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Mühle C, Kornhuber J. Assay to measure sphingomyelinase and ceramidase activities efficiently and safely. J Chromatogr A 2016; 1481:137-144. [PMID: 28012590 DOI: 10.1016/j.chroma.2016.12.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/13/2016] [Accepted: 12/13/2016] [Indexed: 10/20/2022]
Abstract
As part of the sphingomyelin pathway, sphingomyelinases and ceramidases have attracted much attention in basic as well as clinical research. However, current assays still often rely on a radioactive substrate, extensive manual purification steps, and hazardous solvents for chromatographic analysis. We here show the equivalence of a fluorescent sphingomyelin substrate and present a new versatile solvent replacing the chloroform/methanol mixture. By further modifications including the omission of the manual extraction steps, chloroform and methanol are eliminated from the entire procedure and render the assay flexible to repeated analyses at multiple time intervals. These improvements allow for the rapid detection of both enzymes in a high throughput microtiter format. Moreover, we demonstrate the relevance of the plastic assay material and the interchangeability between serum and different plasma sources.
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Affiliation(s)
- Christiane Mühle
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander University of Erlangen-Nuremberg (FAU), Schwabachanlage 6, D-91054, Germany.
| | - Johannes Kornhuber
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander University of Erlangen-Nuremberg (FAU), Schwabachanlage 6, D-91054, Germany.
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2
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Xiong ZJ, Huang J, Poda G, Pomès R, Privé GG. Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis. J Mol Biol 2016; 428:3026-42. [PMID: 27349982 DOI: 10.1016/j.jmb.2016.06.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 06/14/2016] [Accepted: 06/16/2016] [Indexed: 11/29/2022]
Abstract
Acid sphingomyelinase (ASM) is a lysosomal phosphodiesterase that catalyzes the hydrolysis of sphingomyelin to produce ceramide and phosphocholine. While other lysosomal sphingolipid hydrolases require a saposin activator protein for full activity, the ASM polypeptide incorporates a built-in N-terminal saposin domain and does not require an external activator protein. Here, we report the crystal structure of human ASM and describe the organization of the three main regions of the enzyme: the N-terminal saposin domain, the proline-rich connector, and the catalytic domain. The saposin domain is tightly associated along an edge of the large, bowl-shaped catalytic domain and adopts an open form that exposes a hydrophobic concave surface approximately 30Å from the catalytic center. The calculated electrostatic potential of the enzyme is electropositive at the acidic pH of the lysosome, consistent with the strict requirement for the presence of acidic lipids in target membranes. Docking studies indicate that sphingomyelin binds with the ceramide-phosphate group positioned at the binuclear zinc center and molecular dynamic simulations indicate that the intrinsic flexibility of the saposin domain is important for monomer-dimer exchange and for membrane interactions. Overall, ASM uses a combination of electrostatic and hydrophobic interactions to cause local disruptions of target bilayers in order to bring the lipid headgroup to the catalytic center in a membrane-bound reaction.
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Affiliation(s)
- Zi-Jian Xiong
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jingjing Huang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Gennady Poda
- Drug Discovery, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Régis Pomès
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gilbert G Privé
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, Toronto, Ontario, Canada.
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Lim SM, Yeung K, Trésaugues L, Ling TH, Nordlund P. The structure and catalytic mechanism of human sphingomyelin phosphodiesterase like 3a--an acid sphingomyelinase homologue with a novel nucleotide hydrolase activity. FEBS J 2016; 283:1107-23. [PMID: 26783088 DOI: 10.1111/febs.13655] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/29/2015] [Accepted: 01/12/2016] [Indexed: 10/22/2022]
Abstract
UNLABELLED Human sphingomyelinase phosphodiesterase like 3a (SMPDL3a) is a secreted enzyme that shares a conserved catalytic domain with human acid sphingomyelinase (aSMase), the enzyme carrying mutations causative of Niemann-Pick disease. We have solved the structure of SMPDL3a revealing a calcineurin-like fold. A dimetal site, glycosylation pattern and a disulfide bond network are likely to be conserved also in human aSMase. We show that the binuclear site of SMPDL3a is occupied by two Zn(2+) ions and that excess Zn(2+) leads to inhibition of enzyme activity through binding to additional sites. As an extension of recent biochemical work we uncovered that SMPDL3a catalyses the hydrolysis of several modified nucleotides that include cytidine 5'-diphosphocholine, cytidine diphosphate ethanolamine and ADP-ribose, but not the aSMase substrate, sphingomyelin. We subsequently determined the structure of SMPDL3a in complex with the product 5'-cytidine monophosphate (CMP), a structure that is consistent with several distinct coordination modes of the substrate/product in the active site during the reaction cycle. Based on the structure of CMP complexes, we propose a phosphoryl transfer mechanism for SMPDL3a. Finally, a homology model of human aSMase was constructed to allow for the mapping of selected Niemann-Pick disease mutations on a three-dimensional framework to guide further characterization of their effects on aSMase function. DATABASE Structural data are available in the PDB database under the accession numbers 5EBB and 5EBE.
