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Gawden-Bone CM, Lehner PJ, Volkmar N. As a matter of fat: Emerging roles of lipid-sensitive E3 ubiquitin ligases. Bioessays 2023; 45:e2300139. [PMID: 37890275 DOI: 10.1002/bies.202300139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023]
Abstract
The dynamic structure and composition of lipid membranes need to be tightly regulated to control the vast array of cellular processes from cell and organelle morphology to protein-protein interactions and signal transduction pathways. To maintain membrane integrity, sense-and-response systems monitor and adjust membrane lipid composition to the ever-changing cellular environment, but only a relatively small number of control systems have been described. Here, we explore the emerging role of the ubiquitin-proteasome system in monitoring and maintaining membrane lipid composition. We focus on the ER-resident RNF145 E3 ubiquitin ligase, its role in regulating adiponectin receptor 2 (ADIPOR2), its lipid hydrolase substrate, and the broader implications for understanding the homeostatic processes that fine-tune cellular membrane composition.
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Affiliation(s)
- Christian M Gawden-Bone
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Paul J Lehner
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Norbert Volkmar
- Institute for Molecular Systems Biology (IMSB), ETH Zürich, Zürich, Switzerland
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2
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Lup SD, Navarro-Quiles C, Micol JL. Versatile mapping-by-sequencing with Easymap v.2. FRONTIERS IN PLANT SCIENCE 2023; 14:1042913. [PMID: 36778692 PMCID: PMC9909543 DOI: 10.3389/fpls.2023.1042913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Mapping-by-sequencing combines Next Generation Sequencing (NGS) with classical genetic mapping by linkage analysis to establish gene-to-phenotype relationships. Although numerous tools have been developed to analyze NGS datasets, only a few are available for mapping-by-sequencing. One such tool is Easymap, a versatile, easy-to-use package that performs automated mapping of point mutations and large DNA insertions. Here, we describe Easymap v.2, which also maps small insertion/deletions (InDels), and includes workflows to perform QTL-seq and variant density mapping analyses. Each mapping workflow can accommodate different experimental designs, including outcrossing and backcrossing, F2, M2, and M3 mapping populations, chemically induced mutation and natural variant mapping, input files containing single-end or paired-end reads of genomic or complementary DNA sequences, and alternative control sample files in FASTQ and VCF formats. Easymap v.2 can also be used as a variant analyzer in the absence of a mapping algorithm and includes a multi-threading option.
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Ruiz M, Svensk E, Einarsson E, Grahn EP, Pilon M. A small molecule screen for paqr-2 suppressors identifies Tyloxapol as a membrane fluidizer for C. elegans and mammalian cells. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183959. [PMID: 35588889 DOI: 10.1016/j.bbamem.2022.183959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/20/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Defects in cell membrane homeostasis are implicated in numerous disorders, including cancer, neurodegeneration and diabetes. There is therefore a need for a powerful model to study membrane homeostasis and to identify eventual therapeutic routes. The C. elegans gene paqr-2 encodes a homolog of the mammalian AdipoR1 and AdipoR2 proteins that, when mutated, causes a membrane homeostasis defect accompanied by multiple phenotypes such as intolerance to dietary saturated fatty acids, intolerance to cold and a characteristic tail tip morphology defect. We screened a compound library to identify molecules that can suppress the paqr-2 phenotypes. A single positive hit, Tyloxapol, was found that very effectively suppresses multiple paqr-2 phenotypes. Tyloxapol is a non-ionic detergent currently in use clinically as an expectorant. Importantly, we examined the potential of Tyloxapol as a fluidizer in human cells and found that it improves the viability and membrane fluidity of AdipoR2-deficient human cells challenged with palmitic acid, a membrane-rigidifying saturated fatty acid.
