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John Peter AT, Kornmann B. Uncovering mechanisms of interorganelle lipid transport by enzymatic mass tagging. FEBS Lett 2024; 598:1292-1298. [PMID: 38268324 DOI: 10.1002/1873-3468.14810] [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: 10/18/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Lipid trafficking is critical for the biogenesis and expansion of organelle membranes. Lipid transport proteins (LTPs) have been proposed to facilitate lipid transport at contact sites between organelles. Despite the fundamental importance of LTPs in cell physiology, our knowledge on the mechanisms of interorganelle lipid distribution remains poor due to the scarcity of assays to monitor lipid flux in vivo. In this review, we highlight the recent development of a versatile method named METALIC (Mass tagging-Enabled Tracking of Lipids in Cells), which uses a combination of enzymatic mass tagging and mass spectrometry to track lipid flux between organelles inside living cells. We discuss the methodology, its distinct advantages, limitations as well as its potential to unearth the pipelines of lipid transport and LTP function in vivo.
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2
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Reinhard J, Leveille CL, Cornell CE, Merz AJ, Klose C, Ernst R, Keller SL. Remodeling of yeast vacuole membrane lipidomes from the log (one phase) to stationary stage (two phases). Biophys J 2023; 122:1043-1057. [PMID: 36635960 PMCID: PMC10111276 DOI: 10.1016/j.bpj.2023.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/03/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Upon nutrient limitation, budding yeast of Saccharomyces cerevisiae shift from fast growth (the log stage) to quiescence (the stationary stage). This shift is accompanied by liquid-liquid phase separation in the membrane of the vacuole, an endosomal organelle. Recent work indicates that the resulting micrometer-scale domains in vacuole membranes enable yeast to survive periods of stress. An outstanding question is which molecular changes might cause this membrane phase separation. Here, we conduct lipidomics of vacuole membranes in both the log and stationary stages. Isolation of pure vacuole membranes is challenging in the stationary stage, when lipid droplets are in close contact with vacuoles. Immuno-isolation has previously been shown to successfully purify log-stage vacuole membranes with high organelle specificity, but it was not previously possible to immuno-isolate stationary-stage vacuole membranes. Here, we develop Mam3 as a bait protein for vacuole immuno-isolation, and demonstrate low contamination by non-vacuolar membranes. We find that stationary-stage vacuole membranes contain surprisingly high fractions of phosphatidylcholine lipids (∼40%), roughly twice as much as log-stage membranes. Moreover, in the stationary stage, these lipids have higher melting temperatures, due to longer and more saturated acyl chains. Another surprise is that no significant change in sterol content is observed. These lipidomic changes, which are largely reflected on the whole-cell level, fit within the predominant view that phase separation in membranes requires at least three types of molecules to be present: lipids with high melting temperatures, lipids with low melting temperatures, and sterols.
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Affiliation(s)
- John Reinhard
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany; PZMS, Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany
| | | | | | - Alexey J Merz
- Department of Biochemistry, University of Washington, Seattle, WA
| | | | - Robert Ernst
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany; PZMS, Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany.
| | - Sarah L Keller
- Department of Chemistry, University of Washington, Seattle, WA.
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3
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Zhou Q, Zhang F, Kerbl-Knapp J, Korbelius M, Kuentzel KB, Vujić N, Akhmetshina A, Hörl G, Paar M, Steyrer E, Kratky D, Madl T. Phosphatidylethanolamine N-Methyltransferase Knockout Modulates Metabolic Changes in Aging Mice. Biomolecules 2022; 12:1270. [PMID: 36139111 PMCID: PMC9496051 DOI: 10.3390/biom12091270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 12/11/2022] Open
Abstract
Phospholipid metabolism, including phosphatidylcholine (PC) biosynthesis, is crucial for various biological functions and is associated with longevity. Phosphatidylethanolamine N-methyltransferase (PEMT) is a protein that catalyzes the biosynthesis of PC, the levels of which change in various organs such as the brain and kidneys during aging. However, the role of PEMT for systemic PC supply is not fully understood. To address how PEMT affects aging-associated energy metabolism in tissues responsible for nutrient absorption, lipid storage, and energy consumption, we employed NMR-based metabolomics to study the liver, plasma, intestine (duodenum, jejunum, and ileum), brown/white adipose tissues (BAT and WAT), and skeletal muscle of young (9-10 weeks) and old (91-132 weeks) wild-type (WT) and PEMT knockout (KO) mice. We found that the effect of PEMT-knockout was tissue-specific and age-dependent. A deficiency of PEMT affected the metabolome of all tissues examined, among which the metabolome of BAT from both young and aged KO mice was dramatically changed in comparison to the WT mice, whereas the metabolome of the jejunum was only slightly affected. As for aging, the absence of PEMT increased the divergence of the metabolome during the aging of the liver, WAT, duodenum, and ileum and decreased the impact on skeletal muscle. Overall, our results suggest that PEMT plays a previously underexplored, critical role in both aging and energy metabolism.
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Affiliation(s)
- Qishun Zhou
- Research Unit Integrative Structural Biology, Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8010 Graz, Austria
| | - Fangrong Zhang
- Research Unit Integrative Structural Biology, Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8010 Graz, Austria
- Key Laboratory of Gastrointestinal Cancer, Fujian Medical University, Ministry of Education, Fuzhou 350122, China
| | - Jakob Kerbl-Knapp
- Research Unit Integrative Structural Biology, Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8010 Graz, Austria
| | - Melanie Korbelius
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Katharina Barbara Kuentzel
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Nemanja Vujić
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Alena Akhmetshina
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Gerd Hörl
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, 8010 Graz, Austria
| | - Margret Paar
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, 8010 Graz, Austria
| | - Ernst Steyrer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Dagmar Kratky
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Tobias Madl
- Research Unit Integrative Structural Biology, Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
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4
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METALIC reveals interorganelle lipid flux in live cells by enzymatic mass tagging. Nat Cell Biol 2022; 24:996-1004. [PMID: 35654841 PMCID: PMC9203272 DOI: 10.1038/s41556-022-00917-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 04/18/2022] [Indexed: 11/08/2022]
Abstract
The distinct activities of organelles depend on the proper function of their membranes. Coordinated membrane biogenesis of different organelles necessitates lipid transport from their site of synthesis to their destination. Several factors have been proposed to participate in lipid distribution, but despite its basic importance, in vivo evidence linking the absence of putative transport pathways to specific transport defects remains scarce. A reason for this scarcity is the near absence of in vivo lipid trafficking assays. Here we introduce a versatile method named METALIC (Mass tagging-Enabled TrAcking of Lipids In Cells) to track interorganelle lipid flux inside cells. In this strategy, two enzymes, one directed to a 'donor' and the other to an 'acceptor' organelle, add two distinct mass tags to lipids. Mass-spectrometry-based detection of lipids bearing the two mass tags is then used to quantify exchange between the two organelles. By applying this approach, we show that the ERMES and Vps13-Mcp1 complexes have transport activity in vivo, and unravel their relative contributions to endoplasmic reticulum-mitochondria lipid exchange.
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5
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Fang W, Zhu Y, Yang S, Tong X, Ye C. Reciprocal regulation of phosphatidylcholine synthesis and H3K36 methylation programs metabolic adaptation. Cell Rep 2022; 39:110672. [PMID: 35417718 DOI: 10.1016/j.celrep.2022.110672] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/14/2022] [Accepted: 03/22/2022] [Indexed: 11/17/2022] Open
Abstract
Phospholipid biosynthesis plays a role in mediating membrane-to-histone communication that influences metabolic decisions. Upon nutrient deprivation, phospholipid methylation generates a starvation signal in the form of S-adenosylmethionine (SAM) depletion, leading to dynamic changes in histone methylation. Here we show that the SAM-responsive methylation of H3K36 is critical for metabolic adaptation to nutrient starvation in the budding yeast Saccharomyces cerevisiae. We find that mutants deficient in H3K36 methylation exhibit defects in membrane integrity and pyrimidine metabolism and lose viability quickly under starvation. Adjusting the synthesis of phospholipids potently rewires metabolic pathways for nucleotide synthesis and boosts the production of antioxidants, ameliorating the defects resulting from the loss of H3K36 methylation. We further demonstrate that H3K36 methylation reciprocally regulates phospholipid synthesis by influencing redox balance. Our study illustrates an adaptive mechanism whereby phospholipid synthesis entails a histone modification to reprogram metabolism for adaptation in a eukaryotic model organism.
