301
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Neubauer C, Dalleska NF, Cowley ES, Shikuma NJ, Wu CH, Sessions AL, Newman DK. Lipid remodeling in Rhodopseudomonas palustris TIE-1 upon loss of hopanoids and hopanoid methylation. GEOBIOLOGY 2015; 13:443-53. [PMID: 25923996 DOI: 10.1111/gbi.12143] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/23/2015] [Indexed: 05/17/2023]
Abstract
The sedimentary record of molecular fossils (biomarkers) can potentially provide important insights into the composition of ancient organisms; however, it only captures a small portion of their original lipid content. To interpret what remains, it is important to consider the potential for functional overlap between different lipids in living cells, and how the presence of one type might impact the abundance of another. Hopanoids are a diverse class of steroid analogs made by bacteria and found in soils, sediments, and sedimentary rocks. Here, we examine the trade-off between hopanoid production and that of other membrane lipids. We compare lipidomes of the metabolically versatile α-proteobacterium Rhodopseudomonas palustris TIE-1 and two hopanoid mutants, detecting native hopanoids simultaneously with other types of polar lipids by electrospray ionization mass spectrometry. In all strains, the phospholipids contain high levels of unsaturated fatty acids (often >80%). The degree to which unsaturated fatty acids are modified to cyclopropyl fatty acids varies by phospholipid class. Deletion of the capacity for hopanoid production is accompanied by substantive changes to the lipidome, including a several-fold rise of cardiolipins. Deletion of the ability to make methylated hopanoids has a more subtle effect; however, under photoautotrophic growth conditions, tetrahymanols are upregulated twofold. Together, these results illustrate that the 'lipid fingerprint' produced by a micro-organism can vary depending on the growth condition or loss of single genes, reminding us that the absence of a biomarker does not necessarily imply the absence of a particular source organism.
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Affiliation(s)
- C Neubauer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - N F Dalleska
- Environmental Analysis Center, California Institute of Technology, Pasadena, CA, USA
| | - E S Cowley
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - N J Shikuma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - C-H Wu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - A L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - D K Newman
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
- Environmental Analysis Center, California Institute of Technology, Pasadena, CA, USA
- Howard Hughes Medical Institute, Pasadena, CA, USA
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302
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Malinina L, Simanshu DK, Zhai X, Samygina VR, Kamlekar R, Kenoth R, Ochoa-Lizarralde B, Malakhova ML, Molotkovsky JG, Patel DJ, Brown RE. Sphingolipid transfer proteins defined by the GLTP-fold. Q Rev Biophys 2015; 48:281-322. [PMID: 25797198 PMCID: PMC4691851 DOI: 10.1017/s003358351400016x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Glycolipid transfer proteins (GLTPs) originally were identified as small (~24 kDa), soluble, amphitropic proteins that specifically accelerate the intermembrane transfer of glycolipids. GLTPs and related homologs now are known to adopt a unique, helically dominated, two-layer 'sandwich' architecture defined as the GLTP-fold that provides the structural underpinning for the eukaryotic GLTP superfamily. Recent advances now provide exquisite insights into structural features responsible for lipid headgroup selectivity as well as the adaptability of the hydrophobic compartment for accommodating hydrocarbon chains of differing length and unsaturation. A new understanding of the structural versatility and evolutionary premium placed on the GLTP motif has emerged. Human GLTP-motifs have evolved to function not only as glucosylceramide binding/transferring domains for phosphoinositol 4-phosphate adaptor protein-2 during glycosphingolipid biosynthesis but also as selective binding/transfer proteins for ceramide-1-phosphate. The latter, known as ceramide-1-phosphate transfer protein, recently has been shown to form GLTP-fold while critically regulating Group-IV cytoplasmic phospholipase A2 activity and pro-inflammatory eicosanoid production.
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Affiliation(s)
- Lucy Malinina
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
- Structural Biology Unit, CICbioGUNE, Technology Park of Bizkaia, 48160 Derio-Bilbao, Spain
| | - Dhirendra K. Simanshu
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Xiuhong Zhai
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Valeria R. Samygina
- Structural Biology Unit, CICbioGUNE, Technology Park of Bizkaia, 48160 Derio-Bilbao, Spain
| | | | - Roopa Kenoth
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Borja Ochoa-Lizarralde
- Structural Biology Unit, CICbioGUNE, Technology Park of Bizkaia, 48160 Derio-Bilbao, Spain
| | | | - Julian G. Molotkovsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dinshaw J. Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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303
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Grether-Beck S, Felsner I, Koehler T, Farwick M, Lersch P, Rawlings AV, Krutmann J. Topical ceramides neither enhance UVB-induced apoptosis in normal human keratinocytes nor affect viability in UVB-irradiated reconstructed human epidermis. Exp Dermatol 2015; 23:853-5. [PMID: 25078364 DOI: 10.1111/exd.12526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2014] [Indexed: 12/21/2022]
Abstract
Ceramides are the major lipid of lamellar sheets present in intercellular spaces of the stratum corneum contributing to epidermal barrier properties. Therefore, ceramides and their analogues have been studied for barrier enhancing and water-holding properties for decades. In vitro studies have indicated cytotoxic potential for cell-permeable ceramides thereby raising the question whether topical ceramide application might contribute to UVB-induced apoptosis. Phytosphingosine, N-hexanoyl-phytosphingosine and N-stearoylphytosphingosine (ceramide III) in concentrations ≤5 μm have been used for co-stimulation with low (160 J/m(2) ) or high (600 J/m(2) ) UVB doses in subconfluent basal and confluent differentiating keratinocytes. Significantly, increased caspase-3 activity was observed in basal keratinocytes irradiated with 600 J/m(2) UVB and in differentiating keratinocytes with both UVB doses. Co-stimulation with the named ceramides did not further increase (i) caspase-3 activity and (ii) nucleosomal fragmentation in differentiating keratinocytes. Moreover, co-stimulation with 1-mm ceramides did not further affect viability/lactate dehydrogenase release in UVB-irradiated reconstructed human epidermis corroborating the safety of these ceramides.
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Affiliation(s)
- Susanne Grether-Beck
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
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304
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Ikeda A, Muneoka T, Murakami S, Hirota A, Yabuki Y, Karashima T, Nakazono K, Tsuruno M, Pichler H, Shirahige K, Kodama Y, Shimamoto T, Mizuta K, Funato K. Sphingolipids regulate telomere clustering by affecting the transcription of genes involved in telomere homeostasis. J Cell Sci 2015; 128:2454-67. [PMID: 26045446 DOI: 10.1242/jcs.164160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 05/20/2015] [Indexed: 12/14/2022] Open
Abstract
In eukaryotic organisms, including mammals, nematodes and yeasts, the ends of chromosomes, telomeres are clustered at the nuclear periphery. Telomere clustering is assumed to be functionally important because proper organization of chromosomes is necessary for proper genome function and stability. However, the mechanisms and physiological roles of telomere clustering remain poorly understood. In this study, we demonstrate a role for sphingolipids in telomere clustering in the budding yeast Saccharomyces cerevisiae. Because abnormal sphingolipid metabolism causes downregulation of expression levels of genes involved in telomere organization, sphingolipids appear to control telomere clustering at the transcriptional level. In addition, the data presented here provide evidence that telomere clustering is required to protect chromosome ends from DNA-damage checkpoint signaling. As sphingolipids are found in all eukaryotes, we speculate that sphingolipid-based regulation of telomere clustering and the protective role of telomere clusters in maintaining genome stability might be conserved in eukaryotes.
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Affiliation(s)
- Atsuko Ikeda
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Tetsuya Muneoka
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Suguru Murakami
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Ayaka Hirota
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Yukari Yabuki
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Takefumi Karashima
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Kota Nakazono
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Masahiro Tsuruno
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Harald Pichler
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14/2, Graz 8010, Austria
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Institute of Molecular and Cellular Biosciences, the University of Tokyo, Tokyo 113-0032, Japan
| | | | - Toshi Shimamoto
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Keiko Mizuta
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Kouichi Funato
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
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305
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Luttgeharm KD, Cahoon EB, Markham JE. A mass spectrometry-based method for the assay of ceramide synthase substrate specificity. Anal Biochem 2015; 478:96-101. [PMID: 25725359 DOI: 10.1016/j.ab.2015.02.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 02/12/2015] [Accepted: 02/17/2015] [Indexed: 01/24/2023]
Abstract
The acyl composition of sphingolipids is determined by the specificity of the enzyme ceramide synthase (EC 2.3.1.24). Ceramide contains a long-chain base (LCB) linked to a variety of fatty acids to produce a lipid class with potentially hundreds of structural variants. An optimized procedure for the assay of ceramide synthase in yeast microsomes is reported that uses mass spectrometry to detect any possible LCB and fatty acid combination synthesized from unlabeled substrates provided in the reaction. The assay requires the delivery of substrates with bovine serum albumin for maximum activity within defined limits of substrate concentration and specific methods to stop the reaction and extract the lipid that avoid the non-enzymatic synthesis of ceramide. The activity of ceramide synthase in yeast microsomes is demonstrated with the four natural LCBs found in yeast along with six saturated and two unsaturated fatty acyl-coenzyme As from 16 to 26 carbons in length. The procedure allows for the determination of substrate specificity and kinetic parameters toward natural substrates for ceramide synthase from potentially any organism.
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Affiliation(s)
- Kyle D Luttgeharm
- Department of Biochemistry and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Edgar B Cahoon
- Department of Biochemistry and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Jennifer E Markham
- Department of Biochemistry and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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306
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Zhang H, Abraham N, Khan LA, Gobel V. RNAi-based biosynthetic pathway screens to identify in vivo functions of non-nucleic acid-based metabolites such as lipids. Nat Protoc 2015; 10:681-700. [PMID: 25837419 PMCID: PMC5597045 DOI: 10.1038/nprot.2015.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The field of metabolomics continues to catalog new compounds, but their functional analysis remains technically challenging, and roles beyond metabolism are largely unknown. Unbiased genetic/RNAi screens are powerful tools to identify the in vivo functions of protein-encoding genes, but not of nonproteinaceous compounds such as lipids. They can, however, identify the biosynthetic enzymes of these compounds-findings that are usually dismissed, as these typically synthesize multiple products. Here, we provide a method using follow-on biosynthetic pathway screens to identify the endpoint biosynthetic enzyme and thus the compound through which they act. The approach is based on the principle that all subsequently identified downstream biosynthetic enzymes contribute to the synthesis of at least this one end product. We describe how to systematically target lipid biosynthetic pathways; optimize targeting conditions; take advantage of pathway branchpoints; and validate results by genetic assays and biochemical analyses. This approach extends the power of unbiased genetic/RNAi screens to identify in vivo functions of non-nucleic acid-based metabolites beyond their metabolic roles. It will typically require several months to identify a metabolic end product by biosynthetic pathway screens, but this time will vary widely depending, among other factors, on the end product's location in the pathway, which determines the number of screens required for its identification.