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Affiliation(s)
- Mario Ruiz
- Dept. Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, S-405 30 Gothenburg, Sweden
| | - Emma Svensk
- Dept. Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, S-405 30 Gothenburg, Sweden
| | - Elinor Einarsson
- Dept. Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, S-405 30 Gothenburg, Sweden
| | - Erik Podda Grahn
- Dept. Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, S-405 30 Gothenburg, Sweden
| | - Marc Pilon
- Dept. Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, S-405 30 Gothenburg, Sweden.
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4
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Devkota R, Henricsson M, Borén J, Pilon M. The C. elegans PAQR-2 and IGLR-2 membrane homeostasis proteins are uniquely essential for tolerating dietary saturated fats. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158883. [PMID: 33444761 DOI: 10.1016/j.bbalip.2021.158883] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/18/2020] [Accepted: 01/06/2021] [Indexed: 01/07/2023]
Abstract
How cells maintain vital membrane lipid homeostasis while obtaining most of their constituent fatty acids from a varied diet remains largely unknown. Here, we report the first whole-organism (Caenorhabditis elegans) forward genetic screen to identify genes essential for tolerance to dietary saturated fatty acids (SFAs). We found that only the PAQR-2/IGLR-2 pathway, homologous to the human adiponectin receptor 2 (AdipoR2) pathway, is uniquely essential to prevent SFA-mediated toxicity. When provided a SFA-rich diet, worms lacking either protein accumulate an excess of SFAs in their membrane phospholipids, which is accompanied by membrane rigidification. Additionally, we used fluorescence resonance energy transfer (FRET) to show that the interaction between PAQR-2 and IGLR-2 is regulated by membrane fluidity, suggesting a mechanism by which this protein complex senses membrane properties. We also created versions of PAQR-2 that lacked parts of the cytoplasmic N-terminal domain and showed that these were still functional, though still dependent on the interaction with IGLR-2. We conclude that membrane homeostasis via the PAQR-2/IGLR-2 fluidity sensor is the only pathway specifically essential for the non-toxic uptake of dietary SFAs in C. elegans.
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Affiliation(s)
- Ranjan Devkota
- Dept. Chemistry and Molecular Biology, Univ. Gothenburg, 405 30 Gothenburg, Sweden
| | - Marcus Henricsson
- Dept. Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, Univ. of Gothenburg, 405 30 Gothenburg, Sweden
| | - Jan Borén
- Dept. Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, Univ. of Gothenburg, 405 30 Gothenburg, Sweden
| | - Marc Pilon
- Dept. Chemistry and Molecular Biology, Univ. Gothenburg, 405 30 Gothenburg, Sweden.
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5
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Kuo CJ, Hsu YC, Wang ST, Liou BY, Lim SBY, Chen YW, Chen CS. IGLR-2, a Leucine-Rich Repeat Domain Containing Protein, Is Required for the Host Defense in Caenorhabditis elegans. Front Immunol 2020; 11:561337. [PMID: 33329523 PMCID: PMC7734252 DOI: 10.3389/fimmu.2020.561337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/21/2020] [Indexed: 11/13/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC), a human pathogen, also infects Caenorhabditis elegans. We demonstrated previously that C. elegans activates the p38 MAPK innate immune pathway to defend against EHEC infection. However, whether a C. elegans pattern recognition receptor (PRR) exists to regulate the immune pathway remains unknown. PRRs identified in other metazoans contain several conserved domains, including the leucine-rich repeat (LRR). By screening a focused RNAi library, we identified the IGLR-2, a transmembrane protein containing the LRR domain, as a potential immune regulator in C. elegans. Our data showed that iglr-2 regulates the host susceptibility to EHEC infection. Moreover, iglr-2 is required for pathogen avoidance to EHEC. The iglr-2 overexpressed strain, which was more resistant to EHEC originally, showed hypersusceptibility to EHEC upon knockdown of the p38 MAPK pathway. Together, our data suggested that iglr-2 plays an important role in C. elegans to defend EHEC by regulating pathogen-avoidance behavior and the p38 MAPK pathway.