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Affiliation(s)
- Wen Fang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yibing Zhu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Sen Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xiaomeng Tong
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Cunqi Ye
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China; Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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6
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Kopf AH, Lijding O, Elenbaas BOW, Koorengevel MC, Dobruchowska JM, van Walree CA, Killian JA. Synthesis and Evaluation of a Library of Alternating Amphipathic Copolymers to Solubilize and Study Membrane Proteins. Biomacromolecules 2022; 23:743-759. [PMID: 34994549 PMCID: PMC8924871 DOI: 10.1021/acs.biomac.1c01166] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Amphipathic copolymers
such as poly(styrene-maleic acid) (SMA)
are promising tools for the facile extraction of membrane proteins
(MPs) into native nanodiscs. Here, we designed and synthesized a library
of well-defined alternating copolymers of SMA analogues in order to
elucidate polymer properties that are important for MP solubilization
and stability. MP extraction efficiency was determined using KcsA
from E. coli membranes, and general solubilization
efficiency was investigated via turbidimetry experiments on membranes
of E. coli, yeast mitochondria, and synthetic
lipids. Remarkably, halogenation of SMA copolymers dramatically improved
solubilization efficiency in all systems, while substituents on the
copolymer backbone improved resistance to Ca2+. Relevant
polymer properties were found to include hydrophobic balance, size
and positioning of substituents, rigidity, and electronic effects.
The library thus contributes to the rational design of copolymers
for the study of MPs.
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Affiliation(s)
- Adrian H Kopf
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Odette Lijding
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Barend O W Elenbaas
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Martijn C Koorengevel
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Justyna M Dobruchowska
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, and Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Cornelis A van Walree
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - J Antoinette Killian
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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7
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Hu C, Luo W, Xu J, Han X. RECOGNITION AND AVOIDANCE OF ION SOURCE-GENERATED ARTIFACTS IN LIPIDOMICS ANALYSIS. MASS SPECTROMETRY REVIEWS 2022; 41:15-31. [PMID: 32997818 PMCID: PMC8287896 DOI: 10.1002/mas.21659] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/24/2020] [Accepted: 08/31/2020] [Indexed: 05/04/2023]
Abstract
Lipid research is attracting more and more attention as various key roles and novel biological functions of lipids have been demonstrated and discovered in the organism. Mass spectrometry (MS)-based lipidomics approaches are the most powerful and effective tools for analysis of cellular lipidomes with very high sensitivity and specificity. However, the artifacts generated from in-source fragmentation are always present in all kinds of ion sources, even soft ionization techniques (i.e., electrospray ionization and matrix-assisted laser desorption/ionization [MALDI]). These artifacts can cause many problems for lipidomics, especially when the fragment ions correspond to/are isomeric species of other endogenous lipid species in complex biological samples. These commonly observed artifacts could lead to misannotation, false identification, and consequently, incorrect attribution of phenotypes, and will have negative impact on any MS-based lipidomics research including but not limited to biomarker discovery, drug development, etc. Liquid chromatography-MS, shotgun lipidomics, and MALDI-MS imaging are three representative lipidomics approaches in which ion source-generated artifacts are all manifested and are comprehensively summarized in this article. The strategies on how to avoid/reduce the artifacts of in-source fragmentation on lipidomics analysis are also discussed in detail. We believe that with the recognition and avoidance of ion source-generated artifacts, MS-based lipidomics approaches will provide better accuracy on comprehensive analysis of biological samples and will make greater contribution to the research on metabolism and translational/precision medicine (collectively termed functional lipidomics). © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Changfeng Hu
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, 548 Bingwen Road, Hangzhou, Zhejiang 310053, China
| | - Wenqing Luo
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, 548 Bingwen Road, Hangzhou, Zhejiang 310053, China
| | - Jie Xu
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003 China
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229 USA
- Department of Medicine – Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229 USA
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8
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Schlame M, Xu Y, Erdjument-Bromage H, Neubert TA, Ren M. Lipidome-wide 13C flux analysis: a novel tool to estimate the turnover of lipids in organisms and cultures. J Lipid Res 2020; 61:95-104. [PMID: 31712250 PMCID: PMC6939592 DOI: 10.1194/jlr.d119000318] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/07/2019] [Indexed: 01/12/2023] Open
Abstract
Lipid metabolism plays an important role in the regulation of cellular homeostasis. However, because it is difficult to measure the actual rates of synthesis and degradation of individual lipid species, lipid compositions are often used as a surrogate to evaluate lipid metabolism even though they provide only static snapshots of the lipodome. Here, we designed a simple method to determine the turnover rate of phospholipid and acylglycerol species based on the incorporation of 13C6-glucose combined with LC-MS/MS. We labeled adult Drosophila melanogaster with 13C6-glucose that incorporates into the entire lipidome, derived kinetic parameters from mass spectra, and studied effects of deletion of CG6718, the fly homolog of the calcium-independent phospholipase A2β, on lipid metabolism. Although 13C6-glucose gave rise to a complex pattern of 13C incorporation, we were able to identify discrete isotopomers in which 13C atoms were confined to the glycerol group. With these isotopomers, we calculated turnover rate constants, half-life times, and fluxes of the glycerol backbone of multiple lipid species. To perform these calculations, we estimated the fraction of labeled molecules in glycerol-3-phosphate, the lipid precursor, by mass isotopomer distribution analysis of the spectra of phosphatidylglycerol. When we applied this method to D. melanogaster, we found a range of lipid half-lives from 2 to 200 days, demonstrated tissue-specific fluxes of individual lipid species, and identified a novel function of CG6718 in triacylglycerol metabolism. This method provides fluxomics-type data with significant potential to improve the understanding of complex lipid regulation in a variety of research models.
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Affiliation(s)
- Michael Schlame
- Departments of Anesthesiology, New York University School of Medicine, New York, NY 10016; Cell Biology, New York University School of Medicine, New York, NY 10016.
| | - Yang Xu
- Departments of Anesthesiology, New York University School of Medicine, New York, NY 10016
| | - Hediye Erdjument-Bromage
- Cell Biology, New York University School of Medicine, New York, NY 10016; Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016
| | - Thomas A Neubert
- Cell Biology, New York University School of Medicine, New York, NY 10016; Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016
| | - Mindong Ren
- Departments of Anesthesiology, New York University School of Medicine, New York, NY 10016; Cell Biology, New York University School of Medicine, New York, NY 10016
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9
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Patton-Vogt J, de Kroon AIPM. Phospholipid turnover and acyl chain remodeling in the yeast ER. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158462. [PMID: 31146038 PMCID: PMC10716787 DOI: 10.1016/j.bbalip.2019.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/01/2019] [Accepted: 05/15/2019] [Indexed: 12/14/2022]
Abstract
The turnover of phospholipids plays an essential role in membrane lipid homeostasis by impacting both lipid head group and acyl chain composition. This review focusses on the degradation and acyl chain remodeling of the major phospholipid classes present in the ER membrane of the reference eukaryote Saccharomyces cerevisiae, i.e. phosphatidylcholine (PC), phosphatidylinositol (PI) and phosphatidylethanolamine (PE). Phospholipid turnover reactions are introduced, and the occurrence and important functions of phospholipid remodeling in higher eukaryotes are briefly summarized. After presenting an inventory of established mechanisms of phospholipid acyl chain exchange, current knowledge of phospholipid degradation and remodeling by phospholipases and acyltransferases localized to the yeast ER is summarized. PC is subject to the PC deacylation-reacylation remodeling pathway (PC-DRP) involving a phospholipase B, the recently identified glycerophosphocholine acyltransferase Gpc1p, and the broad specificity acyltransferase Ale1p. PI is post-synthetically enriched in C18:0 acyl chains by remodeling reactions involving Cst26p. PE may undergo turnover by the phospholipid: diacylglycerol acyltransferase Lro1p as first step in acyl chain remodeling. Clues as to the functions of phospholipid acyl chain remodeling are discussed.
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Affiliation(s)
- Jana Patton-Vogt
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA, USA
| | - Anton I P M de Kroon
- Membrane Biochemistry & Biophysics, Bijvoet Center and Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands.
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10
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Anaokar S, Kodali R, Jonik B, Renne MF, Brouwers JFHM, Lager I, de Kroon AIPM, Patton-Vogt J. The glycerophosphocholine acyltransferase Gpc1 is part of a phosphatidylcholine (PC)-remodeling pathway that alters PC species in yeast. J Biol Chem 2018; 294:1189-1201. [PMID: 30514764 DOI: 10.1074/jbc.ra118.005232] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/27/2018] [Indexed: 12/22/2022] Open
Abstract
Phospholipase B-mediated hydrolysis of phosphatidylcholine (PC) results in the formation of free fatty acids and glycerophosphocholine (GPC) in the yeast Saccharomyces cerevisiae GPC can be reacylated by the glycerophosphocholine acyltransferase Gpc1, which produces lysophosphatidylcholine (LPC), and LPC can be converted to PC by the lysophospholipid acyltransferase Ale1. Here, we further characterized the regulation and function of this distinct PC deacylation/reacylation pathway in yeast. Through in vitro and in vivo experiments, we show that Gpc1 and Ale1 are the major cellular GPC and LPC acyltransferases, respectively. Importantly, we report that Gpc1 activity affects the PC species profile. Loss of Gpc1 decreased the levels of monounsaturated PC species and increased those of diunsaturated PC species, whereas Gpc1 overexpression had the opposite effects. Of note, Gpc1 loss did not significantly affect phosphatidylethanolamine, phosphatidylinositol, and phosphatidylserine profiles. Our results indicate that Gpc1 is involved in postsynthetic PC remodeling that produces more saturated PC species. qRT-PCR analyses revealed that GPC1 mRNA abundance is regulated coordinately with PC biosynthetic pathways. Inositol availability, which regulates several phospholipid biosynthetic genes, down-regulated GPC1 expression at the mRNA and protein levels and, as expected, decreased levels of monounsaturated PC species. Finally, loss of GPC1 decreased stationary phase viability in inositol-free medium. These results indicate that Gpc1 is part of a postsynthetic PC deacylation/reacylation remodeling pathway (PC-DRP) that alters the PC species profile, is regulated in coordination with other major lipid biosynthetic pathways, and affects yeast growth.