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Affiliation(s)
- Hongjie Zhang
- Mucosal Immunology and Biology Research Center, Department of Pediatrics, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Nessy Abraham
- Mucosal Immunology and Biology Research Center, Department of Pediatrics, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Liakot A Khan
- Mucosal Immunology and Biology Research Center, Department of Pediatrics, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Verena Gobel
- Mucosal Immunology and Biology Research Center, Department of Pediatrics, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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307
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Rispal D, Eltschinger S, Stahl M, Vaga S, Bodenmiller B, Abraham Y, Filipuzzi I, Movva NR, Aebersold R, Helliwell SB, Loewith R. Target of Rapamycin Complex 2 Regulates Actin Polarization and Endocytosis via Multiple Pathways. J Biol Chem 2015; 290:14963-78. [PMID: 25882841 DOI: 10.1074/jbc.m114.627794] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Indexed: 11/06/2022] Open
Abstract
Target of rapamycin is a Ser/Thr kinase that operates in two conserved multiprotein complexes, TORC1 and TORC2. Unlike TORC1, TORC2 is insensitive to rapamycin, and its functional characterization is less advanced. Previous genetic studies demonstrated that TORC2 depletion leads to loss of actin polarization and loss of endocytosis. To determine how TORC2 regulates these readouts, we engineered a yeast strain in which TORC2 can be specifically and acutely inhibited by the imidazoquinoline NVP-BHS345. Kinetic analyses following inhibition of TORC2, supported with quantitative phosphoproteomics, revealed that TORC2 regulates these readouts via distinct pathways as follows: rapidly through direct protein phosphorylation cascades and slowly through indirect changes in the tensile properties of the plasma membrane. The rapid signaling events are mediated in large part through the phospholipid flippase kinases Fpk1 and Fpk2, whereas the slow signaling pathway involves increased plasma membrane tension resulting from a gradual depletion of sphingolipids. Additional hits in our phosphoproteomic screens highlight the intricate control TORC2 exerts over diverse aspects of eukaryote cell physiology.
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Affiliation(s)
- Delphine Rispal
- From the Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 1211 Geneva
| | - Sandra Eltschinger
- From the Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 1211 Geneva
| | - Michael Stahl
- From the Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 1211 Geneva
| | - Stefania Vaga
- the Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich
| | - Bernd Bodenmiller
- the Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich
| | - Yann Abraham
- the Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel
| | - Ireos Filipuzzi
- the Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel
| | - N Rao Movva
- the Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel
| | - Ruedi Aebersold
- the Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, the Faculty of Science, University of Zürich, 8057 Zürich, and
| | - Stephen B Helliwell
- the Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel,
| | - Robbie Loewith
- From the Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 1211 Geneva, the National Centre for Competence in Research Chemical Biology, 1211 Geneva, Switzerland
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308
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Yamagami K, Yamamoto T, Sakai S, Mioka T, Sano T, Igarashi Y, Tanaka K. Inositol depletion restores vesicle transport in yeast phospholipid flippase mutants. PLoS One 2015; 10:e0120108. [PMID: 25781026 PMCID: PMC4363822 DOI: 10.1371/journal.pone.0120108] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 01/19/2015] [Indexed: 12/19/2022] Open
Abstract
In eukaryotic cells, type 4 P-type ATPases function as phospholipid flippases, which translocate phospholipids from the exoplasmic leaflet to the cytoplasmic leaflet of the lipid bilayer. Flippases function in the formation of transport vesicles, but the mechanism remains unknown. Here, we isolate an arrestin-related trafficking adaptor, ART5, as a multicopy suppressor of the growth and endocytic recycling defects of flippase mutants in budding yeast. Consistent with a previous report that Art5p downregulates the inositol transporter Itr1p by endocytosis, we found that flippase mutations were also suppressed by the disruption of ITR1, as well as by depletion of inositol from the culture medium. Interestingly, inositol depletion suppressed the defects in all five flippase mutants. Inositol depletion also partially restored the formation of secretory vesicles in a flippase mutant. Inositol depletion caused changes in lipid composition, including a decrease in phosphatidylinositol and an increase in phosphatidylserine. A reduction in phosphatidylinositol levels caused by partially depleting the phosphatidylinositol synthase Pis1p also suppressed a flippase mutation. These results suggest that inositol depletion changes the lipid composition of the endosomal/TGN membranes, which results in vesicle formation from these membranes in the absence of flippases.
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Affiliation(s)
- Kanako Yamagami
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Japan
| | - Takaharu Yamamoto
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Japan
| | - Shota Sakai
- Laboratory of Biomembrane and Biofunctional Chemistry, Graduate School of Advanced Life Science, and Frontier Research Center for Post-Genome Science and Technology, Hokkaido University, Sapporo, Japan
| | - Tetsuo Mioka
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Japan
| | - Takamitsu Sano
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Japan
| | - Yasuyuki Igarashi
- Laboratory of Biomembrane and Biofunctional Chemistry, Graduate School of Advanced Life Science, and Frontier Research Center for Post-Genome Science and Technology, Hokkaido University, Sapporo, Japan
| | - Kazuma Tanaka
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Japan
- * E-mail:
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309
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Lysosomotropic agents selectively target chronic lymphocytic leukemia cells due to altered sphingolipid metabolism. Leukemia 2015; 30:1290-300. [PMID: 26859075 DOI: 10.1038/leu.2016.4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/04/2015] [Accepted: 11/17/2015] [Indexed: 12/11/2022]
Abstract
Lysosome membrane permeabilization (LMP) mediates cell death in a variety of cancer cells. However, little is known about lysosomes and LMP in chronic lymphocytic leukemia (CLL). Owing to drug resistance and toxicity in CLL patients, better treatment strategies are required. Our results show that CLL cells were sensitive to the lysosomotropic agent siramesine. Furthermore, this drug was more effective in CLL cells, regardless of prognostic factors, compared with normal B cells. Siramesine caused LMP, lipid peroxidation and transcription factor EB nuclear translocation followed by mitochondrial membrane potential loss and reactive oxygen species release. Siramesine-induced cell death was blocked by lipid antioxidants, but not by soluble antioxidants or protease inhibitors. To determine whether CLL cells had altered lysosomes, we investigated sphingolipid metabolism as the lysosome is a hub for lipid metabolism. We found that CLL cells had more lysosomes, increased sphingosine-1-phosphate phosphatase 1 (SPP1) expression, and increased levels of sphingosine compared with normal B cells. Raising sphingosine levels increased LMP and cell death in CLL cells, but not in normal B cells. Together, these results show that excess sphingosine in CLL cells could contribute to their sensitivity toward LMP. Thus, targeting the lysosome could be a novel therapeutic strategy in CLL.
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310
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Bickert A, Ginkel C, Kol M, vom Dorp K, Jastrow H, Degen J, Jacobs RL, Vance DE, Winterhager E, Jiang XC, Dörmann P, Somerharju P, Holthuis JCM, Willecke K. Functional characterization of enzymes catalyzing ceramide phosphoethanolamine biosynthesis in mice. J Lipid Res 2015; 56:821-35. [PMID: 25667419 DOI: 10.1194/jlr.m055269] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Besides bulk amounts of SM, mammalian cells produce small quantities of the SM analog ceramide phosphoethanolamine (CPE). Little is known about the biological role of CPE or enzymes responsible for CPE production. Heterologous expression studies revealed that SM synthase (SMS)2 is a bifunctional enzyme producing both SM and CPE, whereas SMS-related protein (SMSr) serves as monofunctional CPE synthase. Acute disruption of SMSr catalytic activity in cultured cells causes a rise in endoplasmic reticulum (ER) ceramides, fragmentation of ER exit sites, and induction of mitochondrial apoptosis. To address the relevance of CPE biosynthesis in vivo, we analyzed the tissue-specific distribution of CPE in mice and generated mouse lines lacking SMSr and SMS2 catalytic activity. We found that CPE levels were >300-fold lower than SM in all tissues examined. Unexpectedly, combined inactivation of SMSr and SMS2 significantly reduced, but did not eliminate, tissue-specific CPE pools and had no obvious impact on mouse development or fertility. While SMSr is widely expressed and serves as the principal CPE synthase in the brain, blocking its catalytic activity did not affect ceramide levels or secretory pathway integrity in the brain or any other tissue. Our data provide a first inventory of CPE species and CPE-biosynthetic enzymes in mammals.