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Affiliation(s)
- Cheng-Ju Kuo
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Chu Hsu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sin-Tian Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Bang-Yu Liou
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Serene Boon-Yuean Lim
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Wei Chen
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chang-Shi Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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Leveraging a gain-of-function allele of Caenorhabditis elegans paqr-1 to elucidate membrane homeostasis by PAQR proteins. PLoS Genet 2020; 16:e1008975. [PMID: 32750056 PMCID: PMC7428288 DOI: 10.1371/journal.pgen.1008975] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/14/2020] [Accepted: 07/01/2020] [Indexed: 12/12/2022] Open
Abstract
The C. elegans proteins PAQR-2 (a homolog of the human seven-transmembrane domain AdipoR1 and AdipoR2 proteins) and IGLR-2 (a homolog of the mammalian LRIG proteins characterized by a single transmembrane domain and the presence of immunoglobulin domains and leucine-rich repeats in their extracellular portion) form a complex that protects against plasma membrane rigidification by promoting the expression of fatty acid desaturases and the incorporation of polyunsaturated fatty acids into phospholipids, hence increasing membrane fluidity. In the present study, we leveraged a novel gain-of-function allele of PAQR-1, a PAQR-2 paralog, to carry out structure-function studies. We found that the transmembrane domains of PAQR-2 are responsible for its functional requirement for IGLR-2, that PAQR-1 does not require IGLR-2 but acts via the same pathway as PAQR-2, and that the divergent N-terminal cytoplasmic domains of the PAQR-1 and PAQR-2 proteins serve a regulatory function and may regulate access to the catalytic site of these proteins. We also show that overexpression of human AdipoR1 or AdipoR2 alone is sufficient to confer increased palmitic acid resistance in HEK293 cells, and thus act in a manner analogous to the PAQR-1 gain-of-function allele.
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Ruiz M, Bodhicharla R, Ståhlman M, Svensk E, Busayavalasa K, Palmgren H, Ruhanen H, Boren J, Pilon M. Evolutionarily conserved long-chain Acyl-CoA synthetases regulate membrane composition and fluidity. eLife 2019; 8:47733. [PMID: 31769755 PMCID: PMC6901333 DOI: 10.7554/elife.47733] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 11/23/2019] [Indexed: 12/19/2022] Open
Abstract
The human AdipoR1 and AdipoR2 proteins, as well as their C. elegans homolog PAQR-2, protect against cell membrane rigidification by exogenous saturated fatty acids by regulating phospholipid composition. Here, we show that mutations in the C. elegans gene acs-13 help to suppress the phenotypes of paqr-2 mutant worms, including their characteristic membrane fluidity defects. acs-13 encodes a homolog of the human acyl-CoA synthetase ACSL1, and localizes to the mitochondrial membrane where it likely activates long chains fatty acids for import and degradation. Using siRNA combined with lipidomics and membrane fluidity assays (FRAP and Laurdan dye staining) we further show that the human ACSL1 potentiates lipotoxicity by the saturated fatty acid palmitate: silencing ACSL1 protects against the membrane rigidifying effects of palmitate and acts as a suppressor of AdipoR2 knockdown, thus echoing the C. elegans findings. We conclude that acs-13 mutations in C. elegans and ACSL1 knockdown in human cells prevent lipotoxicity by promoting increased levels of polyunsaturated fatty acid-containing phospholipids.