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Affiliation(s)
- Sanket Anaokar
- Departments of Biological Sciences, Pittsburgh, Pennsylvania 15282
| | - Ravindra Kodali
- Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - Benjamin Jonik
- Departments of Biological Sciences, Pittsburgh, Pennsylvania 15282
| | - Mike F Renne
- Department of Membrane Biochemistry & Biophysics, Bijvoet Center and Institute of Biomembranes, 3584 CH Utrecht, The Netherlands
| | - Jos F H M Brouwers
- Department of Biochemistry and Cell Biology, Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Ida Lager
- Department of Plant Breeding, Swedish University of Agricultural Sciences, SE-230 53 Alnarp, Sweden
| | - Anton I P M de Kroon
- Department of Membrane Biochemistry & Biophysics, Bijvoet Center and Institute of Biomembranes, 3584 CH Utrecht, The Netherlands
| | - Jana Patton-Vogt
- Departments of Biological Sciences, Pittsburgh, Pennsylvania 15282.
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11
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Triebl A, Wenk MR. Analytical Considerations of Stable Isotope Labelling in Lipidomics. Biomolecules 2018; 8:biom8040151. [PMID: 30453585 PMCID: PMC6315579 DOI: 10.3390/biom8040151] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 12/26/2022] Open
Abstract
Over the last two decades, lipids have come to be understood as far more than merely components of cellular membranes and forms of energy storage, and are now also being implicated to play important roles in a variety of diseases, with lipid biomarker research one of the most widespread applications of lipidomic techniques both in research and in clinical settings. Stable isotope labelling has become a staple technique in the analysis of small molecule metabolism and dynamics, as it is the only experimental setup by which biosynthesis, remodelling and degradation of biomolecules can be directly measured. Using state-of-the-art analytical technologies such as chromatography-coupled high resolution tandem mass spectrometry, the stable isotope label can be precisely localized and quantified within the biomolecules. The application of stable isotope labelling to lipidomics is however complicated by the diversity of lipids and the complexity of the necessary data analysis. This article discusses key experimental aspects of stable isotope labelling in the field of mass spectrometry-based lipidomics, summarizes current applications and provides an outlook on future developments and potential.
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Affiliation(s)
- Alexander Triebl
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore; Singapore 117596, Singapore.
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore; Singapore 117596, Singapore.
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12
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du Plessis M, Franken J, Bauer FF. Carnitine Requires Choline to Exert Physiological Effects in Saccharomyces cerevisiae. Front Microbiol 2018; 9:1362. [PMID: 30034373 PMCID: PMC6043790 DOI: 10.3389/fmicb.2018.01362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/05/2018] [Indexed: 11/25/2022] Open
Abstract
L-Carnitine is a key metabolite in the energy metabolism of eukaryotic cells, functioning as a shuttling molecule for activated acyl-residues between cellular compartments. In higher eukaryotes this function is essential, and defects in carnitine metabolism has severe effects on fatty acid and carbon metabolism. Carnitine supplementation has been associated with an array of mostly beneficial impacts in higher eukaryotic cells, including stress protection and regulation of redox metabolism in diseased cells. Some of these phenotypes have no obvious link to the carnitine shuttle, and suggest that carnitine has as yet unknown shuttle-independent functions. The existence of shuttle-independent functions has also been suggested in Saccharomyces cerevisiae, including a beneficial effect during hydrogen peroxide stress and a detrimental impact when carnitine is co-supplemented with the reducing agent dithiothreitol (DTT). Here we used these two distinct yeast phenotypes to screen for potential genetic factors that suppress the shuttle independent physiological effects of carnitine. Two deletion strains, Δcho2 and Δopi3, coding for enzymes that catalyze the sequential conversion of phosphatidylethanolamine to phosphatidylcholine were identified for suppressing the phenotypic effects of carnitine. Additional characterisation indicated that the suppression cannot be explained by differences in phospholipid homeostasis. The phenotypes could be reinstated by addition of extracellular choline, but show that the requirement for choline is not based on some overlapping function or the structural similarities of the two molecules. This is the first study to suggest a molecular link between a specific metabolite and carnitine-dependent, but shuttle-independent phenotypes in eukaryotes.
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Affiliation(s)
| | | | - Florian F. Bauer
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch University, Stellenbosch, South Africa
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13
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Haider A, Wei YC, Lim K, Barbosa AD, Liu CH, Weber U, Mlodzik M, Oras K, Collier S, Hussain MM, Dong L, Patel S, Alvarez-Guaita A, Saudek V, Jenkins BJ, Koulman A, Dymond MK, Hardie RC, Siniossoglou S, Savage DB. PCYT1A Regulates Phosphatidylcholine Homeostasis from the Inner Nuclear Membrane in Response to Membrane Stored Curvature Elastic Stress. Dev Cell 2018; 45:481-495.e8. [PMID: 29754800 PMCID: PMC5971203 DOI: 10.1016/j.devcel.2018.04.012] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/27/2018] [Accepted: 04/11/2018] [Indexed: 12/19/2022]
Abstract
Cell and organelle membranes consist of a complex mixture of phospholipids (PLs) that determine their size, shape, and function. Phosphatidylcholine (PC) is the most abundant phospholipid in eukaryotic membranes, yet how cells sense and regulate its levels in vivo remains unclear. Here we show that PCYT1A, the rate-limiting enzyme of PC synthesis, is intranuclear and re-locates to the nuclear membrane in response to the need for membrane PL synthesis in yeast, fly, and mammalian cells. By aligning imaging with lipidomic analysis and data-driven modeling, we demonstrate that yeast PCYT1A membrane association correlates with membrane stored curvature elastic stress estimates. Furthermore, this process occurs inside the nucleus, although nuclear localization signal mutants can compensate for the loss of endogenous PCYT1A in yeast and in fly photoreceptors. These data suggest an ancient mechanism by which nucleoplasmic PCYT1A senses surface PL packing defects on the inner nuclear membrane to control PC homeostasis.
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Affiliation(s)
- Afreen Haider
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Yu-Chen Wei
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Koini Lim
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Antonio D Barbosa
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Che-Hsiung Liu
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Ursula Weber
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Marek Mlodzik
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Kadri Oras
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Simon Collier
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - M Mahmood Hussain
- Departments of Cell Biology and Pediatrics, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA
| | - Liang Dong
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Satish Patel
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Anna Alvarez-Guaita
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Vladimir Saudek
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Benjamin J Jenkins
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Albert Koulman
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Marcus K Dymond
- Division of Chemistry, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK
| | - Roger C Hardie
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Symeon Siniossoglou
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK.
| | - David B Savage
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK.
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14
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Renne MF, de Kroon AIPM. The role of phospholipid molecular species in determining the physical properties of yeast membranes. FEBS Lett 2017; 592:1330-1345. [PMID: 29265372 PMCID: PMC5947837 DOI: 10.1002/1873-3468.12944] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/27/2017] [Accepted: 12/11/2017] [Indexed: 12/18/2022]
Abstract
In most eukaryotes, including Saccharomyces cerevisiae, glycerophospholipids are the main membrane lipid constituents. Besides serving as general membrane ‘building blocks’, glycerophospholipids play an important role in determining the physical properties of the membrane, which are crucial for proper membrane function. To ensure optimal physical properties, membrane glycerophospholipid composition and synthesis are tightly regulated. This review will summarize our current knowledge of factors and processes determining the membrane glycerophospholipid composition of the reference eukaryote S. cerevisiae at the level of molecular species. Extrapolating from relevant model membrane data, we also discuss how modulation of the molecular species composition can regulate membrane physical properties.