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Affiliation(s)
- Andreas Bickert
- Molecular Genetics, Life, and Medical Sciences Institute University of Bonn, 53115 Bonn, Germany
| | - Christina Ginkel
- Molecular Genetics, Life, and Medical Sciences Institute University of Bonn, 53115 Bonn, Germany
| | - Matthijs Kol
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Katharina vom Dorp
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, 53115 Bonn, Germany
| | - Holger Jastrow
- Imaging Center Essen, Electron Microscopy Unit, University Hospital University of Duisburg-Essen, 45147 Essen, Germany
| | - Joachim Degen
- Molecular Genetics, Life, and Medical Sciences Institute University of Bonn, 53115 Bonn, Germany
| | - René L Jacobs
- Departments of Agricultural, Food, and Nutritional Science, Molecular and Cell Biology of Lipids, University of Alberta, T6G 2S2 Edmonton, Canada
| | - Dennis E Vance
- Biochemistry, University of Alberta, T6G 2S2 Edmonton, Canada
| | - Elke Winterhager
- Department of Molecular Biology, University of Duisburg-Essen, 45147 Essen, Germany
| | - Xian-Cheng Jiang
- Department of Anatomy and Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY 11203
| | - Peter Dörmann
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, 53115 Bonn, Germany
| | - Pentti Somerharju
- Medical Biochemistry, Institute of Biomedicine, University of Helsinki, 00014 Helsinki, Finland
| | - Joost C M Holthuis
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Klaus Willecke
- Molecular Genetics, Life, and Medical Sciences Institute University of Bonn, 53115 Bonn, Germany
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311
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Ernst D, Murphy SM, Sathiyanadan K, Wei Y, Othman A, Laurá M, Liu YT, Penno A, Blake J, Donaghy M, Houlden H, Reilly MM, Hornemann T. Novel HSAN1 mutation in serine palmitoyltransferase resides at a putative phosphorylation site that is involved in regulating substrate specificity. Neuromolecular Med 2015; 17:47-57. [PMID: 25567748 PMCID: PMC4326654 DOI: 10.1007/s12017-014-8339-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 12/17/2014] [Indexed: 02/04/2023]
Abstract
1-Deoxysphingolipids (1-deoxySL) are atypical sphingolipids that are formed by the enzyme serine palmitoyltransferase (SPT) due to a promiscuous use of l-alanine over its canonical substrate l-serine. Several mutations in SPT are associated with the hereditary sensory and autonomic neuropathy type I (HSAN1). The current hypothesis is that these mutations induce a permanent shift in the affinity from l-serine toward l-alanine which results in a pathologically increased 1-deoxySL formation in HSAN1 patients. Also, wild-type SPT forms 1-deoxySL under certain conditions, and elevated levels were found in individuals with the metabolic syndrome and diabetes. However, the molecular mechanisms which control the substrate shift of the wild-type enzyme are not understood. Here, we report a novel SPTLC2–S384F variant in two unrelated HSAN1 families. Affected patients showed elevated plasma 1-deoxySL levels and expression of the S384F mutant in HEK293 cells increased 1-deoxySL formation. Previously, S384 has been reported as one of the two (S384 and Y387) putative phosphorylation sites in SPTLC2. The phosphorylation of wild-type SPTLC2 was confirmed by isoelectric focusing. The impact of an S384 phosphorylation on SPT activity was tested by creating mutants mimicking either a constitutively phosphorylated (S384D, S384E) or non-phosphorylated (S384A, Y387F, Y387F+S384A) protein. The S384D but not the S384E variant was associated with increased 1-deoxySL formation. The other mutations had no influence on activity and substrate affinity. In summary, our data show that S384F is a novel mutation in HSAN1 and that the substrate specificity of wild-type SPT might by dynamically regulated by a phosphorylation at this position.
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Affiliation(s)
- Daniela Ernst
- Institute for Clinical Chemistry, University Hospital Zurich, CH-8091 Zurich, Switzerland
- Institute of Physiology and Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, CH-8057 Zurich, Switzerland
| | - Sinéad M. Murphy
- Department of Neurology, Adelaide & Meath Hospitals Incorporating the National Children’s Hospital, Tallaght, Dublin 24, Ireland
- Academic Unit of Neurology, Trinity College Dublin, Dublin, Ireland
- Department of Molecular Neurosciences, MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London, UK
| | | | - Yu Wei
- Institute for Clinical Chemistry, University Hospital Zurich, CH-8091 Zurich, Switzerland
| | - Alaa Othman
- Institute for Clinical Chemistry, University Hospital Zurich, CH-8091 Zurich, Switzerland
- Competence Center for Systems Physiology and Metabolic Diseases, Zuerich, Switzerland
| | - Matilde Laurá
- Department of Molecular Neurosciences, MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London, UK
| | - Yo-Tsen Liu
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
- National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Anke Penno
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Julian Blake
- Department of Clinical Neurophysiology, The National Hospital for Neurology and Neurosurgery, London, UK
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
- Department of Clinical Neurophysiology, Norfolk and Norwich University Hospital, Norwich, UK
| | - Michael Donaghy
- Nuffield Department of Clinical Neuroscience, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Henry Houlden
- Department of Molecular Neurosciences, MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London, UK
| | - Mary M. Reilly
- Department of Molecular Neurosciences, MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London, UK
| | - Thorsten Hornemann
- Institute for Clinical Chemistry, University Hospital Zurich, CH-8091 Zurich, Switzerland
- Institute of Physiology and Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, CH-8057 Zurich, Switzerland
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
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312
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Sphingosine-1-phosphate and ceramide are associated with health and atresia of bovine ovarian antral follicles. Animal 2015; 9:308-12. [DOI: 10.1017/s1751731114002341] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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313
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Schiffmann R. The consequences of genetic and pharmacologic reduction in sphingolipid synthesis. J Inherit Metab Dis 2015; 38:77-84. [PMID: 25164785 DOI: 10.1007/s10545-014-9758-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/28/2014] [Accepted: 07/31/2014] [Indexed: 10/24/2022]
Abstract
A new therapy based on substrate synthesis reduction in sphingolipidoses is showing promise. The consequences of decreasing sphingolipid synthesis depend on the level at which synthetic blockage occurs and on the extent of the blockage. Complete synthetic blockage may be lethal if it includes all sphingolipids, such as in a global knockout of serine palmitoyltransferase. Partial inhibition of sphingolipid synthetic pathways is usually benign and may have beneficial effects in a number of lysosomal diseases and in more common pathologies, as seen in animal models for atherosclerosis, polycystic kidney disease, diabetes, and asthma. Studies of various forms of sphingolipid synthesis reduction serve to highlight not only the cellular role of these lipids but also the potential risks and therapeutic benefits of pharmacological agents to be used in therapy for human diseases.
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Affiliation(s)
- Raphael Schiffmann
- Institute of Metabolic Disease, Baylor Research Institute, 3812 Elm Street, Dallas, TX, USA,
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314
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Olson DK, Fröhlich F, Christiano R, Hannibal-Bach HK, Ejsing CS, Walther TC. Rom2-dependent phosphorylation of Elo2 controls the abundance of very long-chain fatty acids. J Biol Chem 2014; 290:4238-47. [PMID: 25519905 DOI: 10.1074/jbc.m114.629279] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Sphingolipids are essential components of eukaryotic membranes, where they serve to maintain membrane integrity. They are important components of membrane trafficking and function in signaling as messenger molecules. Sphingolipids are synthesized de novo from very long-chain fatty acids (VLCFA) and sphingoid long-chain bases, which are amide linked to form ceramide and further processed by addition of various headgroups. Little is known concerning the regulation of VLCFA levels and how cells coordinate their synthesis with the availability of long-chain bases for sphingolipid synthesis. Here we show that Elo2, a key enzyme of VLCFA synthesis, is controlled by signaling of the guanine nucleotide exchange factor Rom2, initiating at the plasma membrane. This pathway controls Elo2 phosphorylation state and VLCFA synthesis. Our data identify a regulatory mechanism for coordinating VLCFA synthesis with sphingolipid metabolism and link signal transduction pathways from the plasma membrane to the regulation of lipids for membrane homeostasis.
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Affiliation(s)
- Daniel K Olson
- From the Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, the Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06150
| | - Florian Fröhlich
- From the Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115
| | - Romain Christiano
- From the Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115
| | - Hans K Hannibal-Bach
- the Department of Biochemistry and Molecular Biology, University of Southern Denmark, 0230 Odense, Denmark
| | - Christer S Ejsing
- the Department of Biochemistry and Molecular Biology, University of Southern Denmark, 0230 Odense, Denmark
| | - Tobias C Walther
- From the Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, and the Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
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315
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Alexaki A, Gupta SD, Majumder S, Kono M, Tuymetova G, Harmon JM, Dunn TM, Proia RL. Autophagy regulates sphingolipid levels in the liver. J Lipid Res 2014; 55:2521-31. [PMID: 25332431 DOI: 10.1194/jlr.m051862] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Sphingolipid levels are tightly regulated to maintain cellular homeostasis. During pathologic conditions such as in aging, inflammation, and metabolic and neurodegenerative diseases, levels of some sphingolipids, including the bioactive metabolite ceramide, are elevated. Sphingolipid metabolism has been linked to autophagy, a critical catabolic process in both normal cell function and disease; however, the in vivo relevance of the interaction is not well-understood. Here, we show that blocking autophagy in the liver by deletion of the Atg7 gene, which is essential for autophagosome formation, causes an increase in sphingolipid metabolites including ceramide. We also show that overexpression of serine palmitoyltransferase to elevate de novo sphingolipid biosynthesis induces autophagy in the liver. The results reveal autophagy as a process that limits excessive ceramide levels and that is induced by excessive elevation of de novo sphingolipid synthesis in the liver. Dysfunctional autophagy may be an underlying mechanism causing elevations in ceramide that may contribute to pathogenesis in diseases.