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Affiliation(s)
- Sing Mei Lim
- Division of Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kit Yeung
- Division of Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Lionel Trésaugues
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Teo Hsiang Ling
- Division of Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Pär Nordlund
- Division of Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Institute of Molecular and Cell Biology, A*STAR, Singapore city, Singapore
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4
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Gorelik A, Illes K, Superti-Furga G, Nagar B. Structural Basis for Nucleotide Hydrolysis by the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3A. J Biol Chem 2016; 291:6376-85. [PMID: 26792860 DOI: 10.1074/jbc.m115.711085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Indexed: 11/06/2022] Open
Abstract
Sphingomyelin phosphodiesterase, acid-like 3A (SMPDL3A) is a member of a small family of proteins founded by the well characterized lysosomal enzyme, acid sphingomyelinase (ASMase). ASMase converts sphingomyelin into the signaling lipid, ceramide. It was recently discovered that, in contrast to ASMase, SMPDL3A is inactive against sphingomyelin and, surprisingly, can instead hydrolyze nucleoside diphosphates and triphosphates, which may play a role in purinergic signaling. As none of the ASMase-like proteins has been structurally characterized to date, the molecular basis for their substrate preferences is unknown. Here we report crystal structures of murine SMPDL3A, which represent the first structures of an ASMase-like protein. The catalytic domain consists of a central mixed β-sandwich surrounded by α-helices. Additionally, SMPDL3A possesses a unique C-terminal domain formed from a cluster of four α-helices that appears to distinguish this protein family from other phosphoesterases. We show that SMDPL3A is a di-zinc-dependent enzyme with an active site configuration that suggests a mechanism of phosphodiester hydrolysis by a metal-activated water molecule and protonation of the leaving group by a histidine residue. Co-crystal structures of SMPDL3A with AMP and α,β-methylene ADP (AMPCP) reveal that the substrate binding site accommodates nucleotides by establishing interactions with their base, sugar, and phosphate moieties, with the latter the major contributor to binding affinity. Our study provides the structural basis for SMPDL3A substrate specificity and sheds new light on the function of ASMase-like proteins.
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Affiliation(s)
- Alexei Gorelik
- From the Department of Biochemistry and Groupe de Recherche Axe sur la Structure des Proteines, Faculty of Medicine, McGill University, Montreal, Quebec H3G 0B1, Canada and
| | - Katalin Illes
- From the Department of Biochemistry and Groupe de Recherche Axe sur la Structure des Proteines, Faculty of Medicine, McGill University, Montreal, Quebec H3G 0B1, Canada and
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090 Vienna, Austria
| | - Bhushan Nagar
- From the Department of Biochemistry and Groupe de Recherche Axe sur la Structure des Proteines, Faculty of Medicine, McGill University, Montreal, Quebec H3G 0B1, Canada and
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Lowe TM, Ailloud F, Allen C. Hydroxycinnamic Acid Degradation, a Broadly Conserved Trait, Protects Ralstonia solanacearum from Chemical Plant Defenses and Contributes to Root Colonization and Virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:286-97. [PMID: 25423265 PMCID: PMC4329107 DOI: 10.1094/mpmi-09-14-0292-fi] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Plants produce hydroxycinnamic acid (HCA) defense compounds to combat pathogens, such as the bacterium Ralstonia solanacearum. We showed that an HCA degradation pathway is genetically and functionally conserved across diverse R. solanacearum strains. Further, a feruloyl-CoA synthetase (Δfcs) mutant that cannot degrade HCA was less virulent on tomato plants. To understand the role of HCA degradation in bacterial wilt disease, we tested the following hypotheses: HCA degradation helps the pathogen i) grow, as a carbon source; ii) spread, by reducing HCA-derived physical barriers; and iii) survive plant antimicrobial compounds. Although HCA degradation enabled R. solanacearum growth on HCA in vitro, HCA degradation was dispensable for growth in xylem sap and root exudate, suggesting that HCA are not significant carbon sources in planta. Acetyl-bromide quantification of lignin demonstrated that R. solanacearum infections did not affect the gross quantity or distribution of stem lignin. However, the Δfcs mutant was significantly more susceptible to inhibition by two HCA, namely, caffeate and p-coumarate. Finally, plant colonization assays suggested that HCA degradation facilitates early stages of infection and root colonization. Together, these results indicated that ability to degrade HCA contributes to bacterial wilt virulence by facilitating root entry and by protecting the pathogen from HCA toxicity.