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Affiliation(s)
- Mike F. Renne
- Membrane Biochemistry & BiophysicsDepartment of ChemistryBijvoet Center for Biomolecular Research & Institute of BiomembranesUtrecht Universitythe Netherlands
| | - Anton I. P. M. de Kroon
- Membrane Biochemistry & BiophysicsDepartment of ChemistryBijvoet Center for Biomolecular Research & Institute of BiomembranesUtrecht Universitythe Netherlands
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15
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McMaster CR. From yeast to humans - roles of the Kennedy pathway for phosphatidylcholine synthesis. FEBS Lett 2017; 592:1256-1272. [PMID: 29178478 DOI: 10.1002/1873-3468.12919] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 12/13/2022]
Abstract
The major phospholipid present in most eukaryotic membranes is phosphatidylcholine (PC), comprising ~ 50% of phospholipid content. PC metabolic pathways are highly conserved from yeast to humans. The main pathway for the synthesis of PC is the Kennedy (CDP-choline) pathway. In this pathway, choline is converted to phosphocholine by choline kinase, phosphocholine is metabolized to CDP-choline by the rate-determining enzyme for this pathway, CTP:phosphocholine cytidylyltransferase, and cholinephosphotransferase condenses CDP-choline with diacylglycerol to produce PC. This Review discusses how PC synthesis via the Kennedy pathway is regulated, its role in cellular and biological processes, as well as diseases known to be associated with defects in PC synthesis. Finally, we present the first model for the making of a membrane via PC synthesis.
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García E, Coa JC, Otero E, Carda M, Vélez ID, Robledo SM, Cardona WI. Synthesis and antiprotozoal activity of furanchalcone–quinoline, furanchalcone–chromone and furanchalcone–imidazole hybrids. Med Chem Res 2017. [DOI: 10.1007/s00044-017-2076-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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17
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Fernandes BS, Vieira JPF, Contesini FJ, Mantelatto PE, Zaiat M, Pradella JGDC. High value added lipids produced by microorganisms: a potential use of sugarcane vinasse. Crit Rev Biotechnol 2017; 37:1048-1061. [DOI: 10.1080/07388551.2017.1304356] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Bruna Soares Fernandes
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Centre of Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - João Paulo Fernandes Vieira
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Centre of Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Fabiano Jares Contesini
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Centre of Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Paulo Eduardo Mantelatto
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Centre of Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Marcelo Zaiat
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Centre of Research in Energy and Materials (CNPEM), Campinas, Brazil
- Biological Processes Laboratory, Center for Research, Development and Innovation in Environmental Engineering, São Carlos School of Engineering (EESC), University of São Paulo (USP), São Carlos, Brazil
| | - José Geraldo da Cruz Pradella
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Centre of Research in Energy and Materials (CNPEM), Campinas, Brazil
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18
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Lipidomics in research on yeast membrane lipid homeostasis. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:797-799. [PMID: 28219720 DOI: 10.1016/j.bbalip.2017.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 11/21/2022]
Abstract
Mass spectrometry is increasingly used in research on membrane lipid homeostasis, both in analyses of the steady state lipidome at the level of molecular lipid species, and in pulse-chase approaches employing stable isotope-labeled lipid precursors addressing the dynamics of lipid metabolism. Here my experience with, and view on mass spectrometry-based lipid analysis is presented, with emphasis on aspects of quantification of membrane lipid composition of the yeast Saccharomyces cerevisiae. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.
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19
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Oelkers P, Pokhrel K. Four Acyltransferases Uniquely Contribute to Phospholipid Heterogeneity in Saccharomyces cerevisiae. Lipid Insights 2016; 9:31-41. [PMID: 27920551 PMCID: PMC5127605 DOI: 10.4137/lpi.s40597] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/25/2016] [Accepted: 10/25/2016] [Indexed: 11/14/2022] Open
Abstract
Diverse acyl-CoA species and acyltransferase isoenzymes are components of a complex system that synthesizes glycerophospholipids and triacylglycerols. Saccharomyces cerevisiae has four main acyl-CoA species, two main glycerol-3-phosphate 1-O-acyltransferases (Gat1p, Gat2p), and two main 1-acylglycerol-3-phosphate O-acyltransferases (Lpt1p, Slc1p). The in vivo contribution of these isoenzymes to phospholipid heterogeneity was determined using haploids with compound mutations: gat1Δlpt1Δ, gat2Δlpt1Δ, gat1Δslc1Δ, and gat2Δslc1Δ. All mutations mildly reduced [3H]palmitic acid incorporation into phospholipids relative to triacylglycerol. Electrospray ionization tandem mass spectrometry identified few differences from wild type in gat1Δlpt1Δ, dramatic differences in gat2Δslc1Δ, and intermediate changes in gat2Δlpt1Δ and gat1Δslc1Δ. Yeast expressing Gat1p and Lpt1p had phospholipids enriched with acyl chains that were unsaturated, 18 carbons long, and paired for length. These alterations prevented growth at 18.5°C and in 10% ethanol. Therefore, Gat2p and Slc1p dictate phospholipid acyl chain composition in rich media at 30°C. Slc1p selectively pairs acyl chains of different lengths.
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Affiliation(s)
- Peter Oelkers
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, USA
| | - Keshav Pokhrel
- Department of Mathematics and Statistics, University of Michigan-Dearborn, Dearborn, MI, USA
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20
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Synthesis of Novel Quaternary Ammonium Salts and Their in Vitro Antileishmanial Activity and U-937 Cell Cytotoxicity. Molecules 2016; 21:381. [PMID: 27043509 PMCID: PMC6273649 DOI: 10.3390/molecules21040381] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 03/11/2016] [Accepted: 03/14/2016] [Indexed: 01/17/2023] Open
Abstract
This work describes the synthesis of a series of quaternary ammonium salts and the assessment of their in vitro antileishmanial activity and cytotoxicity. A preliminary discussion on a structure-activity relationship of the compounds is also included. Three series of quaternary ammonium salts were prepared: (i) halomethylated quaternary ammonium salts (series I); (ii) non-halogenated quaternary ammonium salts (series II) and (iii) halomethylated choline analogs (series III). Assessments of their in vitro cytotoxicity in human promonocytic cells U-937 and antileishmanial activity in axenic amastigotes of L. (Viannia) panamensis (M/HOM/87/UA140-pIR-eGFP) were carried out using the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide) micromethod. Antileishmanial activity was also tested in intracellular amastigotes of L. (V) panamensis using flow cytometry. High toxicity for human U937 cells was found with most of the compounds, which exhibited Lethal Concentration 50 (LC50) values in the range of 9 to 46 μg/mL. Most of the compounds evidenced antileishmanial activity. In axenic amastigotes, the antileishmanial activity varied from 14 to 57 μg/mL, while in intracellular amastigotes their activity varied from 17 to 50 μg/mL. N-Chloromethyl-N,N-dimethyl-N-(4,4-diphenylbut-3-en-1-yl)ammonium iodide (1a), N-iodomethyl-N,N-dimethyl-N-(4,4-diphenylbut-3-en-1-yl)ammonium iodide (2a), N,N,N-trimethyl-N-(4,4-diphenylbut-3-en-1-yl)ammonium iodide (3a) and N,N,N-trimethyl-N-(5,5-diphenylpent-4-en-1-yl)ammonium iodide (3b) turned out to be the most active compounds against intracellular amastigotes of L. (V) panamensis, with EC50 values varying between 24.7 for compound 3b and 38.4 μg/mL for compound 1a. Thus, these compounds represents new “hits” in the development of leishmanicidal drugs.
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21
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Renne MF, Bao X, De Smet CH, de Kroon AIPM. Lipid Acyl Chain Remodeling in Yeast. Lipid Insights 2016; 8:33-40. [PMID: 26819558 PMCID: PMC4720183 DOI: 10.4137/lpi.s31780] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/21/2015] [Indexed: 11/05/2022] Open
Abstract
Membrane lipid homeostasis is maintained by de novo synthesis, intracellular transport, remodeling, and degradation of lipid molecules. Glycerophospholipids, the most abundant structural component of eukaryotic membranes, are subject to acyl chain remodeling, which is defined as the post-synthetic process in which one or both acyl chains are exchanged. Here, we review studies addressing acyl chain remodeling of membrane glycerophospholipids in Saccharomyces cerevisiae, a model organism that has been successfully used to investigate lipid synthesis and its regulation. Experimental evidence for the occurrence of phospholipid acyl chain exchange in cardiolipin, phosphatidylcholine, phosphatidylinositol, and phosphatidylethanolamine is summarized, including methods and tools that have been used for detecting remodeling. Progress in the identification of the enzymes involved is reported, and putative functions of acyl chain remodeling in yeast are discussed.
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Affiliation(s)
- Mike F Renne
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Xue Bao
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Cedric H De Smet
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands.; Present address: Division of Cell Biology, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Anton I P M de Kroon
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
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22
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da Silveira Dos Santos AX, Riezman I, Aguilera-Romero MA, David F, Piccolis M, Loewith R, Schaad O, Riezman H. Systematic lipidomic analysis of yeast protein kinase and phosphatase mutants reveals novel insights into regulation of lipid homeostasis. Mol Biol Cell 2014; 25:3234-46. [PMID: 25143408 PMCID: PMC4196872 DOI: 10.1091/mbc.e14-03-0851] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The regulatory pathways required to maintain eukaryotic lipid homeostasis are largely unknown. We developed a systematic approach to uncover new players in the regulation of lipid homeostasis. Through an unbiased mass spectrometry-based lipidomic screening, we quantified hundreds of lipid species, including glycerophospholipids, sphingolipids, and sterols, from a collection of 129 mutants in protein kinase and phosphatase genes of Saccharomyces cerevisiae. Our approach successfully identified known kinases involved in lipid homeostasis and uncovered new ones. By clustering analysis, we found connections between nutrient-sensing pathways and regulation of glycerophospholipids. Deletion of members of glucose- and nitrogen-sensing pathways showed reciprocal changes in glycerophospholipid acyl chain lengths. We also found several new candidates for the regulation of sphingolipid homeostasis, including a connection between inositol pyrophosphate metabolism and complex sphingolipid homeostasis through transcriptional regulation of AUR1 and SUR1. This robust, systematic lipidomic approach constitutes a rich, new source of biological information and can be used to identify novel gene associations and function.