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Affiliation(s)
- Aikaterini Alexaki
- Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Sita D Gupta
- Departments of Biochemistry Uniformed Services University of the Health Sciences, Bethesda, MD 20184
| | - Saurav Majumder
- Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Mari Kono
- Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Galina Tuymetova
- Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Jeffrey M Harmon
- Molecular Biology and Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, MD 20184
| | - Teresa M Dunn
- Departments of Biochemistry Uniformed Services University of the Health Sciences, Bethesda, MD 20184
| | - Richard L Proia
- Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
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316
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Muir A, Ramachandran S, Roelants FM, Timmons G, Thorner J. TORC2-dependent protein kinase Ypk1 phosphorylates ceramide synthase to stimulate synthesis of complex sphingolipids. eLife 2014; 3. [PMID: 25279700 PMCID: PMC4217029 DOI: 10.7554/elife.03779] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/02/2014] [Indexed: 12/14/2022] Open
Abstract
Plasma membrane lipid composition must be maintained during growth and under environmental insult. In yeast, signaling mediated by TOR Complex 2 (TORC2)-dependent protein kinase Ypk1 controls lipid abundance and distribution in response to membrane stress. Ypk1, among other actions, alleviates negative regulation of L-serine:palmitoyl-CoA acyltransferase, upregulating production of long-chain base precursors to sphingolipids. To explore other roles for TORC2-Ypk1 signaling in membrane homeostasis, we devised a three-tiered genome-wide screen to identify additional Ypk1 substrates, which pinpointed both catalytic subunits of the ceramide synthase complex. Ypk1-dependent phosphorylation of both proteins increased upon either sphingolipid depletion or heat shock and was important for cell survival. Sphingolipidomics, other biochemical measurements and genetic analysis demonstrated that these modifications of ceramide synthase increased its specific activity and stimulated channeling of long-chain base precursors into sphingolipid end-products. Control at this branch point also prevents accumulation of intermediates that could compromise cell growth by stimulating autophagy. DOI:http://dx.doi.org/10.7554/eLife.03779.001 Cells are enclosed by a plasma membrane that separates and protects each cell from its environment. These membranes are made of a variety of proteins and fatty molecules called lipids, which are carefully organized throughout the membrane. When cells experience stresses such as heat or excessive pressure, the plasma membrane changes to help protect the cell. In particular, more of a group of lipids called sphingolipids are incorporated into the membrane under stress conditions. In yeast cells, a protein called Ypk1 plays an important role in protecting the cell from stress. Ypk1 controls the activity of a number of proteins that are responsible for balancing the amounts of different types of lipids in cell membranes. The combined action of these Ypk1-dependent proteins leads to the remodelling of the cell membrane to protect against stress. While several proteins that work with Ypk1 are known, some of the changes that serve to protect the plasma membrane cannot be explained by the action of these proteins alone. To provide a more comprehensive picture of how Ypk1 helps cells to respond to changes in the environment, Muir et al. developed a new approach that combines biochemical, genetic and bioinformatics techniques to survey the yeast genome for proteins that could be Ypk1 targets. Muir et al. first produced a list of potential candidate proteins by searching for proteins with features similar to known Ypk1 targets, and then considered those that are known to be involved in processes that also involve Ypk1. To filter the potential targets further, Muir et al. performed experiments in yeast cells to see which proteins prevented normal cell growth if they were over-produced. Further experiments investigating which of these proteins interact with Ypk1 when purified identified 12 new proteins that are most likely targets of the Ypk1 protein. Two of these newly identified Ypk1 target proteins form part of an enzyme complex called ceramide synthase, which produces a family of waxy lipid molecules from which more complex sphingolipids are built. Muir et al. discovered that during stress, Ypk1 enhances the activity of the ceramide synthase enzyme, which increases lipid production and the amount of sphingolipid deposited in the cell membrane. If this process is interrupted at any stage, cells struggle to survive under stress conditions. The other candidate proteins identified by Muir et al. remain to be validated and characterized as Ypk1 targets. Nevertheless, the techniques used have conclusively identified some new Ypk1 targets and could also be applied to similar searches for proteins targeted in other biological processes. DOI:http://dx.doi.org/10.7554/eLife.03779.002
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Affiliation(s)
- Alexander Muir
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Subramaniam Ramachandran
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Françoise M Roelants
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Garrett Timmons
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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317
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Assies J, Mocking RJT, Lok A, Ruhé HG, Pouwer F, Schene AH. Effects of oxidative stress on fatty acid- and one-carbon-metabolism in psychiatric and cardiovascular disease comorbidity. Acta Psychiatr Scand 2014; 130:163-80. [PMID: 24649967 PMCID: PMC4171779 DOI: 10.1111/acps.12265] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/20/2014] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Cardiovascular disease (CVD) is the leading cause of death in severe psychiatric disorders (depression, schizophrenia). Here, we provide evidence of how the effects of oxidative stress on fatty acid (FA) and one-carbon (1-C) cycle metabolism, which may initially represent adaptive responses, might underlie comorbidity between CVD and psychiatric disorders. METHOD We conducted a literature search and integrated data in a narrative review. RESULTS Oxidative stress, mainly generated in mitochondria, is implicated in both psychiatric and cardiovascular pathophysiology. Oxidative stress affects the intrinsically linked FA and 1-C cycle metabolism: FAs decrease in chain length and unsaturation (particularly omega-3 polyunsaturated FAs), and lipid peroxidation products increase; the 1-C cycle shifts from the methylation to transsulfuration pathway (lower folate and higher homocysteine and antioxidant glutathione). Interestingly, corresponding alterations were reported in psychiatric disorders and CVD. Potential mechanisms through which FA and 1-C cycle metabolism may be involved in brain (neurocognition, mood regulation) and cardiovascular system functioning (inflammation, thrombosis) include membrane peroxidizability and fluidity, eicosanoid synthesis, neuroprotection and epigenetics. CONCLUSION While oxidative-stress-induced alterations in FA and 1-C metabolism may initially enhance oxidative stress resistance, persisting chronically, they may cause damage possibly underlying (co-occurrence of) psychiatric disorders and CVD. This might have implications for research into diagnosis and (preventive) treatment of (CVD in) psychiatric patients.
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Affiliation(s)
- J Assies
- Program for Mood Disorders, Department of Psychiatry, Academic Medical Center, Amsterdam
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318
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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: 5.3] [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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319
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Hurlock AK, Roston RL, Wang K, Benning C. Lipid trafficking in plant cells. Traffic 2014; 15:915-32. [PMID: 24931800 DOI: 10.1111/tra.12187] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/12/2014] [Accepted: 06/12/2014] [Indexed: 12/29/2022]
Abstract
Plant cells contain unique organelles such as chloroplasts with an extensive photosynthetic membrane. In addition, specialized epidermal cells produce an extracellular cuticle composed primarily of lipids, and storage cells accumulate large amounts of storage lipids. As lipid assembly is associated only with discrete membranes or organelles, there is a need for extensive lipid trafficking within plant cells, more so in specialized cells and sometimes also in response to changing environmental conditions such as phosphate deprivation. Because of the complexity of plant lipid metabolism and the inherent recalcitrance of membrane lipid transporters, the mechanisms of lipid transport within plant cells are not yet fully understood. Recently, several new proteins have been implicated in different aspects of plant lipid trafficking. While these proteins provide only first insights into limited aspects of lipid transport phenomena in plant cells, they represent exciting opportunities for further studies.
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Affiliation(s)
- Anna K Hurlock
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA; Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
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320
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Shen H, Giordano F, Wu Y, Chan J, Zhu C, Milosevic I, Wu X, Yao K, Chen B, Baumgart T, Sieburth D, De Camilli P. Coupling between endocytosis and sphingosine kinase 1 recruitment. Nat Cell Biol 2014; 16:652-62. [PMID: 24929359 PMCID: PMC4230894 DOI: 10.1038/ncb2987] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 05/09/2014] [Indexed: 12/13/2022]
Abstract
Genetic studies have suggested a functional link between cholesterol/sphingolipid metabolism and endocytic membrane traffic. Here we show that perturbing the cholesterol/sphingomyelin balance in the plasma membrane results in the massive formation of clusters of narrow endocytic tubular invaginations positive for N-BAR proteins. These tubules are intensely positive for sphingosine kinase 1 (SPHK1). SPHK1 is also targeted to physiologically occurring early endocytic intermediates, and is highly enriched in nerve terminals, which are cellular compartments specialized for exo/endocytosis. Membrane recruitment of SPHK1 involves a direct, curvature-sensitive interaction with the lipid bilayer mediated by a hydrophobic patch on the enzyme's surface. The knockdown of SPHKs results in endocytic recycling defects, and a mutation that disrupts the hydrophobic patch of Caenorhabditis elegans SPHK fails to rescue the neurotransmission defects in loss-of-function mutants of this enzyme. Our studies support a role for sphingosine phosphorylation in endocytic membrane trafficking beyond the established function of sphingosine-1-phosphate in intercellular signalling.
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Affiliation(s)
- Hongying Shen
- 1] Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06510, USA [2] Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510, USA [3]
| | - Francesca Giordano
- 1] Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06510, USA [2] Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510, USA [3]
| | - Yumei Wu
- 1] Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06510, USA [2] Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Jason Chan
- 1] Zilkha Neurogenetic Institute, Department of Cell and Neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA [2]
| | - Chen Zhu
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ira Milosevic
- 1] Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06510, USA [2] Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Xudong Wu
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Kai Yao
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Bo Chen
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Derek Sieburth
- Zilkha Neurogenetic Institute, Department of Cell and Neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Pietro De Camilli
- 1] Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06510, USA [2] Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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321
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Siamer S, Guillas I, Shimobayashi M, Kunz C, Hall MN, Barny MA. Expression of the bacterial type III effector DspA/E in Saccharomyces cerevisiae down-regulates the sphingolipid biosynthetic pathway leading to growth arrest. J Biol Chem 2014; 289:18466-77. [PMID: 24828506 DOI: 10.1074/jbc.m114.562769] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Erwinia amylovora, the bacterium responsible for fire blight, relies on a type III secretion system and a single injected effector, DspA/E, to induce disease in host plants. DspA/E belongs to the widespread AvrE family of type III effectors that suppress plant defense responses and promote bacterial growth following infection. Ectopic expression of DspA/E in plant or in Saccharomyces cerevisiae is toxic, indicating that DspA/E likely targets a cellular process conserved between yeast and plant. To unravel the mode of action of DspA/E, we screened the Euroscarf S. cerevisiae library for mutants resistant to DspA/E-induced growth arrest. The most resistant mutants (Δsur4, Δfen1, Δipt1, Δskn1, Δcsg1, Δcsg2, Δorm1, and Δorm2) were impaired in the sphingolipid biosynthetic pathway. Exogenously supplied sphingolipid precursors such as the long chain bases (LCBs) phytosphingosine and dihydrosphingosine also suppressed the DspA/E-induced yeast growth defect. Expression of DspA/E in yeast down-regulated LCB biosynthesis and induced a rapid decrease in LCB levels, indicating that serine palmitoyltransferase (SPT), the first and rate-limiting enzyme of the sphingolipid biosynthetic pathway, was repressed. SPT down-regulation was mediated by dephosphorylation and activation of Orm proteins that negatively regulate SPT. A Δcdc55 mutation affecting Cdc55-PP2A protein phosphatase activity prevented Orm dephosphorylation and suppressed DspA/E-induced growth arrest.
