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Aisyah R, Ohshima N, Watanabe D, Nakagawa Y, Sakuma T, Nitschke F, Nakamura M, Sato K, Nakahata K, Yokoyama C, Marchioni CR, Kumrungsee T, Shimizu T, Sotomaru Y, Takeo T, Nakagata N, Izumi T, Miura S, Minassian BA, Yamamoto T, Wada M, Yanaka N. GDE5/Gpcpd1 activity determines phosphatidylcholine composition in skeletal muscle and regulates contractile force in mice. Commun Biol 2024; 7:604. [PMID: 38769369 PMCID: PMC11106330 DOI: 10.1038/s42003-024-06298-z] [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: 07/11/2023] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
Glycerophosphocholine (GPC) is an important precursor for intracellular choline supply in phosphatidylcholine (PC) metabolism. GDE5/Gpcpd1 hydrolyzes GPC into choline and glycerol 3-phosphate; this study aimed to elucidate its physiological function in vivo. Heterozygous whole-body GDE5-deficient mice reveal a significant GPC accumulation across tissues, while homozygous whole-body knockout results in embryonic lethality. Skeletal muscle-specific GDE5 deletion (Gde5 skKO) exhibits reduced passive force and improved fatigue resistance in electrically stimulated gastrocnemius muscles in vivo. GDE5 deficiency also results in higher glycolytic metabolites and glycogen levels, and glycerophospholipids alteration, including reduced levels of phospholipids that bind polyunsaturated fatty acids (PUFAs), such as DHA. Interestingly, this PC fatty acid compositional change is similar to that observed in skeletal muscles of denervated and Duchenne muscular dystrophy mouse models. These are accompanied by decrease of GDE5 expression, suggesting a regulatory role of GDE5 activity for glycerophospholipid profiles. Furthermore, a DHA-rich diet enhances contractile force and lowers fatigue resistance, suggesting a functional relationship between PC fatty acid composition and muscle function. Finally, skinned fiber experiments show that GDE5 loss increases the probability of the ryanodine receptor opening and lowers the maximum Ca2+-activated force. Collectively, GDE5 activity plays roles in PC and glucose/glycogen metabolism in skeletal muscle.
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Affiliation(s)
- Rahmawati Aisyah
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | | | - Daiki Watanabe
- Graduate School of Humanities and Social Sciences, Hiroshima University, Hiroshima, Japan
- Graduate School of Sport and Health Sciences, Osaka University of Health and Sport Sciences, Osaka, Japan
| | - Yoshiko Nakagawa
- Center for Animal Resources and Development (CARD), Kumamoto University, Kumamoto, Japan
| | - Tetsushi Sakuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Felix Nitschke
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Minako Nakamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Koji Sato
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Kaori Nakahata
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Chihiro Yokoyama
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Charlotte R Marchioni
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Takahiko Shimizu
- Aging Stress Response Research Project Team, National Center for Geriatrics and Gerontology, Aichi, Japan
| | - Yusuke Sotomaru
- Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima, Japan
| | - Toru Takeo
- Center for Animal Resources and Development (CARD), Kumamoto University, Kumamoto, Japan
| | - Naomi Nakagata
- Center for Animal Resources and Development (CARD), Kumamoto University, Kumamoto, Japan
| | - Takashi Izumi
- Graduate School of Medicine, Gunma University, Gunma, Japan
- Faculty of Health Care, Teikyo Heisei University, Tokyo, Japan
| | - Shinji Miura
- Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka, Japan
| | - Berge A Minassian
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Takashi Yamamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Masanobu Wada
- Graduate School of Humanities and Social Sciences, Hiroshima University, Hiroshima, Japan
| | - Noriyuki Yanaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan.
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Wang J, Li J, Fu Y, Zhu Y, Lin L, Li Y. Research progress, challenges and perspectives of phospholipids metabolism in the LXR‑LPCAT3 signaling pathway and its relation to NAFLD (Review). Int J Mol Med 2024; 53:32. [PMID: 38362962 PMCID: PMC10903931 DOI: 10.3892/ijmm.2024.5356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/16/2024] [Indexed: 02/17/2024] Open
Abstract
Phospholipids (PLs) are principle constituents of biofilms, with their fatty acyl chain composition significantly impacting the biophysical properties of membranes, thereby influencing biological processes. Recent studies have elucidated that fatty acyl chains, under the enzymatic action of lyso‑phosphatidyl‑choline acyltransferases (LPCATs), expedite incorporation into the sn‑2 site of phosphatidyl‑choline (PC), profoundly affecting pathophysiology. Accumulating evidence suggests that alterations in LPCAT activity are implicated in various diseases, including non‑alcoholic fatty liver disease (NAFLD), hepatitis C, atherosclerosis and cancer. Specifically, LPCAT3 is instrumental in maintaining systemic lipid homeostasis through its roles in hepatic lipogenesis, intestinal lipid absorption and lipoprotein secretion. The liver X receptor (LXR), pivotal in lipid homeostasis, modulates cholesterol, fatty acid (FA) and PL metabolism. LXR's capacity to modify PL composition in response to cellular sterol fluctuations is a vital mechanism for protecting biofilms against lipid stress. Concurrently, LXR activation enhances LPCAT3 expression on cell membranes and elevates polyunsaturated PL levels. This activation can ameliorate saturated free FA effects in vitro or endoplasmic reticulum stress in vivo due to lipid accumulation in hepatic cells. Pharmacological interventions targeting LXR, LPCAT and membrane PL components could offer novel therapeutic directions for NAFLD management. The present review primarily focused on recent advancements in understanding the LPCAT3 signaling pathway's role in lipid metabolism related to NAFLD, aiming to identify new treatment targets for the disease.
