to the occurrence of spleen inflammation.
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Affiliation(s)
- Li Dong
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Junli Xiang
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Jingyi Guo
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Guangdi Chen
- Bioelectromagnetics Laboratory, School of Medicine, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Institute of Environmental Health, School of Public Health, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Guoqing Di
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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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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Ulengin-Talkish I, Parson MAH, Jenkins ML, Roy J, Shih AZL, St-Denis N, Gulyas G, Balla T, Gingras AC, Várnai P, Conibear E, Burke JE, Cyert MS. Palmitoylation targets the calcineurin phosphatase to the phosphatidylinositol 4-kinase complex at the plasma membrane. Nat Commun 2021; 12:6064. [PMID: 34663815 PMCID: PMC8523714 DOI: 10.1038/s41467-021-26326-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/29/2021] [Indexed: 11/25/2022] Open
Abstract
Calcineurin, the conserved protein phosphatase and target of immunosuppressants, is a critical mediator of Ca2+ signaling. Here, to discover calcineurin-regulated processes we examined an understudied isoform, CNAβ1. We show that unlike canonical cytosolic calcineurin, CNAβ1 localizes to the plasma membrane and Golgi due to palmitoylation of its divergent C-terminal tail, which is reversed by the ABHD17A depalmitoylase. Palmitoylation targets CNAβ1 to a distinct set of membrane-associated interactors including the phosphatidylinositol 4-kinase (PI4KA) complex containing EFR3B, PI4KA, TTC7B and FAM126A. Hydrogen-deuterium exchange reveals multiple calcineurin-PI4KA complex contacts, including a calcineurin-binding peptide motif in the disordered tail of FAM126A, which we establish as a calcineurin substrate. Calcineurin inhibitors decrease PI4P production during Gq-coupled GPCR signaling, suggesting that calcineurin dephosphorylates and promotes PI4KA complex activity. In sum, this work discovers a calcineurin-regulated signaling pathway which highlights the PI4KA complex as a regulatory target and reveals that dynamic palmitoylation confers unique localization, substrate specificity and regulation to CNAβ1.
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Affiliation(s)
| | - Matthew A H Parson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Jagoree Roy
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Alexis Z L Shih
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nicole St-Denis
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, University of Toronto, Toronto, Canada
- High-Fidelity Science Communications, Summerside, PE, Canada
| | - Gergo Gulyas
- Section on Molecular Signal Transduction, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Péter Várnai
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Elizabeth Conibear
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
- Department of Biochemistry, The University of British Columbia, Vancouver, BC, Canada
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA, USA.
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Wigington CP, Roy J, Damle NP, Yadav VK, Blikstad C, Resch E, Wong CJ, Mackay DR, Wang JT, Krystkowiak I, Bradburn DA, Tsekitsidou E, Hong SH, Kaderali MA, Xu SL, Stearns T, Gingras AC, Ullman KS, Ivarsson Y, Davey NE, Cyert MS. Systematic Discovery of Short Linear Motifs Decodes Calcineurin Phosphatase Signaling. Mol Cell 2020; 79:342-358.e12. [PMID: 32645368 DOI: 10.1016/j.molcel.2020.06.029] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 03/24/2020] [Accepted: 05/26/2020] [Indexed: 12/17/2022]
Abstract
Short linear motifs (SLiMs) drive dynamic protein-protein interactions essential for signaling, but sequence degeneracy and low binding affinities make them difficult to identify. We harnessed unbiased systematic approaches for SLiM discovery to elucidate the regulatory network of calcineurin (CN)/PP2B, the Ca2+-activated phosphatase that recognizes LxVP and PxIxIT motifs. In vitro proteome-wide detection of CN-binding peptides, in vivo SLiM-dependent proximity labeling, and in silico modeling of motif determinants uncovered unanticipated CN interactors, including NOTCH1, which we establish as a CN substrate. Unexpectedly, CN shows SLiM-dependent proximity to centrosomal and nuclear pore complex (NPC) proteins-structures where Ca2+ signaling is largely uncharacterized. CN dephosphorylates human and yeast NPC proteins and promotes accumulation of a nuclear transport reporter, suggesting conserved NPC regulation by CN. The CN network assembled here provides a resource to investigate Ca2+ and CN signaling and demonstrates synergy between experimental and computational methods, establishing a blueprint for examining SLiM-based networks.