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Affiliation(s)
- Sabrina Siamer
- From the Institut National de la Recherche Agronomique UMR1392, Institut d'Ecologie et des Sciences de l'Environnement, Université Pierre et Marie Curie (UPMC), Bât A 7ème Etage Case 237, 7 Quai St.-Bernard, 75252 Paris, France, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Isabelle Guillas
- Sorbonne Universités, UMR1166, Institut National de la Santé et de la recherche médicale-UPMC, Pitié-Salpétrière University Hospital, F75013, Paris, France
| | | | - Caroline Kunz
- Sorbonne Universités, UPMC University Paris 06, UFR 927, F-75005 Paris, France, and Muséum National d'Histoire Naturelle, UMR7245, Molécules de Communication et Adaptation des Micro-organismes, F-75005 Paris, France
| | - Michael N Hall
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Marie-Anne Barny
- From the Institut National de la Recherche Agronomique UMR1392, Institut d'Ecologie et des Sciences de l'Environnement, Université Pierre et Marie Curie (UPMC), Bât A 7ème Etage Case 237, 7 Quai St.-Bernard, 75252 Paris, France,
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322
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Aguilera-Romero A, Gehin C, Riezman H. Sphingolipid homeostasis in the web of metabolic routes. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:647-56. [DOI: 10.1016/j.bbalip.2013.10.014] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 10/17/2013] [Accepted: 10/19/2013] [Indexed: 10/26/2022]
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323
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Low YS, Bircham PW, Maass DR, Atkinson PH. Kinetochore genes are required to fully activate secretory pathway expansion in S. cerevisiae under induced ER stress. MOLECULAR BIOSYSTEMS 2014; 10:1790-802. [PMID: 24722431 DOI: 10.1039/c3mb70414a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Basal ER stress occurs when proteins misfold in normal physiological conditions and are corrected by the unfolded protein response (UPR). Elevated ER stress occurs when misfolding is refractory as found in numerous diseases such as atherosclerosis, Type II diabetes and some cancers. In elevated ER stress it is unclear whether cells utilise the same or different networks of genes as in basal levels of ER stress. To probe this question, we used secretory pathway reporters Yip3p-GFP, Erv29p-GFP, Orm2p-GFP and UPREpr-GFP placed on the yeast deletion mutant array (DMA) genetic background. The reporter's expression levels, measured by automated microscopy, at basal versus elevated ER stress induced by the over-expression of CPY* were compared. A novel group of kinetochore genes (CTF19 complex) were found to be uniquely required for full induction of all four ER stress reporters in elevated stress. A follow-up reporter screen was developed by mating the ctf19Δ kinetochore gene deletion strain into the genome-wide XXXp-GFP tagged library then testing with over-expressed CPY*. This screen identified Bcy1p and Bfr1p as possible signalling points that down-regulate the UPR and secretory pathway when kinetochore proteins are absent under elevated stress conditions. Bfr1p appears to be a checkpoint that monitors the integrity of kinetochores at increased levels of ER stress. This study concludes that functional kinetochores are required for full activation of the secretory pathway in elevated ER stress and that the responses to basal and elevated levels of ER stress require different networks of genes.
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Affiliation(s)
- Yee S Low
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington, New Zealand.
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324
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Liu Y, Samuel BS, Breen PC, Ruvkun G. Caenorhabditis elegans pathways that surveil and defend mitochondria. Nature 2014; 508:406-10. [PMID: 24695221 PMCID: PMC4102179 DOI: 10.1038/nature13204] [Citation(s) in RCA: 239] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 03/04/2014] [Indexed: 01/11/2023]
Abstract
Mitochondrial function is challenged by toxic by-products of metabolism as well as by pathogen attack. Caenorhabditis elegans normally responds to mitochondrial dysfunction with activation of mitochondrial-repair, drug-detoxification and pathogen-response pathways. Here, from a genome-wide RNA interference (RNAi) screen, we identified 45 C. elegans genes that are required to upregulate detoxification, pathogen-response and mitochondrial-repair pathways after inhibition of mitochondrial function by drug-induced or genetic disruption. Animals defective in ceramide biosynthesis are deficient in mitochondrial surveillance, and addition of particular ceramides can rescue the surveillance defects. Ceramide can also rescue the mitochondrial surveillance defects of other gene inactivations, mapping these gene activities upstream of ceramide. Inhibition of the mevalonate pathway, either by RNAi or statin drugs, also disrupts mitochondrial surveillance. Growth of C. elegans with a significant fraction of bacterial species from their natural habitat causes mitochondrial dysfunction. Other bacterial species inhibit C. elegans defence responses to a mitochondrial toxin, revealing bacterial countermeasures to animal defence.
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Affiliation(s)
- Ying Liu
- 1] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [3] State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Buck S Samuel
- 1] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter C Breen
- 1] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Gary Ruvkun
- 1] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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325
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Abstract
Lipids are unevenly distributed within and between cell membranes, thus defining organelle identity. Such distribution relies on local metabolic branches and mechanisms that move lipids. These processes are regulated by feedback mechanisms that decipher topographical information in organelle membranes and then regulate lipid levels or flows. In the endoplasmic reticulum, the major lipid source, transcriptional regulators and enzymes sense changes in membrane features to modulate lipid production. At the Golgi apparatus, lipid-synthesizing, lipid-flippase, and lipid-transport proteins (LTPs) collaborate to control lipid balance and distribution within the membrane to guarantee remodeling processes crucial for vesicular trafficking. Open questions exist regarding LTPs, which are thought to be lipid sensors that regulate lipid synthesis or carriers that transfer lipids between organelles across long distances or in contact sites. A novel model is that LTPs, by exchanging two different lipids, exploit one lipid gradient between two distinct membranes to build a second lipid gradient.
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Affiliation(s)
- Guillaume Drin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and CNRS, 06560 Valbonne, France;
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326
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Worgall TS, Veerappan A, Sung B, Kim BI, Weiner E, Bholah R, Silver RB, Jiang XC, Worgall S. Impaired sphingolipid synthesis in the respiratory tract induces airway hyperreactivity. Sci Transl Med 2014; 5:186ra67. [PMID: 23698380 DOI: 10.1126/scitranslmed.3005765] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Asthma is a clinically heterogeneous genetic disease, and its pathogenesis is incompletely understood. Genome-wide association studies link ORM (yeast)-Like protein isoform 3 [corrected] (ORMDL3), a member of the ORM gene family, to nonallergic childhood-onset asthma. Orm proteins negatively regulate sphingolipid (SL) synthesis by acting as homeostatic regulators of serine palmitoyl-CoA transferase (SPT), the rate-limiting enzyme of de novo SL synthesis, but it is not known how SPT activity or SL synthesis is related to asthma. The present study analyzes the effect of decreased de novo SL synthesis in the lung on airway reactivity after administration of myriocin, an inhibitor of SPT, and in SPT heterozygous knockout mice. We show that, in both models, decreased de novo SL synthesis increases bronchial reactivity in the absence of inflammation. Decreased SPT activity affected intracellular magnesium homeostasis and altered the bronchial sensitivity to magnesium. This functionally links decreased de novo SL synthesis to asthma and so identifies this metabolic pathway as a potential target for therapeutic interventions.
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Affiliation(s)
- Tilla S Worgall
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA.
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327
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The response to inositol: regulation of glycerolipid metabolism and stress response signaling in yeast. Chem Phys Lipids 2014; 180:23-43. [PMID: 24418527 DOI: 10.1016/j.chemphyslip.2013.12.013] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 12/26/2013] [Indexed: 12/13/2022]
Abstract
This article focuses on discoveries of the mechanisms governing the regulation of glycerolipid metabolism and stress response signaling in response to the phospholipid precursor, inositol. The regulation of glycerolipid lipid metabolism in yeast in response to inositol is highly complex, but increasingly well understood, and the roles of individual lipids in stress response are also increasingly well characterized. Discoveries that have emerged over several decades of genetic, molecular and biochemical analyses of metabolic, regulatory and signaling responses of yeast cells, both mutant and wild type, to the availability of the phospholipid precursor, inositol are discussed.
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328
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Sphingolipid biosynthetic pathway genes FEN1 and SUR4 modulate amphotericin B resistance. Antimicrob Agents Chemother 2014; 58:2409-14. [PMID: 24395234 DOI: 10.1128/aac.02130-13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Deletants of the sphingolipid biosynthetic pathway genes FEN1 and SUR4 of Saccharomyces cerevisiae, as well as deletants of their orthologs in Candida albicans, were found to be 2- to 5-fold-more sensitive to amphotericin B (AmB) than parent strains. The inhibition of sphingolipid biosynthesis in parent strains by myriocin sensitized them to AmB, which can be reversed by providing phytosphingosine, an intermediate in the sphingolipid pathway. These results indicate that sphingolipids modulate AmB resistance, with implications for mechanisms underlying AmB action and resistance.
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329
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Zauber H, Burgos A, Garapati P, Schulze WX. Plasma membrane lipid-protein interactions affect signaling processes in sterol-biosynthesis mutants in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2014; 5:78. [PMID: 24672530 PMCID: PMC3957024 DOI: 10.3389/fpls.2014.00078] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 02/18/2014] [Indexed: 05/06/2023]
Abstract
The plasma membrane is an important organelle providing structure, signaling and transport as major biological functions. Being composed of lipids and proteins with different physicochemical properties, the biological functions of membranes depend on specific protein-protein and protein-lipid interactions. Interactions of proteins with their specific sterol and lipid environment were shown to be important factors for protein recruitment into sub-compartmental structures of the plasma membrane. System-wide implications of altered endogenous sterol levels for membrane functions in living cells were not studied in higher plant cells. In particular, little is known how alterations in membrane sterol composition affect protein and lipid organization and interaction within membranes. Here, we conducted a comparative analysis of the plasma membrane protein and lipid composition in Arabidopsis sterol-biosynthesis mutants smt1 and ugt80A2;B1. smt1 shows general alterations in sterol composition while ugt80A2;B1 is significantly impaired in sterol glycosylation. By systematically analyzing different cellular fractions and combining proteomic with lipidomic data we were able to reveal contrasting alterations in lipid-protein interactions in both mutants, with resulting differential changes in plasma membrane signaling status.
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Affiliation(s)
- Henrik Zauber
- Max Planck Institute of Molecular Plant PhysiologyGolm, Germany
- Max-Delbrück-Centrum für Molekulare MedizinBerlin-Buch, Germany
| | - Asdrubal Burgos
- Max Planck Institute of Molecular Plant PhysiologyGolm, Germany
| | | | - Waltraud X. Schulze
- Max Planck Institute of Molecular Plant PhysiologyGolm, Germany
- Plant Systems Biology, University of HohenheimStuttgart, Germany
- *Correspondence: Waltraud X. Schulze, Plant Systems Biology, University of Hohenheim, Garbenstrasse 30, Stuttgart 70593, Germany e-mail:
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330
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Ono JG, Worgall TS, Worgall S. 17q21 locus and ORMDL3: an increased risk for childhood asthma. Pediatr Res 2014; 75:165-70. [PMID: 24165737 DOI: 10.1038/pr.2013.186] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 05/09/2013] [Indexed: 01/09/2023]
Abstract
Genetic variations in the 17q21 locus are strongly associated with childhood nonallergic asthma. Expression of the 17q21 genes, orosomucoid like 3 (ORMDL3) and gasdermin B (GSMDB), is affected by these disease-associated variants. However, until recently, no functional connection of the protein products coded by these genes with asthma was known. Lately, it has been identified that ORMDL3 function has been related to various cellular processes that could be relevant for the pathogenesis of asthma. This includes dysregulation of the unfolded protein response (UPR) associated with airway remodeling and also an effect of ORMDL3-dysregulated sphingolipid synthesis on bronchial hyperreactivity. These findings are crucial for a better understanding of the mechanism of childhood asthma and may lead to asthma therapeutics that target pathways previously not thought to be related to this common pediatric respiratory disease. Furthermore, this may validate the unbiased genome-wide association study (GWAS) approach for complex diseases such as asthma, to better define pathomechanisms and drug targets.