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Affiliation(s)
- Aline Xavier da Silveira Dos Santos
- Department of Biochemistry, University of Geneva, Geneva CH-1211, Switzerland National Centre of Competence in Research "Chemical Biology,", University of Geneva, Geneva CH-1211, Switzerland
| | - Isabelle Riezman
- Department of Biochemistry, University of Geneva, Geneva CH-1211, Switzerland
| | - Maria-Auxiliadora Aguilera-Romero
- Department of Biochemistry, University of Geneva, Geneva CH-1211, Switzerland National Centre of Competence in Research "Chemical Biology,", University of Geneva, Geneva CH-1211, Switzerland
| | - Fabrice David
- École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Manuele Piccolis
- Department of Molecular Biology, University of Geneva, Geneva CH-1211, Switzerland
| | - Robbie Loewith
- National Centre of Competence in Research "Chemical Biology,", University of Geneva, Geneva CH-1211, Switzerland Department of Molecular Biology, University of Geneva, Geneva CH-1211, Switzerland
| | - Olivier Schaad
- Department of Biochemistry, University of Geneva, Geneva CH-1211, Switzerland
| | - Howard Riezman
- Department of Biochemistry, University of Geneva, Geneva CH-1211, Switzerland National Centre of Competence in Research "Chemical Biology,", University of Geneva, Geneva CH-1211, Switzerland
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23
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de Ghellinck A, Schaller H, Laux V, Haertlein M, Sferrazza M, Maréchal E, Wacklin H, Jouhet J, Fragneto G. Production and analysis of perdeuterated lipids from Pichia pastoris cells. PLoS One 2014; 9:e92999. [PMID: 24747350 PMCID: PMC3991571 DOI: 10.1371/journal.pone.0092999] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/27/2014] [Indexed: 01/18/2023] Open
Abstract
Probing molecules using perdeuteration (i.e deuteration in which all hydrogen atoms are replaced by deuterium) is extremely useful in a wide range of biophysical techniques. In the case of lipids, the synthesis of the biologically relevant unsaturated perdeuterated lipids is challenging and not usually pursued. In this work, perdeuterated phospholipids and sterols from the yeast Pichia pastoris grown in deuterated medium are extracted and analyzed as derivatives by gas chromatography and mass spectrometry respectively. When yeast cells are grown in a deuterated environment, the phospholipid homeostasis is maintained but the fatty acid unsaturation level is modified while the ergosterol synthesis is not affected by the deuterated culture medium. Our results confirm that the production of well defined natural unsaturated perdeuterated lipids is possible and gives also new insights about the process of desaturase enzymes.
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Affiliation(s)
- Alexis de Ghellinck
- Institut Laue-Langevin, Grenoble, France
- Service des polymères, Université Libre de Bruxelles, Brussels, Belgium
| | - Hubert Schaller
- Institut de Biologie Moléculaire des Plantes du CNRS, Strasbourg, France
| | | | | | - Michele Sferrazza
- Service des polymères, Université Libre de Bruxelles, Brussels, Belgium
| | - Eric Maréchal
- Laboratoire de physiologie cellulaire et végétale, CNRS/CEA/Univ. Grenoble Alpes/INRA, Grenoble, France
| | - Hanna Wacklin
- European Spallation Source ESS AB, Lund, Sweden
- Chemistry Department, University of Copenhagen, Copenhagen, Denmark
| | - Juliette Jouhet
- Laboratoire de physiologie cellulaire et végétale, CNRS/CEA/Univ. Grenoble Alpes/INRA, Grenoble, France
- * E-mail:
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24
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Kishino H, Eguchi H, Takagi K, Horiuchi H, Fukuda R, Ohta A. Acyl-chain remodeling of dioctanoyl-phosphatidylcholine in Saccharomyces cerevisiae mutant defective in de novo and salvage phosphatidylcholine synthesis. Biochem Biophys Res Commun 2014; 445:289-93. [PMID: 24491568 DOI: 10.1016/j.bbrc.2014.01.136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 01/25/2014] [Indexed: 10/25/2022]
Abstract
A yeast strain, in which endogenous phosphatidylcholine (PC) synthesis is controllable, was constructed by the replacement of the promoter of PCT1, encoding CTP:phosphocholine cytidylyltransferase, with GAL1 promoter in a double deletion mutant of PEM1 and PEM2, encoding phosphatidylethanolamine methyltransferase and phospholipid methyltransferase, respectively. This mutant did not grow in the glucose-containing medium, but the addition of dioctanoyl-phosphatidylcholine (diC8PC) supported its growth. Analyses of the metabolism of (13)C-labeled diC8PC ((methyl-(13)C)3-diC8PC) in this strain using electrospray ionization tandem mass spectrometry revealed that it was converted to PC species containing acyl residues of 16 or 18 carbons at both sn-1 and sn-2 positions. In addition, both acyl residues of (methyl-(13)C)3-diC8PC were replaced with 16:1 acyl chains in the in vitro reaction using the yeast cell extract in the presence of palmitoleoyl-CoA. These results indicate that PC containing short acyl residues was remodeled to those with acyl chains of physiological length in yeast.
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Affiliation(s)
- Hideyuki Kishino
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroki Eguchi
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Keiko Takagi
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroyuki Horiuchi
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryouichi Fukuda
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akinori Ohta
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.
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25
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Application of stable isotopes to investigate the metabolism of fatty acids, glycerophospholipid and sphingolipid species. Prog Lipid Res 2014; 54:14-31. [PMID: 24462586 DOI: 10.1016/j.plipres.2014.01.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 12/30/2013] [Accepted: 01/07/2014] [Indexed: 11/22/2022]
Abstract
Nature provides an enormous diversity of lipid molecules that originate from various pathways. To gain insight into the metabolism and dynamics of lipid species, the application of stable isotope-labeled tracers combined with mass spectrometric analysis represents a perfect tool. This review provides an overview of strategies to track fatty acid, glycerophospholipid, and sphingolipid metabolism. In particular, the selection of stable isotope-labeled precursors and their mass spectrometric analysis is discussed. Furthermore, examples of metabolic studies that were performed in cell culture, animal and clinical experiments are presented.
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26
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The turnover of glycerol and acyl moieties of cardiolipin. Chem Phys Lipids 2013; 179:17-24. [PMID: 24184572 DOI: 10.1016/j.chemphyslip.2013.10.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 10/14/2013] [Accepted: 10/16/2013] [Indexed: 01/30/2023]
Abstract
The dynamical behavior of mitochondria has attracted much attention, but little is known about the dynamics of mitochondrial lipids, specifically cardiolipin (CL). Here, we estimated the turnover of select molecular species of CL in mammalian cell cultures and compared it to the turnover of other lipids, including phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylinositol. Cells were labeled with myristic acid, 9,10-²H₂-oleic acid, or D-[U-¹³C₆]-glucose and analyzed by mass spectrometry at different time points of pulse-chase experiments. The turnover of glycerol groups was monitored by specific isotopologues that carried ¹³C primarily in the glycerol carbons, whereas the turnover of acyl groups was monitored by molecular species that carried myristoyl or ²H₂-oleoyl groups. We found that the turnover of CL, but not of mitochondrial PC and PE, was substantially slower than the turnover of other cellular phospholipids. In dioleoyl-PC and dioleoyl-PE, the acyl turnover was faster than the glycerol turnover, indicating continuous deacylation and reacylation of the oleoyl residues. In contrast, the acyl turnover was similar to the glycerol turnover in tetraoleoyl-CL, suggesting that oleoyl remodeling did not take place continuously in endogenous CL. We conclude that CL, once assembled in mitochondrial membranes, remains largely inert to degradation and acyl remodeling.