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Affiliation(s)
- Tiffany M. Lowe
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Florent Ailloud
- Peuplements Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT), INRA-CIRAD, Saint Pierre, La Réunion, France
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
- Corresponding Author: Caitilyn Allen; ; 608-262-9578
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Traini M, Quinn CM, Sandoval C, Johansson E, Schroder K, Kockx M, Meikle PJ, Jessup W, Kritharides L. Sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A) is a novel nucleotide phosphodiesterase regulated by cholesterol in human macrophages. J Biol Chem 2014; 289:32895-913. [PMID: 25288789 DOI: 10.1074/jbc.m114.612341] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cholesterol-loaded foam cell macrophages are prominent in atherosclerotic lesions and play complex roles in both inflammatory signaling and lipid metabolism, which are underpinned by large scale reprogramming of gene expression. We performed a microarray study of primary human macrophages that showed that transcription of the sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A) gene is up-regulated after cholesterol loading. SMPDL3A protein expression in and secretion from primary macrophages are stimulated by cholesterol loading, liver X receptor ligands, and cyclic AMP, and N-glycosylated SMPDL3A protein is detectable in circulating blood. We demonstrate for the first time that SMPDL3A is a functional phosphodiesterase with an acidic pH optimum. We provide evidence that SMPDL3A is not an acid sphingomyelinase but unexpectedly is active against nucleotide diphosphate and triphosphate substrates at acidic and neutral pH. SMPDL3A is a major source of nucleotide phosphodiesterase activity secreted by liver X receptor-stimulated human macrophages. Extracellular nucleotides such as ATP may activate pro-inflammatory responses in immune cells. Increased expression and secretion of SMPDL3A by cholesterol-loaded macrophage foam cells in lesions may decrease local concentrations of pro-inflammatory nucleotides and potentially represent a novel anti-inflammatory axis linking lipid metabolism with purinergic signaling in atherosclerosis.
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Affiliation(s)
- Mathew Traini
- From the Atherosclerosis Laboratory, ANZAC Research Institute, University of Sydney, Sydney, New South Wales 2139,
| | - Carmel M Quinn
- the Centre for Vascular Research, University of New South Wales, Sydney, New South Wales 2052
| | - Cecilia Sandoval
- the Centre for Vascular Research, University of New South Wales, Sydney, New South Wales 2052
| | - Erik Johansson
- From the Atherosclerosis Laboratory, ANZAC Research Institute, University of Sydney, Sydney, New South Wales 2139
| | - Kate Schroder
- the Institute for Molecular Bioscience, University of Queensland, Queensland 4072
| | - Maaike Kockx
- From the Atherosclerosis Laboratory, ANZAC Research Institute, University of Sydney, Sydney, New South Wales 2139
| | - Peter J Meikle
- the Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, and
| | - Wendy Jessup
- From the Atherosclerosis Laboratory, ANZAC Research Institute, University of Sydney, Sydney, New South Wales 2139
| | - Leonard Kritharides
- From the Atherosclerosis Laboratory, ANZAC Research Institute, University of Sydney, Sydney, New South Wales 2139, the Department of Cardiology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia
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