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Affiliation(s)
- Jennie G Ono
- Department of Pediatrics, Weill Cornell Medical College, New York, New York
| | - Tilla S Worgall
- 1] Department of Pathology and Cell Biology, Columbia University, New York, New York [2] Department of Pediatrics, Columbia University, New York, New York [3] Institute of Human Nutrition, Columbia University, New York, New York
| | - Stefan Worgall
- 1] Department of Pediatrics, Weill Cornell Medical College, New York, New York [2] Department of Genetic Medicine, Weill Cornell Medical College, New York, New York
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331
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Zauber H, Burgos A, Garapati P, Schulze WX. Plasma membrane lipid-protein interactions affect signaling processes in sterol-biosynthesis mutants in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2014; 5:78. [PMID: 24672530 DOI: 10.3389/fpls.2014.00078014.00078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 02/18/2014] [Indexed: 05/22/2023]
Abstract
The plasma membrane is an important organelle providing structure, signaling and transport as major biological functions. Being composed of lipids and proteins with different physicochemical properties, the biological functions of membranes depend on specific protein-protein and protein-lipid interactions. Interactions of proteins with their specific sterol and lipid environment were shown to be important factors for protein recruitment into sub-compartmental structures of the plasma membrane. System-wide implications of altered endogenous sterol levels for membrane functions in living cells were not studied in higher plant cells. In particular, little is known how alterations in membrane sterol composition affect protein and lipid organization and interaction within membranes. Here, we conducted a comparative analysis of the plasma membrane protein and lipid composition in Arabidopsis sterol-biosynthesis mutants smt1 and ugt80A2;B1. smt1 shows general alterations in sterol composition while ugt80A2;B1 is significantly impaired in sterol glycosylation. By systematically analyzing different cellular fractions and combining proteomic with lipidomic data we were able to reveal contrasting alterations in lipid-protein interactions in both mutants, with resulting differential changes in plasma membrane signaling status.
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Affiliation(s)
- Henrik Zauber
- Max Planck Institute of Molecular Plant Physiology Golm, Germany ; Max-Delbrück-Centrum für Molekulare Medizin Berlin-Buch, Germany
| | - Asdrubal Burgos
- Max Planck Institute of Molecular Plant Physiology Golm, Germany
| | | | - Waltraud X Schulze
- Max Planck Institute of Molecular Plant Physiology Golm, Germany ; Plant Systems Biology, University of Hohenheim Stuttgart, Germany
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332
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Cohen Y, Megyeri M, Chen OCW, Condomitti G, Riezman I, Loizides-Mangold U, Abdul-Sada A, Rimon N, Riezman H, Platt FM, Futerman AH, Schuldiner M. The yeast p5 type ATPase, spf1, regulates manganese transport into the endoplasmic reticulum. PLoS One 2013; 8:e85519. [PMID: 24392018 PMCID: PMC3877380 DOI: 10.1371/journal.pone.0085519] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Accepted: 11/27/2013] [Indexed: 12/13/2022] Open
Abstract
The endoplasmic reticulum (ER) is a large, multifunctional and essential organelle. Despite intense research, the function of more than a third of ER proteins remains unknown even in the well-studied model organism Saccharomyces cerevisiae. One such protein is Spf1, which is a highly conserved, ER localized, putative P-type ATPase. Deletion of SPF1 causes a wide variety of phenotypes including severe ER stress suggesting that this protein is essential for the normal function of the ER. The closest homologue of Spf1 is the vacuolar P-type ATPase Ypk9 that influences Mn(2+) homeostasis. However in vitro reconstitution assays with Spf1 have not yielded insight into its transport specificity. Here we took an in vivo approach to detect the direct and indirect effects of deleting SPF1. We found a specific reduction in the luminal concentration of Mn(2+) in ∆spf1 cells and an increase following it's overexpression. In agreement with the observed loss of luminal Mn(2+) we could observe concurrent reduction in many Mn(2+)-related process in the ER lumen. Conversely, cytosolic Mn(2+)-dependent processes were increased. Together, these data support a role for Spf1p in Mn(2+) transport in the cell. We also demonstrate that the human sequence homologue, ATP13A1, is a functionally conserved orthologue. Since ATP13A1 is highly expressed in developing neuronal tissues and in the brain, this should help in the study of Mn(2+)-dependent neurological disorders.
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Affiliation(s)
- Yifat Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Márton Megyeri
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Oscar C. W. Chen
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Giuseppe Condomitti
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Isabelle Riezman
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | | | - Alaa Abdul-Sada
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Nitzan Rimon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Howard Riezman
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
- National Centre of Competence in Research (NCCR) Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Frances M. Platt
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Anthony H. Futerman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
- The Joseph Meyerhoff Professor of Biochemistry at the Weizmann Institute of Science, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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333
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Swinnen E, Wilms T, Idkowiak-Baldys J, Smets B, De Snijder P, Accardo S, Ghillebert R, Thevissen K, Cammue B, De Vos D, Bielawski J, Hannun YA, Winderickx J. The protein kinase Sch9 is a key regulator of sphingolipid metabolism in Saccharomyces cerevisiae. Mol Biol Cell 2013; 25:196-211. [PMID: 24196832 PMCID: PMC3873890 DOI: 10.1091/mbc.e13-06-0340] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Sphingolipids play crucial roles in the determination of growth and survival of eukaryotic cells. The budding yeast protein kinase Sch9 is not only an effector, but also a regulator of sphingolipid metabolism. This new function provides a crucial link between nutrient and sphingolipid signaling. The Saccharomyces cerevisiae protein kinase Sch9 is an in vitro and in vivo effector of sphingolipid signaling. This study examines the link between Sch9 and sphingolipid metabolism in S. cerevisiae in vivo based on the observation that the sch9Δ mutant displays altered sensitivity to different inhibitors of sphingolipid metabolism, namely myriocin and aureobasidin A. Sphingolipid profiling indicates that sch9Δ cells have increased levels of long-chain bases and long-chain base-1 phosphates, decreased levels of several species of (phyto)ceramides, and altered ratios of complex sphingolipids. We show that the target of rapamycin complex 1–Sch9 signaling pathway functions to repress the expression of the ceramidase genes YDC1 and YPC1, thereby revealing, for the first time in yeast, a nutrient-dependent transcriptional mechanism involved in the regulation of sphingolipid metabolism. In addition, we establish that Sch9 affects the activity of the inositol phosphosphingolipid phospholipase C, Isc1, which is required for ceramide production by hydrolysis of complex sphingolipids. Given that sphingolipid metabolites play a crucial role in the regulation of stress tolerance and longevity of yeast cells, our data provide a model in which Sch9 regulates the latter phenotypes by acting not only as an effector but also as a regulator of sphingolipid metabolism.
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Affiliation(s)
- Erwin Swinnen
- Functional Biology, KU Leuven, 3001 Heverlee, Belgium Centre for Surface Chemistry and Catalysis, KU Leuven, 3001 Heverlee, Belgium Centre of Microbial and Plant Genetics, KU Leuven, 3001 Heverlee, Belgium Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29403
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334
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The pyridoxal 5'-phosphate (PLP)-dependent enzyme serine palmitoyltransferase (SPT): effects of the small subunits and insights from bacterial mimics of human hLCB2a HSAN1 mutations. BIOMED RESEARCH INTERNATIONAL 2013; 2013:194371. [PMID: 24175284 PMCID: PMC3794620 DOI: 10.1155/2013/194371] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 07/22/2013] [Indexed: 12/03/2022]
Abstract
The pyridoxal 5′-phosphate (PLP)-dependent enzyme serine palmitoyltransferase (SPT) catalyses the first step of de novo sphingolipid biosynthesis. The core human enzyme is a membrane-bound heterodimer composed of two subunits (hLCB1 and hLCB2a/b), and mutations in both hLCB1 (e.g., C133W and C133Y) and hLCB2a (e.g., V359M, G382V, and I504F) have been identified in patients with hereditary sensory and autonomic neuropathy type I (HSAN1), an inherited disorder that affects sensory and autonomic neurons. These mutations result in substrate promiscuity, leading to formation of neurotoxic deoxysphingolipids found in affected individuals. Here we measure the activities of the hLCB2a mutants in the presence of ssSPTa and ssSPTb and find that all decrease enzyme activity. High resolution structural data of the homodimeric SPT enzyme from the bacterium Sphingomonas paucimobilis (Sp SPT) provides a model to understand the impact of the hLCB2a mutations on the mechanism of SPT. The three human hLCB2a HSAN1 mutations map onto Sp SPT (V246M, G268V, and G385F), and these mutant mimics reveal that the amino acid changes have varying impacts; they perturb the PLP cofactor binding, reduce the affinity for both substrates, decrease the enzyme activity, and, in the most severe case, cause the protein to be expressed in an insoluble form.
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335
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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: 659] [Impact Index Per Article: 54.9] [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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336
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Xia Y, Peng L. Photoactivatable Lipid Probes for Studying Biomembranes by Photoaffinity Labeling. Chem Rev 2013; 113:7880-929. [DOI: 10.1021/cr300419p] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yi Xia
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
| | - Ling Peng
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
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337
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Huang X, Withers BR, Dickson RC. Sphingolipids and lifespan regulation. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1841:657-64. [PMID: 23954556 DOI: 10.1016/j.bbalip.2013.08.006] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 08/01/2013] [Accepted: 08/06/2013] [Indexed: 02/08/2023]
Abstract
Diseases including cancer, type 2 diabetes, cardiovascular and immune dysfunction and neurodegeneration become more prevalent as we age, and combined with the increase in average human lifespan, place an ever increasing burden on the health care system. In this chapter we focus on finding ways of modulating sphingolipids to prevent the development of age-associated diseases or delay their onset, both of which could improve health in elderly, fragile people. Reducing the incidence of or delaying the onset of diseases of aging has blossomed in the past decade because of advances in understanding signal transduction pathways and cellular processes, especially in model organisms, that are largely conserved in most eukaryotes and that can be modulated to reduce signs of aging and increase health span. In model organisms such interventions must also increase lifespan to be considered significant, but this is not a requirement for use in humans. The most encouraging interventions in model organisms involve lowering the concentration of one or more sphingolipids so as to reduce the activity of key signaling pathways, one of the most promising being the Target of Rapamycin Complex 1 (TORC1) protein kinase pathway. Other potential ways in which modulating sphingolipids may contribute to improving the health profile of the elderly is by reducing oxidative stresses, inflammatory responses and growth factor signaling. Lastly, perhaps the most interesting way to modulate sphingolipids and promote longevity is by lowering the activity of serine palmitoyltransferase, the first enzyme in the de novo sphingolipid biosynthesis pathway. Available data in yeasts and rodents are encouraging and as we gain insights into molecular mechanisms the strategies for improving human health by modulating sphingolipids will become more apparent. This article is part of a Special Issue entitled New Frontiers in Sphingolipid Biology.