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27
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Horvath SE, Daum G. Lipids of mitochondria. Prog Lipid Res 2013; 52:590-614. [PMID: 24007978 DOI: 10.1016/j.plipres.2013.07.002] [Citation(s) in RCA: 606] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 07/31/2013] [Indexed: 01/06/2023]
Abstract
A unique organelle for studying membrane biochemistry is the mitochondrion whose functionality depends on a coordinated supply of proteins and lipids. Mitochondria are capable of synthesizing several lipids autonomously such as phosphatidylglycerol, cardiolipin and in part phosphatidylethanolamine, phosphatidic acid and CDP-diacylglycerol. Other mitochondrial membrane lipids such as phosphatidylcholine, phosphatidylserine, phosphatidylinositol, sterols and sphingolipids have to be imported. The mitochondrial lipid composition, the biosynthesis and the import of mitochondrial lipids as well as the regulation of these processes will be main issues of this review article. Furthermore, interactions of lipids and mitochondrial proteins which are highly important for various mitochondrial processes will be discussed. Malfunction or loss of enzymes involved in mitochondrial phospholipid biosynthesis lead to dysfunction of cell respiration, affect the assembly and stability of the mitochondrial protein import machinery and cause abnormal mitochondrial morphology or even lethality. Molecular aspects of these processes as well as diseases related to defects in the formation of mitochondrial membranes will be described.
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Affiliation(s)
- Susanne E Horvath
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, A-8010 Graz, Austria
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Qiao B, Lu H, Cao YX, Chen R, Yuan YJ. Phospholipid profiles ofPenicillium chrysogenumin different scales of fermentations. Eng Life Sci 2013. [DOI: 10.1002/elsc.201200139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Bin Qiao
- Key Laboratory of Systems Bioengineering, Ministry of Education; School of Chemical Engineering and Technology, Tianjin University; Tianjin P. R. China
| | - Hua Lu
- Key Laboratory of Systems Bioengineering, Ministry of Education; School of Chemical Engineering and Technology, Tianjin University; Tianjin P. R. China
- Hebei Zhongrun Pharmaceutical Co., Ltd; China, Shijiazhuang Pharmaceutical Group Co., Ltd. (CSPC); Shijiazhuang P. R. China
| | - Ying-Xiu Cao
- Key Laboratory of Systems Bioengineering, Ministry of Education; School of Chemical Engineering and Technology, Tianjin University; Tianjin P. R. China
| | - Rao Chen
- Hebei Zhongrun Pharmaceutical Co., Ltd; China, Shijiazhuang Pharmaceutical Group Co., Ltd. (CSPC); Shijiazhuang P. R. China
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering, Ministry of Education; School of Chemical Engineering and Technology, Tianjin University; Tianjin P. R. China
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Lipid droplets and peroxisomes: key players in cellular lipid homeostasis or a matter of fat--store 'em up or burn 'em down. Genetics 2013; 193:1-50. [PMID: 23275493 PMCID: PMC3527239 DOI: 10.1534/genetics.112.143362] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Lipid droplets (LDs) and peroxisomes are central players in cellular lipid homeostasis: some of their main functions are to control the metabolic flux and availability of fatty acids (LDs and peroxisomes) as well as of sterols (LDs). Both fatty acids and sterols serve multiple functions in the cell—as membrane stabilizers affecting membrane fluidity, as crucial structural elements of membrane-forming phospholipids and sphingolipids, as protein modifiers and signaling molecules, and last but not least, as a rich carbon and energy source. In addition, peroxisomes harbor enzymes of the malic acid shunt, which is indispensable to regenerate oxaloacetate for gluconeogenesis, thus allowing yeast cells to generate sugars from fatty acids or nonfermentable carbon sources. Therefore, failure of LD and peroxisome biogenesis and function are likely to lead to deregulated lipid fluxes and disrupted energy homeostasis with detrimental consequences for the cell. These pathological consequences of LD and peroxisome failure have indeed sparked great biomedical interest in understanding the biogenesis of these organelles, their functional roles in lipid homeostasis, interaction with cellular metabolism and other organelles, as well as their regulation, turnover, and inheritance. These questions are particularly burning in view of the pandemic development of lipid-associated disorders worldwide.
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Checks and balances in membrane phospholipid class and acyl chain homeostasis, the yeast perspective. Prog Lipid Res 2013; 52:374-94. [PMID: 23631861 DOI: 10.1016/j.plipres.2013.04.006] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 03/28/2013] [Accepted: 04/16/2013] [Indexed: 11/24/2022]
Abstract
Glycerophospholipids are the most abundant membrane lipid constituents in most eukaryotic cells. As a consequence, phospholipid class and acyl chain homeostasis are crucial for maintaining optimal physical properties of membranes that in turn are crucial for membrane function. The topic of this review is our current understanding of membrane phospholipid homeostasis in the reference eukaryote Saccharomyces cerevisiae. After introducing the physical parameters of the membrane that are kept in optimal range, the properties of the major membrane phospholipids and their contributions to membrane structure and dynamics are summarized. Phospholipid metabolism and known mechanisms of regulation are discussed, including potential sensors for monitoring membrane physical properties. Special attention is paid to processes that maintain the phospholipid class specific molecular species profiles, and to the interplay between phospholipid class and acyl chain composition when yeast membrane lipid homeostasis is challenged. Based on the reviewed studies, molecular species selectivity of the lipid metabolic enzymes, and mass action in acyl-CoA metabolism are put forward as important intrinsic contributors to membrane lipid homeostasis.
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De Smet CH, Cox R, Brouwers JF, de Kroon AIPM. Yeast cells accumulate excess endogenous palmitate in phosphatidylcholine by acyl chain remodeling involving the phospholipase B Plb1p. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1831:1167-76. [PMID: 23501167 DOI: 10.1016/j.bbalip.2013.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 03/01/2013] [Accepted: 03/04/2013] [Indexed: 11/18/2022]
Abstract
In the yeast Saccharomyces cerevisiae, the molecular species profile of the major membrane glycerophospholipid phosphatidylcholine (PC) is determined by the molecular species-selectivity of the biosynthesis routes and by acyl chain remodeling. Overexpression of the glycerol-3-phosphate acyltransferase Sct1p was recently shown to induce a strong increase in the cellular content of palmitate (C16:0). Using stable isotope labeling and mass spectrometry, the present study shows that wild type yeast overexpressing Sct1p incorporates excess C16:0 into PC via the methylation of PE, the CDP-choline route, and post-synthetic acyl chain remodeling. Overexpression of Sct1p increased the extent of remodeling of PE-derived PC, providing a novel tool to perform mechanistic studies on PC acyl chain exchange. The exchange of acyl chains occurred at both the sn-1 and sn-2 positions of the glycerol backbone of PC, and required the phospholipase B Plb1p for optimal efficiency. Sct1p-catalyzed acyl chain exchange, the acyl-CoA binding protein Acb1p, the Plb1p homologue Plb2p, and the glycerophospholipid:triacylglycerol transacylase Lro1p were not required for PC remodeling. The results indicate that PC serves as a buffer for excess cellular C16:0.
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Qiao B, Tian HC, Yuan YJ. Comparative lipidomic analysis of S. cerevisiae cells during industrial bioethanol fermentation. Front Chem Sci Eng 2012. [DOI: 10.1007/s11705-012-1223-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Klose C, Surma MA, Gerl MJ, Meyenhofer F, Shevchenko A, Simons K. Flexibility of a eukaryotic lipidome--insights from yeast lipidomics. PLoS One 2012; 7:e35063. [PMID: 22529973 PMCID: PMC3329542 DOI: 10.1371/journal.pone.0035063] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 03/12/2012] [Indexed: 11/20/2022] Open
Abstract
Mass spectrometry-based shotgun lipidomics has enabled the quantitative and comprehensive assessment of cellular lipid compositions. The yeast Saccharomyces cerevisiae has proven to be a particularly valuable experimental system for studying lipid-related cellular processes. Here, by applying our shotgun lipidomics platform, we investigated the influence of a variety of commonly used growth conditions on the yeast lipidome, including glycerophospholipids, triglycerides, ergosterol as well as complex sphingolipids. This extensive dataset allowed for a quantitative description of the intrinsic flexibility of a eukaryotic lipidome, thereby providing new insights into the adjustments of lipid biosynthetic pathways. In addition, we established a baseline for future lipidomic experiments in yeast. Finally, flexibility of lipidomic features is proposed as a new parameter for the description of the physiological state of an organism.
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Affiliation(s)
- Christian Klose
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michal A. Surma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Mathias J. Gerl
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Felix Meyenhofer
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Kai Simons
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- * E-mail:
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De Smet CH, Vittone E, Scherer M, Houweling M, Liebisch G, Brouwers JF, de Kroon AIPM. The yeast acyltransferase Sct1p regulates fatty acid desaturation by competing with the desaturase Ole1p. Mol Biol Cell 2012; 23:1146-56. [PMID: 22323296 PMCID: PMC3315803 DOI: 10.1091/mbc.e11-07-0624] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The glycerol-3-phosphate acyltransferase Sct1p/Gat2p is shown to regulate fatty acyl chain desaturation by competing with the fatty acid desaturase Ole1p for C16:0-CoA. The activity of Sct1p depends on the level of expression and the phosphorylation state. The acyltransferase Cst26p regulates the phosphorylation of Sct1p. The degree of fatty acid unsaturation, that is, the ratio of unsaturated versus saturated fatty acyl chains, determines membrane fluidity. Regulation of expression of the fatty acid desaturase Ole1p was hitherto the only known mechanism governing the degree of fatty acid unsaturation in Saccharomyces cerevisiae. We report a novel mechanism for the regulation of fatty acid desaturation that is based on competition between Ole1p and the glycerol-3-phosphate acyltransferase Sct1p/Gat2p for the common substrate C16:0-CoA. Deletion of SCT1 decreases the content of saturated fatty acids, whereas overexpression of SCT1 dramatically decreases the desaturation of fatty acids and affects phospholipid composition. Whereas overexpression of Ole1p increases desaturation, co-overexpression of Ole1p and Sct1p results in a fatty acid composition intermediate between those obtained upon overexpression of the enzymes separately. On the basis of these results, we propose that Sct1p sequesters C16:0-CoA into lipids, thereby shielding it from desaturation by Ole1p. Taking advantage of the growth defect conferred by overexpressing SCT1, we identified the acyltransferase Cst26p/Psi1p as a regulator of Sct1p activity by affecting the phosphorylation state and overexpression level of Sct1p. The level of Sct1p phosphorylation is increased when cells are supplemented with saturated fatty acids, demonstrating the physiological relevance of our findings.