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Affiliation(s)
| | - Jagoree Roy
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Nikhil P Damle
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Vikash K Yadav
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Cecilia Blikstad
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Eduard Resch
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology TMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Cassandra J Wong
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Douglas R Mackay
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jennifer T Wang
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Izabella Krystkowiak
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | | | | | - Su Hyun Hong
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Malika Amyn Kaderali
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Shou-Ling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Tim Stearns
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, M5S 3H7 ON, Canada
| | - Katharine S Ullman
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fullham Road, London SW3 6JB, UK
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA, USA.
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8
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Li X, Li J, Martinez EC, Froese A, Passariello CL, Henshaw K, Rusconi F, Li Y, Yu Q, Thakur H, Nikolaev VO, Kapiloff MS. Calcineurin Aβ-Specific Anchoring Confers Isoform-Specific Compartmentation and Function in Pathological Cardiac Myocyte Hypertrophy. Circulation 2020; 142:948-962. [PMID: 32611257 DOI: 10.1161/circulationaha.119.044893] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND The Ca2+/calmodulin-dependent phosphatase calcineurin is a key regulator of cardiac myocyte hypertrophy in disease. An unexplained paradox is how the β isoform of the calcineurin catalytic A-subunit (CaNAβ) is required for induction of pathological myocyte hypertrophy, despite calcineurin Aα expression in the same cells. It is unclear how the pleiotropic second messenger Ca2+ drives excitation-contraction coupling while not stimulating hypertrophy by calcineurin in the normal heart. Elucidation of the mechanisms conferring this selectivity in calcineurin signaling should reveal new strategies for targeting the phosphatase in disease. METHODS Primary adult rat ventricular myocytes were studied for morphology and intracellular signaling. New Förster resonance energy transfer reporters were used to assay Ca2+ and calcineurin activity in living cells. Conditional gene deletion and adeno-associated virus-mediated gene delivery in the mouse were used to study calcineurin signaling after transverse aortic constriction in vivo. RESULTS CIP4 (Cdc42-interacting protein 4)/TRIP10 (thyroid hormone receptor interactor 10) was identified as a new polyproline domain-dependent scaffold for CaNAβ2 by yeast 2-hybrid screen. Cardiac myocyte-specific CIP4 gene deletion in mice attenuated pressure overload-induced pathological cardiac remodeling and heart failure. Blockade of CaNAβ polyproline-dependent anchoring using a competing peptide inhibited concentric hypertrophy in cultured myocytes; disruption of anchoring in vivo using an adeno-associated virus gene therapy vector inhibited cardiac hypertrophy and improved systolic function after pressure overload. Live cell Förster resonance energy transfer biosensor imaging of cultured myocytes revealed that Ca2+ levels and calcineurin activity associated with the CIP4 compartment were increased by neurohormonal stimulation, but minimally by pacing. Conversely, Ca2+ levels and calcineurin activity detected by nonlocalized Förster resonance energy transfer sensors were induced by pacing and minimally by neurohormonal stimulation, providing functional evidence for differential intracellular compartmentation of Ca2+ and calcineurin signal transduction. CONCLUSIONS These results support a structural model for Ca2+ and CaNAβ compartmentation in cells based on an isoform-specific mechanism for calcineurin protein-protein interaction and localization. This mechanism provides an explanation for the specific role of CaNAβ in hypertrophy and its selective activation under conditions of pathologic stress. Disruption of CaNAβ polyproline-dependent anchoring constitutes a rational strategy for therapeutic targeting of CaNAβ-specific signaling responsible for pathological cardiac remodeling in cardiovascular disease deserving of further preclinical investigation.