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Affiliation(s)
- Xinhe Huang
- Department of Molecular and Cellular Biochemistry and the Lucille Markey Cancer Center, University of Kentucky College of Medicine, 741 S. Limestone, Lexington, KY 40536, USA
| | - Bradley R Withers
- Department of Molecular and Cellular Biochemistry and the Lucille Markey Cancer Center, University of Kentucky College of Medicine, 741 S. Limestone, Lexington, KY 40536, USA
| | - Robert C Dickson
- Department of Molecular and Cellular Biochemistry and the Lucille Markey Cancer Center, University of Kentucky College of Medicine, 741 S. Limestone, Lexington, KY 40536, USA.
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338
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Flis VV, Daum G. Lipid transport between the endoplasmic reticulum and mitochondria. Cold Spring Harb Perspect Biol 2013; 5:5/6/a013235. [PMID: 23732475 DOI: 10.1101/cshperspect.a013235] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Mitochondria are partially autonomous organelles that depend on the import of certain proteins and lipids to maintain cell survival and membrane formation. Although phosphatidylglycerol, cardiolipin, and phosphatidylethanolamine are synthesized by mitochondrial enzymes, phosphatidylcholine, phosphatidylinositol, phosphatidylserine, and sterols need to be imported from other organelles. The origin of most lipids imported into mitochondria is the endoplasmic reticulum, which requires interaction of these two subcellular compartments. Recently, protein complexes that are involved in membrane contact between endoplasmic reticulum and mitochondria were identified, but their role in lipid transport is still unclear. In the present review, we describe components involved in lipid translocation between the endoplasmic reticulum and mitochondria and discuss functional as well as regulatory aspects that are important for lipid homeostasis.
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Affiliation(s)
- Vid V Flis
- Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria
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339
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Sphingosine 1-phosphate and cancer: lessons from thyroid cancer cells. Biomolecules 2013; 3:303-15. [PMID: 24970169 PMCID: PMC4030848 DOI: 10.3390/biom3020303] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 02/03/2023] Open
Abstract
Sphingomyelin is found in the cell membrane of all eukaryotic cells, and was for a long time considered merely as a structural component. However, during the last two decades, metabolites of sphingomyelin, especially sphingosine 1-phosphate (S1P), have proven to be physiologically significant regulators of cell function. Through its five different G protein-coupled receptors, S1P regulates a wide array of cellular processes, ranging from stimulating cellular proliferation and migration, to the inhibition of apoptosis and induction of angiogenesis and modulation of cellular calcium homeostasis. Many of the processes regulated by S1P are important for normal cell physiology, but may also induce severe pathological conditions, especially in malignancies like cancer. Thus, understanding S1P signaling mechanisms has been the aim of a multitude of investigations. Great interest has also been shown in understanding the action of sphingosine kinase (SphK), i.e., the kinase phosphorylating sphingosine to S1P, and the interactions between S1P and growth factor signaling. In the present review, we will discuss recent findings regarding the possible importance of S1P and SphK in the etiology of thyroid cancer. Although clinical data is still scarce, our in vitro findings suggest that S1P may function as a “double-edged sword”, as the receptor profile of thyroid cancer cells largely determines whether S1P stimulates or blocks cellular migration. We will also discuss the interactions between S1P- and VEGF-evoked signaling, and the importance of a S1P1-VEGF receptor 2 complex in thyroid cancer cells.
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340
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Romano JD, Sonda S, Bergbower E, Smith ME, Coppens I. Toxoplasma gondii salvages sphingolipids from the host Golgi through the rerouting of selected Rab vesicles to the parasitophorous vacuole. Mol Biol Cell 2013; 24:1974-95. [PMID: 23615442 PMCID: PMC3681701 DOI: 10.1091/mbc.e12-11-0827] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The obligate intracellular protozoan Toxoplasma gondii actively invades mammalian cells and, upon entry, forms its own membrane-bound compartment, named the parasitophorous vacuole (PV). Within the PV, the parasite replicates and scavenges nutrients, including lipids, from host organelles. Although T. gondii can synthesize sphingolipids de novo, it also scavenges these lipids from the host Golgi. How the parasite obtains sphingolipids from the Golgi remains unclear, as the PV avoids fusion with host organelles. In this study, we explore the host Golgi-PV interaction and evaluate the importance of host-derived sphingolipids for parasite growth. We demonstrate that the PV preferentially localizes near the host Golgi early during infection and remains closely associated with this organelle throughout infection. The parasite subverts the structure of the host Golgi, resulting in its fragmentation into numerous ministacks, which surround the PV, and hijacks host Golgi-derived vesicles within the PV. These vesicles, marked with Rab14, Rab30, or Rab43, colocalize with host-derived sphingolipids in the vacuolar space. Scavenged sphingolipids contribute to parasite replication since alterations in host sphingolipid metabolism are detrimental for the parasite's growth. Thus our results reveal that T. gondii relies on host-derived sphingolipids for its development and scavenges these lipids via Golgi-derived vesicles.
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Affiliation(s)
- Julia D Romano
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA.
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341
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Abstract
Sphingolipids are a diverse group of lipids that have essential cellular roles as structural components of membranes and as potent signaling molecules. In recent years, a detailed picture has emerged of the basic biochemistry of sphingolipids-from their initial synthesis in the endoplasmic reticulum (ER), to their elaboration into complex glycosphingolipids, to their turnover and degradation. However, our understanding of how sphingolipid metabolism is regulated in response to metabolic demand and physiologic cues remains incomplete. Here I discuss new insights into the mechanisms that ensure sphingolipid homeostasis, with an emphasis on the ER as a critical regulatory site in sphingolipid metabolism. In particular, Orm family proteins have recently emerged as key ER-localized mediators of sphingolipid homeostasis. A detailed understanding of how cells sense and control sphingolipid production promises to provide key insights into membrane function in health and disease.
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Affiliation(s)
- David K Breslow
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94035-5345, USA.
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342
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Forrest S, Chai A, Sanhueza M, Marescotti M, Parry K, Georgiev A, Sahota V, Mendez-Castro R, Pennetta G. Increased levels of phosphoinositides cause neurodegeneration in a Drosophila model of amyotrophic lateral sclerosis. Hum Mol Genet 2013; 22:2689-704. [PMID: 23492670 PMCID: PMC3674808 DOI: 10.1093/hmg/ddt118] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Vesicle-associated membrane protein (VAMP)-Associated Protein B (VAPB) is the causative gene of amyotrophic lateral sclerosis 8 (ALS8) in humans. Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease characterized by selective death of motor neurons leading to spasticity, muscle atrophy and paralysis. VAP proteins have been implicated in various cellular processes, including intercellular signalling, synaptic remodelling, lipid transport and membrane trafficking and yet, the molecular mechanisms underlying ALS8 pathogenesis remain poorly understood. We identified the conserved phosphoinositide phosphatase Sac1 as a Drosophila VAP (DVAP)-binding partner and showed that DVAP is required to maintain normal levels of phosphoinositides. Downregulating either Sac1 or DVAP disrupts axonal transport, synaptic growth, synaptic microtubule integrity and the localization of several postsynaptic components. Expression of the disease-causing allele (DVAP-P58S) in a fly model for ALS8 induces neurodegeneration, elicits synaptic defects similar to those of DVAP or Sac1 downregulation and increases phosphoinositide levels. Consistent with a role for Sac1-mediated increase of phosphoinositide levels in ALS8 pathogenesis, we found that Sac1 downregulation induces neurodegeneration in a dosage-dependent manner. In addition, we report that Sac1 is sequestered into the DVAP-P58S-induced aggregates and that reducing phosphoinositide levels rescues the neurodegeneration and suppresses the synaptic phenotypes associated with DVAP-P58S transgenic expression. These data underscore the importance of DVAP–Sac1 interaction in controlling phosphoinositide metabolism and provide mechanistic evidence for a crucial role of phosphoinositide levels in VAP-induced ALS.
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Affiliation(s)
- Stuart Forrest
- Center for Integrative Physiology and Euan MacDonald Center for Motor Neuron Disease Research, School of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
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343
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Schuldiner M, Weissman JS. The contribution of systematic approaches to characterizing the proteins and functions of the endoplasmic reticulum. Cold Spring Harb Perspect Biol 2013; 5:a013284. [PMID: 23359093 DOI: 10.1101/cshperspect.a013284] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The endoplasmic reticulum (ER) is a complex organelle responsible for a range of functions including protein folding and secretion, lipid biosynthesis, and ion homeostasis. Despite its central and essential roles in eukaryotic cells during development, growth, and disease, many ER proteins are poorly characterized. Moreover, the range of biochemical reactions that occur within the ER membranes, let alone how these different activities are coordinated, is not yet defined. In recent years, focused studies on specific ER functions have been complemented by systematic approaches and innovative technologies for high-throughput analysis of the location, levels, and biological impact of given components. This article focuses on the recent progress of these efforts, largely pioneered in the budding yeast Saccharomyces cerevisiae, and also addresses how future systematic studies can be geared to uncover the "dark matter" of uncharted ER functions.
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Affiliation(s)
- Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel 76100.