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Affiliation(s)
- Cedric H De Smet
- Membrane Enzymology, Bijvoet Center and Institute of Biomembranes, Utrecht University, Utrecht, Netherlands
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35
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Quantitative profiling of PE, MMPE, DMPE, and PC lipid species by multiple precursor ion scanning: A tool for monitoring PE metabolism. Biochim Biophys Acta Mol Cell Biol Lipids 2011; 1811:1081-9. [DOI: 10.1016/j.bbalip.2011.09.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 09/17/2011] [Accepted: 09/29/2011] [Indexed: 11/23/2022]
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Abstract
The yeast Saccharomyces cerevisiae, with its full complement of organelles, synthesizes membrane phospholipids by pathways that are generally common to those found in higher eukaryotes. Phospholipid synthesis in yeast is regulated in response to a variety of growth conditions (e.g., inositol supplementation, zinc depletion, and growth stage) by a coordination of genetic (e.g., transcriptional activation and repression) and biochemical (e.g., activity modulation and localization) mechanisms. Phosphatidate (PA), whose cellular levels are controlled by the activities of key phospholipid synthesis enzymes, plays a central role in the transcriptional regulation of phospholipid synthesis genes. In addition to the regulation of gene expression, phosphorylation of key phospholipid synthesis catalytic and regulatory proteins controls the metabolism of phospholipid precursors and products.
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Affiliation(s)
- George M Carman
- Department of Food Science and Rutgers Center for Lipid Research, Rutgers University, New Brunswick, New Jersey 08901, USA.
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37
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Homocysteine as a risk factor for atherosclerosis: is its conversion to s-adenosyl-L-homocysteine the key to deregulated lipid metabolism? J Lipids 2011; 2011:702853. [PMID: 21837278 PMCID: PMC3151505 DOI: 10.1155/2011/702853] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 06/04/2011] [Indexed: 11/17/2022] Open
Abstract
Homocysteine (Hcy) has been recognized for the past five decades as a risk factor for atherosclerosis. However, the role of Hcy in the pathological changes associated with atherosclerosis as well as the pathological mechanisms triggered by Hcy accumulation is
poorly understood. Due to the reversal of the physiological direction of the reaction catalyzed by S-adenosyl-L-homocysteine
hydrolase Hcy accumulation leads to the synthesis of S-adenosyl-L-homocysteine (AdoHcy). AdoHcy is a strong product
inhibitor of S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases, and to date more than 50 AdoMet-dependent
methyltransferases that methylate a broad spectrum of cellular compounds including nucleic acids, proteins and lipids have been
identified. Phospholipid methylation is the major consumer of AdoMet, both in mammals and in yeast. AdoHcy accumulation induced
either by Hcy supplementation or due to S-adenosyl-L-homocysteine hydrolase deficiency results in inhibition of phospholipid
methylation in yeast. Moreover, yeast cells accumulating AdoHcy also massively accumulate triacylglycerols (TAG). Similarly, Hcy
supplementation was shown to lead to increased TAG and sterol synthesis as well as to the induction of the unfolded protein
response (UPR) in mammalian cells. In this review a model of deregulation of lipid metabolism in response to accumulation of
AdoHcy in Hcy-associated pathology is proposed.
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Serricchio M, Bütikofer P. Trypanosoma brucei: a model micro-organism to study eukaryotic phospholipid biosynthesis. FEBS J 2011; 278:1035-46. [DOI: 10.1111/j.1742-4658.2011.08012.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Genome-wide screen for inositol auxotrophy in Saccharomyces cerevisiae implicates lipid metabolism in stress response signaling. Mol Genet Genomics 2010; 285:125-49. [PMID: 21136082 DOI: 10.1007/s00438-010-0592-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 11/20/2010] [Indexed: 12/13/2022]
Abstract
Inositol auxotrophy (Ino(-) phenotype) in budding yeast has classically been associated with misregulation of INO1 and other genes involved in lipid metabolism. To identify all non-essential yeast genes that are necessary for growth in the absence of inositol, we carried out a genome-wide phenotypic screening for deletion mutants exhibiting Ino(-) phenotypes under one or more growth conditions. We report the identification of 419 genes, including 385 genes not previously reported, which exhibit this phenotype when deleted. The identified genes are involved in a wide range of cellular processes, but are particularly enriched in those affecting transcription, protein modification, membrane trafficking, diverse stress responses, and lipid metabolism. Among the Ino(-) mutants involved in stress response, many exhibited phenotypes that are strengthened at elevated temperature and/or when choline is present in the medium. The role of inositol in regulation of lipid metabolism and stress response signaling is discussed.
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Zhou X, Zhou J, Tian H, Yuan Y. Dynamic Lipidomic Insights into the Adaptive Responses ofSaccharomyces cerevisiaeto the Repeated Vacuum Fermentation. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2010; 14:563-74. [DOI: 10.1089/omi.2010.0016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Xiao Zhou
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jian Zhou
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Hongchi Tian
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Yingjin Yuan
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
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41
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Balgoma D, Montero O, Balboa MA, Balsinde J. Lipidomic approaches to the study of phospholipase A2-regulated phospholipid fatty acid incorporation and remodeling. Biochimie 2010; 92:645-50. [DOI: 10.1016/j.biochi.2009.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Accepted: 11/26/2009] [Indexed: 12/21/2022]
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42
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Déchamps S, Wengelnik K, Berry-Sterkers L, Cerdan R, Vial HJ, Gannoun-Zaki L. The Kennedy phospholipid biosynthesis pathways are refractory to genetic disruption in Plasmodium berghei and therefore appear essential in blood stages. Mol Biochem Parasitol 2010; 173:69-80. [PMID: 20478340 DOI: 10.1016/j.molbiopara.2010.05.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 05/04/2010] [Accepted: 05/08/2010] [Indexed: 12/15/2022]
Abstract
Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) are the main membrane phospholipids (PLs) of Plasmodium parasites and can be generated by the de novo (Kennedy) CDP-choline and CDP-ethanolamine pathways and by the CDP-diacylglycerol dependent pathway. The Kennedy pathways initiate from exogenous choline and ethanolamine involving choline kinase (CK) and ethanolamine kinase (EK), followed by the choline-phosphate cytidylyltransferase (CCT) and ethanolamine-phosphate cytidylyltransferase (ECT) that catalyse the formation of CDP-choline and CDP-ethanolamine. Finally, in Plasmodium, PC and PE are apparently synthesized by a common choline/ethanolamine-phosphotransferase (CEPT). Here, we have studied the essential nature of the Kennedy pathways in Plasmodium berghei, a rodent malaria parasite. Sequence analysis of the P. berghei CEPT, CCT, ECT and CK enzymes revealed the presence of all catalytic domains and essential residues and motifs necessary for enzymatic activities. Constructs were designed for the generation of gene knockout and GFP-fusions of the cept, cct, ect and ck genes in P. berghei. We found that all four genes were consistently refractory to knockout attempts. At the same time, successful tagging of these proteins with GFP demonstrated that the loci were targetable and indicated that these genes are essential in P. berghei blood stage parasites. GFP-fusions of CCT, ECT and CK were found in the cytosol whereas the GFP-CEPT mainly localised in the endoplasmic reticulum. These results indicate that both CDP-choline and CDP-ethanolamine de novo pathways are essential for asexual P. berghei development and are non-redundant with other possible sources of PC and PE.