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Affiliation(s)
- Xiaofeng Li
- Interdisciplinary Stem Cell Institute, Department of Pediatrics, Leonard M. Miller School of Medicine, University of Miami, FL (X.L., J.L., E.C.M., C.L.P., K.H., F.R., H.T., M.S.K.)
| | - Jinliang Li
- Interdisciplinary Stem Cell Institute, Department of Pediatrics, Leonard M. Miller School of Medicine, University of Miami, FL (X.L., J.L., E.C.M., C.L.P., K.H., F.R., H.T., M.S.K.).,Departments of Ophthalmology and Medicine, Stanford Cardiovascular Institute, Stanford University, Palo Alto, CA (J.L., Y.L., Q.Y., H.T., M.S.K.)
| | - Eliana C Martinez
- Interdisciplinary Stem Cell Institute, Department of Pediatrics, Leonard M. Miller School of Medicine, University of Miami, FL (X.L., J.L., E.C.M., C.L.P., K.H., F.R., H.T., M.S.K.)
| | - Alexander Froese
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany (A.F., V.O.N.)
| | - Catherine L Passariello
- Interdisciplinary Stem Cell Institute, Department of Pediatrics, Leonard M. Miller School of Medicine, University of Miami, FL (X.L., J.L., E.C.M., C.L.P., K.H., F.R., H.T., M.S.K.)
| | - Kathryn Henshaw
- Interdisciplinary Stem Cell Institute, Department of Pediatrics, Leonard M. Miller School of Medicine, University of Miami, FL (X.L., J.L., E.C.M., C.L.P., K.H., F.R., H.T., M.S.K.)
| | - Francesca Rusconi
- Interdisciplinary Stem Cell Institute, Department of Pediatrics, Leonard M. Miller School of Medicine, University of Miami, FL (X.L., J.L., E.C.M., C.L.P., K.H., F.R., H.T., M.S.K.)
| | - Yang Li
- Departments of Ophthalmology and Medicine, Stanford Cardiovascular Institute, Stanford University, Palo Alto, CA (J.L., Y.L., Q.Y., H.T., M.S.K.)
| | - Qian Yu
- Departments of Ophthalmology and Medicine, Stanford Cardiovascular Institute, Stanford University, Palo Alto, CA (J.L., Y.L., Q.Y., H.T., M.S.K.)
| | - Hrishikesh Thakur
- Interdisciplinary Stem Cell Institute, Department of Pediatrics, Leonard M. Miller School of Medicine, University of Miami, FL (X.L., J.L., E.C.M., C.L.P., K.H., F.R., H.T., M.S.K.).,Departments of Ophthalmology and Medicine, Stanford Cardiovascular Institute, Stanford University, Palo Alto, CA (J.L., Y.L., Q.Y., H.T., M.S.K.)
| | - Viacheslav O Nikolaev
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany (A.F., V.O.N.)
| | - Michael S Kapiloff
- Interdisciplinary Stem Cell Institute, Department of Pediatrics, Leonard M. Miller School of Medicine, University of Miami, FL (X.L., J.L., E.C.M., C.L.P., K.H., F.R., H.T., M.S.K.).,Departments of Ophthalmology and Medicine, Stanford Cardiovascular Institute, Stanford University, Palo Alto, CA (J.L., Y.L., Q.Y., H.T., M.S.K.)