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344
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Bohdanowicz M, Grinstein S. Role of Phospholipids in Endocytosis, Phagocytosis, and Macropinocytosis. Physiol Rev 2013; 93:69-106. [DOI: 10.1152/physrev.00002.2012] [Citation(s) in RCA: 213] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Endocytosis, phagocytosis, and macropinocytosis are fundamental processes that enable cells to sample their environment, eliminate pathogens and apoptotic bodies, and regulate the expression of surface components. While a great deal of effort has been devoted over many years to understanding the proteins involved in these processes, the important contribution of phospholipids has only recently been appreciated. This review is an attempt to collate and analyze the rapidly emerging evidence documenting the role of phospholipids in clathrin-mediated endocytosis, phagocytosis, and macropinocytosis. A primer on phospholipid biosynthesis, catabolism, subcellular distribution, and transport is presented initially, for reference, together with general considerations of the effects of phospholipids on membrane curvature and charge. This is followed by a detailed analysis of the critical functions of phospholipids in the internalization processes and in the maturation of the resulting vesicles and vacuoles as they progress along the endo-lysosomal pathway.
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Affiliation(s)
- Michal Bohdanowicz
- Division of Cell Biology, Hospital for Sick Children, and Institute of Medical Sciences, University of Toronto, Toronto, Canada
| | - Sergio Grinstein
- Division of Cell Biology, Hospital for Sick Children, and Institute of Medical Sciences, University of Toronto, Toronto, Canada
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345
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Lester RL, Withers BR, Schultz MA, Dickson RC. Iron, glucose and intrinsic factors alter sphingolipid composition as yeast cells enter stationary phase. Biochim Biophys Acta Mol Cell Biol Lipids 2012; 1831:726-36. [PMID: 23286903 DOI: 10.1016/j.bbalip.2012.12.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 12/11/2012] [Accepted: 12/19/2012] [Indexed: 11/24/2022]
Abstract
Survival of Saccharomyces cerevisiae cells, like most microorganisms, requires switching from a rapidly dividing to a non-dividing or stationary state. To further understand how cells navigate this switch, we examined sphingolipids since they are key structural elements of membranes and also regulate signaling pathways vital for survival. During and after the switch to a non-dividing state there is a large increase in total free and sphingolipid-bound long chain-bases and an even larger increase in free and bound C20-long-chain bases, which are nearly undetectable in dividing cells. These changes are due to intrinsic factors including Orm1 and Orm2, ceramide synthase, Lcb4 kinase and the Tsc3 subunit of serine palmitoyltransferase as well as extrinsic factors including glucose and iron. Lowering the concentration of glucose, a form of calorie restriction, decreases the level of LCBs, which is consistent with the idea that reducing the level of some sphingolipids enhances lifespan. In contrast, iron deprivation increases LCB levels and decreases long term survival; however, these phenomena may not be related because iron deprivation disrupts many metabolic pathways. The correlation between increased LCBs and shorter lifespan is unsupported at this time. The physiological rise in LCBs that we observe may serve to modulate nutrient transporters and possibly other membrane phenomena that contribute to enhanced stress resistance and survival in stationary phase.
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Affiliation(s)
- Robert L Lester
- Department of Molecular and Cellular Biochemistry and the Lucille Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA
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346
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Kolter T. Ganglioside biochemistry. ISRN BIOCHEMISTRY 2012; 2012:506160. [PMID: 25969757 PMCID: PMC4393008 DOI: 10.5402/2012/506160] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 10/09/2012] [Indexed: 01/21/2023]
Abstract
Gangliosides are sialic acid-containing glycosphingolipids. They occur especially on the cellular surfaces of neuronal cells, where they form a complex pattern, but are also found in many other cell types. The paper provides a general overview on their structures, occurrence, and metabolism. Key functional, biochemical, and pathobiochemical aspects are summarized.
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Affiliation(s)
- Thomas Kolter
- Program Unit Membrane Biology & Lipid Biochemistry, LiMES, University of Bonn, Gerhard-Domagk Straße 1, 53121 Bonn, Germany
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347
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Degenkolbe T, Giavalisco P, Zuther E, Seiwert B, Hincha DK, Willmitzer L. Differential remodeling of the lipidome during cold acclimation in natural accessions of Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:972-82. [PMID: 23061922 DOI: 10.1111/tpj.12007] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Freezing injury is a major factor limiting the geographical distribution of plant species and the growth and yield of crop plants. Plants from temperate climates are able to increase their freezing tolerance during exposure to low but non-freezing temperatures in a process termed cold acclimation. Damage to cellular membranes is the major cause of freezing injury in plants, and membrane lipid composition is strongly modified during cold acclimation. Forward and reverse genetic approaches have been used to probe the role of specific lipid-modifying enzymes in the freezing tolerance of plants. In the present paper we describe an alternative ecological genomics approach that relies on the natural genetic variation within a species. Arabidopsis thaliana has a wide geographical range throughout the Northern Hemisphere with significant natural variation in freezing tolerance that was used for a comparative analysis of the lipidomes of 15 Arabidopsis accessions using ultra-performance liquid chromatography coupled to Fourier-transform mass spectrometry, allowing the detection of 180 lipid species. After 14 days of cold acclimation at 4°C the plants from most accessions had accumulated massive amounts of storage lipids, with most of the changes in long-chain unsaturated triacylglycerides, while the total amount of membrane lipids was only slightly changed. Nevertheless, major changes in the relative amounts of different membrane lipids were also evident. The relative abundance of several lipid species was highly correlated with the freezing tolerance of the accessions, allowing the identification of possible marker lipids for plant freezing tolerance.
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Affiliation(s)
- Thomas Degenkolbe
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
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348
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Pantoja M, Fischer KA, Ieronimakis N, Reyes M, Ruohola-Baker H. Genetic elevation of sphingosine 1-phosphate suppresses dystrophic muscle phenotypes in Drosophila. Development 2012; 140:136-46. [PMID: 23154413 DOI: 10.1242/dev.087791] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Duchenne muscular dystrophy is a lethal genetic disease characterized by the loss of muscle integrity and function over time. Using Drosophila, we show that dystrophic muscle phenotypes can be significantly suppressed by a reduction of wunen, a homolog of lipid phosphate phosphatase 3, which in higher animals can dephosphorylate a range of phospholipids. Our suppression analyses include assessing the localization of Projectin protein, a titin homolog, in sarcomeres as well as muscle morphology and functional movement assays. We hypothesize that wunen-based suppression is through the elevation of the bioactive lipid Sphingosine 1-phosphate (S1P), which promotes cell proliferation and differentiation in many tissues, including muscle. We confirm the role of S1P in suppression by genetically altering S1P levels via reduction of S1P lyase (Sply) and by upregulating the serine palmitoyl-CoA transferase catalytic subunit gene lace, the first gene in the de novo sphingolipid biosynthetic pathway and find that these manipulations also reduce muscle degeneration. Furthermore, we show that reduction of spinster (which encodes a major facilitator family transporter, homologs of which in higher animals have been shown to transport S1P) can also suppress dystrophic muscle degeneration. Finally, administration to adult flies of pharmacological agents reported to elevate S1P signaling significantly suppresses dystrophic muscle phenotypes. Our data suggest that localized intracellular S1P elevation promotes the suppression of muscle wasting in flies.
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Affiliation(s)
- Mario Pantoja
- Department of Biochemistry, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, USA
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349
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Siow DL, Wattenberg BW. Mammalian ORMDL proteins mediate the feedback response in ceramide biosynthesis. J Biol Chem 2012; 287:40198-204. [PMID: 23066021 DOI: 10.1074/jbc.c112.404012] [Citation(s) in RCA: 288] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND The yeast Orm1/2 proteins regulate ceramide biosynthesis. RESULTS Depletion of the mammalian Orm1/2 homologues, ORMDL1-3, eliminates the negative feedback of exogenous ceramide on ceramide biosynthesis in HeLa cells. CONCLUSION ORMDL proteins are the primary regulators of ceramide biosynthesis in mammalian cells. SIGNIFICANCE Therapeutically manipulating levels of the pro-death lipid, ceramide, requires a molecular understanding of its regulation. The mammalian ORMDL proteins are orthologues of the yeast Orm proteins (Orm1/2), which are regulators of ceramide biosynthesis. In mammalian cells, ceramide is a proapoptotic signaling sphingolipid, but it is also an obligate precursor to essential higher order sphingolipids. Therefore levels of ceramide are expected to be tightly controlled. We tested the three ORMDL isoforms for their role in homeostatically regulating ceramide biosynthesis in mammalian cells. Treatment of cells with a short chain (C6) ceramide or sphingosine resulted in a dramatic inhibition of ceramide biosynthesis. This inhibition was almost completely eliminated by ORMDL knockdown. This establishes that the ORMDL proteins mediate the feedback regulation of ceramide biosynthesis in mammalian cells. The ORMDL proteins are functionally redundant. Knockdown of all three isoforms simultaneously was required to alleviate the sphingolipid-mediated inhibition of ceramide biosynthesis. The lipid sensed by the ORMDL-mediated feedback mechanism is medium or long chain ceramide or a higher order sphingolipid. Treatment of permeabilized cells with C6-ceramide resulted in ORMDL-mediated inhibition of the rate-limiting enzyme in sphingolipid biosynthesis, serine palmitoyltransferase. This indicates that C6-ceramide inhibition requires only membrane-bound elements and does not involve diffusible proteins or small molecules. We also tested the atypical sphingomyelin synthase isoform, SMSr, for its role in the regulation of ceramide biosynthesis. This unusual enzyme has been reported to regulate ceramide levels in the endoplasmic reticulum. We were unable to detect a role for SMSr in regulating ceramide biosynthesis. We suggest that the role of SMSr may be in the regulation of downstream metabolism of ceramide.
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Affiliation(s)
- Deanna L Siow
- James Graham Brown Cancer Center, Louisville, KY 40202, USA
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350
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Hla T, Dannenberg AJ. Sphingolipid signaling in metabolic disorders. Cell Metab 2012; 16:420-34. [PMID: 22982021 PMCID: PMC3466368 DOI: 10.1016/j.cmet.2012.06.017] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 05/29/2012] [Accepted: 06/20/2012] [Indexed: 01/01/2023]
Abstract
Sphingolipids, ubiquitous membrane lipids in eukaryotes, carry out a myriad of critical cellular functions. The past two decades have seen significant advances in sphingolipid research, and in 2010 a first sphingolipid receptor modulator was employed as a human therapeutic. Furthermore, cellular signaling mechanisms regulated by sphingolipids are being recognized as critical players in metabolic diseases. This review focuses on recent advances in cellular and physiological mechanisms of sphingolipid regulation and how sphingolipid signaling influences metabolic diseases. Progress in this area may contribute to new understanding and therapeutic options in complex diseases such as atherosclerosis, diabetes, metabolic syndromes, and cancer.
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Affiliation(s)
- Timothy Hla
- Center for Vascular Biology, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA.
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