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Affiliation(s)
- Mario Ruiz
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Rakesh Bodhicharla
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Marcus Ståhlman
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Emma Svensk
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Kiran Busayavalasa
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Henrik Palmgren
- Metabolism BioScience, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Hanna Ruhanen
- Helsinki University Lipidomics Unit, Helsinki Institute for Life Science, Helsinki, Finland.,Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jan Boren
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Marc Pilon
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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de Mendoza D, Pilon M. Control of membrane lipid homeostasis by lipid-bilayer associated sensors: A mechanism conserved from bacteria to humans. Prog Lipid Res 2019; 76:100996. [DOI: 10.1016/j.plipres.2019.100996] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/25/2019] [Accepted: 06/28/2019] [Indexed: 12/31/2022]
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9
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Ruiz M, Ståhlman M, Borén J, Pilon M. AdipoR1 and AdipoR2 maintain membrane fluidity in most human cell types and independently of adiponectin. J Lipid Res 2019; 60:995-1004. [PMID: 30890562 PMCID: PMC6495173 DOI: 10.1194/jlr.m092494] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/07/2019] [Indexed: 12/16/2022] Open
Abstract
The FA composition of phospholipids must be tightly regulated to maintain optimal cell membrane properties and compensate for a highly variable supply of dietary FAs. Previous studies have shown that AdipoR2 and its homologue PAQR-2 are important regulators of phospholipid FA composition in HEK293 cells and Caenorhabditiselegans, respectively. Here we show that both AdipoR1 and AdipoR2 are essential for sustaining desaturase expression and high levels of unsaturated FAs in membrane phospholipids of many human cell types, including primary human umbilical vein endothelial cells, and for preventing membrane rigidification in cells challenged with exogenous palmitate, a saturated FA. Three independent methods confirm the role of the AdipoRs as regulators of membrane composition and fluidity: fluorescence recovery after photobleaching, measurements of Laurdan dye generalized polarization, and mass spectrometry to determine the FA composition of phospholipids. Furthermore, we show that the AdipoRs can prevent lipotoxicity in the complete absence of adiponectin, their putative ligand. We propose that the primary cellular function of AdipoR1 and AdipoR2 is to maintain membrane fluidity in most human cell types and that adiponectin is not required for this function.
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Affiliation(s)
- Mario Ruiz
- Department of Chemistry and Molecular Biology; University of Gothenburg, Gothenburg, Sweden
| | - Marcus Ståhlman
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Jan Borén
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Marc Pilon
- Department of Chemistry and Molecular Biology; University of Gothenburg, Gothenburg, Sweden.
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Ruiz M, Bodhicharla R, Svensk E, Devkota R, Busayavalasa K, Palmgren H, Ståhlman M, Boren J, Pilon M. Membrane fluidity is regulated by the C. elegans transmembrane protein FLD-1 and its human homologs TLCD1/2. eLife 2018; 7:e40686. [PMID: 30509349 PMCID: PMC6279351 DOI: 10.7554/elife.40686] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/04/2018] [Indexed: 12/15/2022] Open
Abstract
Dietary fatty acids are the main building blocks for cell membranes in animals, and mechanisms must therefore exist that compensate for dietary variations. We isolated C. elegans mutants that improved tolerance to dietary saturated fat in a sensitized genetic background, including eight alleles of the novel gene fld-1 that encodes a homolog of the human TLCD1 and TLCD2 transmembrane proteins. FLD-1 is localized on plasma membranes and acts by limiting the levels of highly membrane-fluidizing long-chain polyunsaturated fatty acid-containing phospholipids. Human TLCD1/2 also regulate membrane fluidity by limiting the levels of polyunsaturated fatty acid-containing membrane phospholipids. FLD-1 and TLCD1/2 do not regulate the synthesis of long-chain polyunsaturated fatty acids but rather limit their incorporation into phospholipids. We conclude that inhibition of FLD-1 or TLCD1/2 prevents lipotoxicity by allowing increased levels of membrane phospholipids that contain fluidizing long-chain polyunsaturated fatty acids. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Mario Ruiz
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden
| | - Rakesh Bodhicharla
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden
| | - Emma Svensk
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden
| | - Ranjan Devkota
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden
| | - Kiran Busayavalasa
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden
| | - Henrik Palmgren
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden
- Diabetes Bioscience, Cardiovascular, Renal and Metabolism, IMED Biotech UnitAstraZenecaGothenburgSweden
| | - Marcus Ståhlman
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of MedicineUniversity of GothenburgGothenburgSweden
| | - Jan Boren
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of MedicineUniversity of GothenburgGothenburgSweden
| | - Marc Pilon
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden
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