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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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10
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Xu H, Fang T, Omran RP, Whiteway M, Jiang L. RNA sequencing reveals an additional Crz1-binding motif in promoters of its target genes in the human fungal pathogen Candida albicans. Cell Commun Signal 2020; 18:1. [PMID: 31900175 PMCID: PMC6942403 DOI: 10.1186/s12964-019-0473-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/25/2019] [Indexed: 02/06/2023] Open
Abstract
Background The calcium/calcineurin signaling pathway is mediated by the transcription factors NFAT (nuclear factor of activated T cells) in mammals and Crz1 (calcineurin-responsive zinc finger 1) in yeasts and other lower eukaryotes. A previous microarray analysis identified a putative Crz1-binding motif in promoters of its target genes in Candida albicans, but it has not been experimentally demonstrated. Methods An inactivation mutant for CaCRZ1 was generated through CRISPR/Cas9 approach. Transcript profiling was carried out by RNA sequencing of the wild type and the inactivation mutant for CaCRZ1 in response to 0.2 M CaCl2. Gene promoters were scanned by the online MEME (Multiple Em for Motif Elicitation) software. Gel electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) analysis were used for in vitro and in vivo CaCrz1-binding experiments, respectively. Results RNA sequencing reveals that expression of 219 genes is positively, and expression of 59 genes is negatively, controlled by CaCrz1 in response to calcium stress. These genes function in metabolism, cell cycling, protein fate, cellular transport, signal transduction, transcription, and cell wall biogenesis. Forty of these positively regulated 219 genes have previously been identified by DNA microarray analysis. Promoter analysis of these common 40 genes reveals a consensus motif [5′-GGAGGC(G/A)C(T/A)G-3′], which is different from the putative CaCrz1-binding motif [5′-G(C/T)GGT-3′] identified in the previous study, but similar to Saccharomyces cerevisiae ScCrz1-binding motif [5′-GNGGC(G/T)CA-3′]. EMSA and ChIP assays indicate that CaCrz1 binds in vitro and in vivo to both motifs in the promoter of its target gene CaUTR2. Promoter mutagenesis demonstrates that these two CaCrz1-binding motifs play additive roles in the regulation of CaUTR2 expression. In addition, the CaCRZ1 gene is positively regulated by CaCrz1. CaCrz1 can bind in vitro and in vivo to its own promoter, suggesting an autoregulatory mechanism for CaCRZ1 expression. Conclusions CaCrz1 differentially binds to promoters of its target genes to regulate their expression in response to calcium stress. CaCrz1 also regulates its own expression through the 5′-TGAGGGACTG-3′ site in its promoter. Video abstract
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Affiliation(s)
- Huihui Xu
- Laboratory for Yeast Molecular and Cell Biology, Department of Food Science, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, China
| | - Tianshu Fang
- Laboratory for Yeast Molecular and Cell Biology, Department of Food Science, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, China
| | - Raha Parvizi Omran
- Department of Biology, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Malcolm Whiteway
- Department of Biology, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Linghuo Jiang
- Laboratory for Yeast Molecular and Cell Biology, Department of Food Science, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, China.
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Xu H, Whiteway M, Jiang L. The tricarboxylic acid cycle, cell wall integrity pathway, cytokinesis and intracellular pH homeostasis are involved in the sensitivity of Candida albicans cells to high levels of extracellular calcium. Genomics 2019; 111:1226-1230. [DOI: 10.1016/j.ygeno.2018.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/19/2018] [Accepted: 08/02/2018] [Indexed: 12/15/2022]
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Villalobo A, González-Muñoz M, Berchtold MW. Proteins with calmodulin-like domains: structures and functional roles. Cell Mol Life Sci 2019; 76:2299-2328. [PMID: 30877334 PMCID: PMC11105222 DOI: 10.1007/s00018-019-03062-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 02/26/2019] [Accepted: 03/07/2019] [Indexed: 12/21/2022]
Abstract
The appearance of modular proteins is a widespread phenomenon during the evolution of proteins. The combinatorial arrangement of different functional and/or structural domains within a single polypeptide chain yields a wide variety of activities and regulatory properties to the modular proteins. In this review, we will discuss proteins, that in addition to their catalytic, transport, structure, localization or adaptor functions, also have segments resembling the helix-loop-helix EF-hand motifs found in Ca2+-binding proteins, such as calmodulin (CaM). These segments are denoted CaM-like domains (CaM-LDs) and play a regulatory role, making these CaM-like proteins sensitive to Ca2+ transients within the cell, and hence are able to transduce the Ca2+ signal leading to specific cellular responses. Importantly, this arrangement allows to this group of proteins direct regulation independent of other Ca2+-sensitive sensor/transducer proteins, such as CaM. In addition, this review also covers CaM-binding proteins, in which their CaM-binding site (CBS), in the absence of CaM, is proposed to interact with other segments of the same protein denoted CaM-like binding site (CLBS). CLBS are important regulatory motifs, acting either by keeping these CaM-binding proteins inactive in the absence of CaM, enhancing the stability of protein complexes and/or facilitating their dimerization via CBS/CLBS interaction. The existence of proteins containing CaM-LDs or CLBSs substantially adds to the enormous versatility and complexity of Ca2+/CaM signaling.