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Affiliation(s)
- Sandrine Déchamps
- Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235, CNRS-Universite Montpellier 2, Place Eugene Bataillon, cc107, Montpellier 34095, Cedex 05, France
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Li Y, Zou W, Yan Q, Xu Y, Xia Q, Tsui Z, Ma K. Over-expression of pemt2 into rat hepatoma cells contributes to the mitochondrial apoptotic pathway. IUBMB Life 2009; 61:846-52. [PMID: 19517528 DOI: 10.1002/iub.222] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We previously established a line of phosphatidylethanolamine N-methyltransferase 2 (pemt2) -stably transfected CBRH-7919 hepatoma cells, and showed that pemt2 over-expression inhibited cell proliferation and induced apoptosis. This study was aimed to further elucidate the cellular mechanisms leading to this apoptosis in these cells. Fatty acid compositions of phosphatidylcholine (PC) in pemt2 over-expressed cells and control cells, and the location of PC synthesized by PEMT2 pathway were analyzed with lipid extraction, high-performance thin layer chromatography, high-performance gas chromatography (HPGC), and [(3)H]-ethanolamine tracing. The effects of pemt2 over-expression on the mitochondrial membrane fluidity, the release of cytochrome C from mitochondria, and the activity of caspases were determined by Western blot. Newly synthesized PC by PEMT2 contained more acyl groups of oleic acid (P < 0.01) and was mainly located in mitochondria; pemt2 over-expression increased the mitochondrial membrane fluidity and the release of cytochrome C from the mitochondria into the cytoplasma, which in turn activated caspase-9 and caspase-3, the key molecules in the mitochondrial apoptotic pathway. We demonstrated that, in rat hepatoma cells, PEMT2-induced apoptosis proceeds through mitochondria.
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Affiliation(s)
- Yali Li
- Department of Biochemistry, Dalian Medical University, Dalian 116044, People's Republic of China
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44
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Postle AD, Hunt AN. Dynamic lipidomics with stable isotope labelling. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:2716-21. [DOI: 10.1016/j.jchromb.2009.03.046] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 03/29/2009] [Accepted: 03/30/2009] [Indexed: 01/22/2023]
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45
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Rijken PJ, Houtkooper RH, Akbari H, Brouwers JF, Koorengevel MC, de Kruijff B, Frentzen M, Vaz FM, de Kroon AIPM. Cardiolipin molecular species with shorter acyl chains accumulate in Saccharomyces cerevisiae mutants lacking the acyl coenzyme A-binding protein Acb1p: new insights into acyl chain remodeling of cardiolipin. J Biol Chem 2009; 284:27609-19. [PMID: 19656950 DOI: 10.1074/jbc.m109.016311] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The function of the mitochondrial phospholipid cardiolipin (CL) is thought to depend on its acyl chain composition. The present study aims at a better understanding of the way the CL species profile is established in Saccharomyces cerevisiae by using depletion of the acyl-CoA-binding protein Acb1p as a tool to modulate the cellular acyl chain content. Despite the presence of an intact CL remodeling system, acyl chains shorter than 16 carbon atoms (C16) were found to accumulate in CL in cells lacking Acb1p. Further experiments revealed that Taz1p, a key CL remodeling enzyme, was not responsible for the shortening of CL in the absence of Acb1p. This left de novo CL synthesis as the only possible source of acyl chains shorter than C16 in CL. Experiments in which the substrate specificity of the yeast cardiolipin synthase Crd1p and the acyl chain composition of individual short CL species were investigated, indicated that both CL precursors (i.e. phosphatidylglycerol and CDP-diacylglycerol) contribute to comparable extents to the shorter acyl chains in CL in acb1 mutants. Based on the findings, we conclude that the fatty acid composition of mature CL in yeast is governed by the substrate specificity of the CL-specific lipase Cld1p and the fatty acid composition of the Taz1p substrates.
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Affiliation(s)
- Pieter J Rijken
- Department of Biochemistry of Membranes, Bijvoet Institute and Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
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46
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A role for SCT1/GAT2 in acyl chain remodeling of phosphatidylcholine. Chem Phys Lipids 2009. [DOI: 10.1016/j.chemphyslip.2009.06.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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Mina JG, Pan SY, Wansadhipathi NK, Bruce CR, Shams-Eldin H, Schwarz RT, Steel PG, Denny PW. The Trypanosoma brucei sphingolipid synthase, an essential enzyme and drug target. Mol Biochem Parasitol 2009; 168:16-23. [PMID: 19545591 DOI: 10.1016/j.molbiopara.2009.06.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 06/10/2009] [Accepted: 06/11/2009] [Indexed: 12/29/2022]
Abstract
Sphingolipids are important components of eukaryotic membranes, particularly the plasma membrane, and are involved in a diverse array of signal transduction processes. In the Eukaryota the biosynthetic pathway for the formation of these lipid species is largely conserved. However, in contrast to mammals which produce sphingomyelin (SM), several pathogenic fungi and protozoa synthesize inositol phosphorylceramide (IPC) as the primary phosphosphingolipid. This process is catalyzed by the enzyme IPC synthase, a recognized target for anti-fungals encoded by the AUR1 gene in yeast. Recently, functional orthologues of the AUR1p have been identified in a group of insect vector-borne pathogenic protozoa, the Kinetoplastida, which are responsible for a range of so-called neglected diseases. Of these the Trypanosoma brucei species are the causative agents of human African trypanosomiasis in many of the most under-developed regions of Africa. The available treatments for these diseases are limited, of decreasing efficacy, and often demonstrate severe side-effects. Against this background the T. brucei sphingolipid synthase, an orthologue of the yeast AUR1p, may represent a promising target for novel anti-protozoals. Our studies identify an isoform of this protein as a novel bi-functional enzyme capable of catalyzing the synthesis of both IPC and SM, both known to be present in the parasite. Furthermore, the synthase is essential for parasite growth and can be inhibited by a known anti-fungal at low nanomolar levels in vitro. Most notably this drug demonstrates trypanocidal activity against cultured bloodstream form parasites. Thus, the T. brucei sphingolipid synthase represents a valid and promising drug target.
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Affiliation(s)
- John G Mina
- Centre for Bioactive Chemistry, Department of Chemistry and School of Biological and Biomedical Sciences, Durham University, Durham, UK
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48
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From lipids analysis towards lipidomics, a new challenge for the analytical chemistry of the 21st century. Part II: Analytical lipidomics. Trends Analyt Chem 2009. [DOI: 10.1016/j.trac.2008.12.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Xia JM, Yuan YJ. Comparative lipidomics of four strains of Saccharomyces cerevisiae reveals different responses to furfural, phenol, and acetic acid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:99-108. [PMID: 19049411 DOI: 10.1021/jf802720t] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
To reveal differences between inhibitor-resistant Saccharomyces cerevisiae strains and their parental strain and to investigate the response of S. cerevisiae to furfural, phenol, and acetic acid, comparative lipidomics strategy was employed using an LC-ESI/MS(n) technique on four S. cerevisiae strains, which include an industrial strain (SC) and three tolerant strains screened by this laboratory by step adaptationa furfural-tolerant strain (SCF), a phenol-tolerant strain (SCP), and an acetic acid-tolerant strain (SCA). Lipidome data were then analyzed using wavelet transform-principal component analysis (WT-PCA). Results revealed that phosphatidylcholines (PCs), phosphatidylinositols (PIs), and phosphatidic acids (PAs) were biomarkers for discriminating SC from SCF, SCP, and SCA, respectively. PIs were believed to be extraordinarily important in all inhibitor-tolerant processes because they were the biomarkers responsible for the discrimination of all four different strains. Further analysis of the distribution of different hydrocarbon chains revealed that both the saturation and the length of the chains helped in maintaining proper fluidity of membranes.
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Affiliation(s)
- Jin-Mei Xia
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
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MacKinnon MA, Curwin AJ, Gaspard GJ, Suraci AB, Fernández-Murray JP, McMaster CR. The Kap60-Kap95 karyopherin complex directly regulates phosphatidylcholine synthesis. J Biol Chem 2009; 284:7376-84. [PMID: 19141610 DOI: 10.1074/jbc.m809117200] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Phosphatidylcholine is the major phospholipid in eukaryotic cells. There are two main pathways for the synthesis of phosphatidylcholine: the CDP-choline pathway present in all eukaryotes and the phosphatidylethanolamine methylation pathway present in mammalian hepatocytes and some single celled eukaryotes, including the yeast Saccharomyces cerevisiae. In S. cerevisiae, the rate-determining step in the synthesis of phosphatidylcholine via the CDP-choline pathway is catalyzed by Pct1. Pct1 converts phosphocholine and CTP to CDP-choline and pyrophosphate. In this study, we determined that Pct1 is in the nucleoplasm and at endoplasmic reticulum and nuclear membranes. Pct1 directly interacts with the alpha-importin Kap60 via a bipartite basic region in Pct1, and this region of Pct1 was required for its entry into the nucleus. Pct1 also interacted with the beta-importin Kap95 in cell extracts, implying a model whereby Pct1 interacts with Kap60 and Kap95 with this tripartite complex transiting the nuclear pore. Exclusion of Pct1 from the nucleus by elimination of its nuclear localization signal or by decreasing Kap60 function did not affect the level of phosphatidylcholine synthesis. Diminution of Kap95 function resulted in almost complete ablation of phosphatidylcholine synthesis under conditions where Pct1 was extranuclear. The beta-importin Kap95 is a direct regulator membrane synthesis.
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Affiliation(s)
- Melissa A MacKinnon
- Department of Pediatrics, Atlantic Research Centre, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
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