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Affiliation(s)
- Antonio Villalobo
- Department of Cancer Biology, Instituto de Investigaciones Biomédicas, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Arturo Duperier 4, 28029, Madrid, Spain.
- Instituto de Investigaciones Sanitarias, Hospital Universitario La Paz, Edificio IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain.
| | - María González-Muñoz
- Department of Cancer Biology, Instituto de Investigaciones Biomédicas, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Arturo Duperier 4, 28029, Madrid, Spain
| | - Martin W Berchtold
- Department of Biology, University of Copenhagen, 13 Universitetsparken, 2100, Copenhagen, Denmark.
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Soczewka P, Kolakowski D, Smaczynska-de Rooij I, Rzepnikowska W, Ayscough KR, Kaminska J, Zoladek T. Yeast-model-based study identified myosin- and calcium-dependent calmodulin signalling as a potential target for drug intervention in chorea-acanthocytosis. Dis Model Mech 2019; 12:dmm.036830. [PMID: 30635263 PMCID: PMC6361151 DOI: 10.1242/dmm.036830] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/07/2019] [Indexed: 01/03/2023] Open
Abstract
Chorea-acanthocytosis (ChAc) is a rare neurodegenerative disease associated with mutations in the human VPS13A gene. The mechanism of ChAc pathogenesis is unclear. A simple yeast model was used to investigate the function of the single yeast VSP13 orthologue, Vps13. Vps13, like human VPS13A, is involved in vesicular protein transport, actin cytoskeleton organisation and phospholipid metabolism. A newly identified phenotype of the vps13Δ mutant, sodium dodecyl sulphate (SDS) hypersensitivity, was used to screen a yeast genomic library for multicopy suppressors. A fragment of the MYO3 gene, encoding Myo3-N (the N-terminal part of myosin, a protein involved in the actin cytoskeleton and in endocytosis), was isolated. Myo3-N protein contains a motor head domain and a linker. The linker contains IQ motifs that mediate the binding of calmodulin, a negative regulator of myosin function. Amino acid substitutions that disrupt the interaction of Myo3-N with calmodulin resulted in the loss of vps13Δ suppression. Production of Myo3-N downregulated the activity of calcineurin, a protein phosphatase regulated by calmodulin, and alleviated some defects in early endocytosis events. Importantly, ethylene glycol tetraacetic acid (EGTA), which sequesters calcium and thus downregulates calmodulin and calcineurin, was a potent suppressor of vps13Δ. We propose that Myo3-N acts by sequestering calmodulin, downregulating calcineurin and increasing activity of Myo3, which is involved in endocytosis and, together with Osh2/3 proteins, functions in endoplasmic reticulum-plasma membrane contact sites. These results show that defects associated with vps13Δ could be overcome, and point to a functional connection between Vps13 and calcium signalling as a possible target for chemical intervention in ChAc. Yeast ChAc models may uncover the underlying pathological mechanisms, and may also serve as a platform for drug testing. This article has an associated First Person interview with the first author of the paper. Summary: Using the vps13Δ strain, a yeast model of the neurodegenerative disorder chorea-acanthocytosis, we found that its defects can be overcome by reduction of calcineurin activity and/or type-I-myosin activation.
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Affiliation(s)
- Piotr Soczewka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Genetics, Pawinskiego 5A, 02106 Warsaw, Poland
| | - Damian Kolakowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Genetics, Pawinskiego 5A, 02106 Warsaw, Poland
| | | | - Weronika Rzepnikowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Genetics, Pawinskiego 5A, 02106 Warsaw, Poland
| | - Kathryn R Ayscough
- Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Joanna Kaminska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Genetics, Pawinskiego 5A, 02106 Warsaw, Poland
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Genetics, Pawinskiego 5A, 02106 Warsaw, Poland
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The protein kinase Cmk2 negatively regulates the calcium/calcineurin signalling pathway and expression of calcium pump genes PMR1 and PMC1 in budding yeast. Cell Commun Signal 2019; 17:7. [PMID: 30665402 PMCID: PMC6341702 DOI: 10.1186/s12964-019-0320-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 01/14/2019] [Indexed: 12/16/2022] Open
Abstract
Through a genome-wide screen we have identified calcium-tolerant deletion mutants for five genes in the budding yeast Saccharomyces cerevisiae. In addition to CNB1 and RCN1 that are known to play a role in the calcium signalling pathway, the protein kinase gene CMK2, the sphingolipid homeostasis-related gene ORM2 and the gene SIF2 encoding the WD40 repeat-containing subunit of Set3C histone deacetylase complex are involved in the calcium sensitivity of yeast cells to extracellular calcium. Cmk2 and the transcription factor Crz1 have opposite functions in the response of yeast cells to calcium stress. Deletion of CMK2 elevates the level of calcium/calcineurin signalling and increases the expression level of PMR1 and PMC1, which is dependent on Crz1. Effects of Cmk2 on calcium sensitivity and calcium/calcineurin signalling are dependent on its kinase activity. Therefore, Cmk2 is a negative feedback controller of the calcium/calcineurin signalling pathway. Furthermore, the cmk2 crz1 double deletion mutant is more resistant than the crz1 deletion mutant, suggesting that Cmk2 has an additional Crz1-independent role in promoting calcium tolerance.
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Tian J, Gan Y, Pan C, Zhang M, Wang X, Tang X, Peng X. Nerol-induced apoptosis associated with the generation of ROS and Ca 2+ overload in saprotrophic fungus Aspergillus flavus. Appl Microbiol Biotechnol 2018; 102:6659-6672. [PMID: 29860589 DOI: 10.1007/s00253-018-9125-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/10/2018] [Accepted: 05/12/2018] [Indexed: 12/12/2022]
Abstract
The contamination of food with Aspergillus flavus and subsequent aflatoxins is one of the most serious safety problems in the world. In this study of nerol (NEL)'s antifungal mechanism of action, we observed morphological and physiological changes in Aspergillus flavus. We found that NEL resulted in elevated levels of reactive oxygen species (ROS) and calcium ions (Ca2+). On ROS assays, compared with the controls, the proportion of fluorescent cells treated with concentrations of 0.25, 0.5, 1, and 2 μL/mL NEL increased to 8.4 ± 1.07%, 10.2 ± 1.72%, 13.4 ± 0.50%, and 26.2 ± 4.21%, respectively. Increased mitochondrial dysfunction and oxidative stress induced by the interactions between Ca2+ and ROS subsequently activate the release of cytochrome c and caspase activity. Characteristic changes of apoptosis were also observed via various detection methods, including phosphatidylserine externalization, nuclear condensation, and DNA fragmentation. Meanwhile, we found that the expression of CaMKs increased significantly in NEL-treated cells. In conclusion, our findings indicate that NEL has great potential as an eco-friendly antifungal agent for food preservation.
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Affiliation(s)
- Jun Tian
- College of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, People's Republic of China. .,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, People's Republic of China. .,Key Lab for New Drug Research of TCM and Shenzhen Branch, State R&D Centre for Viro-Biotech, Research Institute of Tsinghua University in Shenzhen, Shenzhen, 518057, Guangdong, People's Republic of China.
| | - Yeyun Gan
- College of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, People's Republic of China
| | - Chao Pan
- College of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, People's Republic of China
| | - Man Zhang
- College of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, People's Republic of China
| | - Xueyan Wang
- Key Lab for New Drug Research of TCM and Shenzhen Branch, State R&D Centre for Viro-Biotech, Research Institute of Tsinghua University in Shenzhen, Shenzhen, 518057, Guangdong, People's Republic of China
| | - Xudong Tang
- Key Lab for New Drug Research of TCM and Shenzhen Branch, State R&D Centre for Viro-Biotech, Research Institute of Tsinghua University in Shenzhen, Shenzhen, 518057, Guangdong, People's Republic of China.
| | - Xue Peng
- College of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, People's Republic of China.
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