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Affiliation(s)
- Junmin Wang
- Department of Gastroenterology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, P.R. China
| | - Jiacheng Li
- Department of Gastroenterology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, P.R. China
| | - Yugang Fu
- Department of Gastroenterology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, P.R. China
| | - Yingying Zhu
- Department of Gastroenterology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, P.R. China
| | - Liubing Lin
- Department of Gastroenterology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, P.R. China
| | - Yong Li
- Department of Gastroenterology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, P.R. China
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Wang K, Zhou Y, Cao L, Lin L, Ledesma-Amaro R, Ji XJ. Engineering Yarrowia lipolytica for Sustainable Production of the Pomegranate Seed Oil-Derived Punicic Acid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3088-3098. [PMID: 38282297 DOI: 10.1021/acs.jafc.3c08718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Punicic acid is a conjugated linolenic acid with various biological activities including antiobesity, antioxidant, anticancer, and anti-inflammatory effects. It is often used as a nutraceutical, dietary additive, and animal feed. Currently, punicic acid is primarily extracted from pomegranate seed oil, but it is restricted due to the extended growth cycle, climatic limitations, and low recovery level. There have also been reports on the chemical synthesis of punicic acid, but it resulted in a mixture of structurally similar isomers, requiring additional purification/separation steps. In this study, a comprehensive strategy for the production of punicic acid in Yarrowia lipolytica was implemented by pushing the supply of linoleic acid precursors in a high-oleic oil strain, expressing multiple copies of the fatty acid conjugase gene from Punica granatum, engineering the acyl-editing pathway to improve the phosphatidylcholine pool, and promoting the assembly of punicic acid in the form of triglycerides. The optimal strain with high oil production capacity and a significantly increased punicic acid ratio accumulated 3072.72 mg/L punicic acid, accounting for 6.19% of total fatty acids in fed-batch fermentation, providing a viable, sustainable, and green approach for punicic acid production to substitute plant extraction and chemical synthesis production.
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Affiliation(s)
- Kaifeng Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Yueyue Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Lizhen Cao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Lu Lin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
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King WR, Singer J, Warman M, Wilson D, Hube B, Lager I, Patton-Vogt J. The glycerophosphocholine acyltransferase Gpc1 contributes to phosphatidylcholine biosynthesis, long-term viability, and embedded hyphal growth in Candida albicans. J Biol Chem 2024; 300:105543. [PMID: 38072057 PMCID: PMC10790099 DOI: 10.1016/j.jbc.2023.105543] [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: 05/21/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/21/2023] Open
Abstract
Candida albicans is a commensal fungus, opportunistic pathogen, and the most common cause of fungal infection in humans. The biosynthesis of phosphatidylcholine (PC), a major eukaryotic glycerophospholipid, occurs through two primary pathways. In Saccharomyces cerevisiae and some plants, a third PC synthesis pathway, the PC deacylation/reacylation pathway (PC-DRP), has been characterized. PC-DRP begins with the acylation of the lipid turnover product, glycerophosphocholine (GPC), by the GPC acyltransferase, Gpc1, to form Lyso-PC. Lyso-PC is then acylated by lysolipid acyltransferase, Lpt1, to produce PC. Importantly, GPC, the substrate for Gpc1, is a ubiquitous metabolite available within the host. GPC is imported by C. albicans, and deletion of the major GPC transporter, Git3, leads to decreased virulence in a murine model. Here we report that GPC can be directly acylated in C. albicans by the protein product of orf19.988, a homolog of ScGpc1. Through lipidomic studies, we show loss of Gpc1 leads to a decrease in PC levels. This decrease occurs in the absence of exogenous GPC, indicating that the impact on PC levels may be greater in the human host where GPC is available. A gpc1Δ/Δ strain exhibits several sensitivities to antifungals that target lipid metabolism. Furthermore, loss of Gpc1 results in both a hyphal growth defect in embedded conditions and a decrease in long-term cell viability. These results demonstrate for the first time the importance of Gpc1 and this alternative PC biosynthesis route (PC-DRP) to the physiology of a pathogenic fungus.
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Affiliation(s)
- William R King
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Justin Singer
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Mitchell Warman
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Duncan Wilson
- Department of Biosciences, University of Exeter, Exeter, England
| | - Bernard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Products and Infection Biology Hans Knöll Institute, Jena, Germany
| | - Ida Lager
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Jana Patton-Vogt
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA.
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Prasad SS, Taylor MC, Colombo V, Yeap HL, Pandey G, Lee SF, Taylor PW, Oakeshott JG. Patterns of Variation in the Usage of Fatty Acid Chains among Classes of Ester and Ether Neutral Lipids and Phospholipids in the Queensland Fruit Fly. INSECTS 2023; 14:873. [PMID: 37999072 PMCID: PMC10672513 DOI: 10.3390/insects14110873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023]
Abstract
Modern lipidomics has the power and sensitivity to elucidate the role of insects' lipidomes in their adaptations to the environment at a mechanistic molecular level. However, few lipidomic studies have yet been conducted on insects beyond model species such as Drosophila melanogaster. Here, we present the lipidome of adult males of another higher dipteran frugivore, Bactrocera tryoni. We describe 421 lipids across 15 classes of ester neutral lipids and phospholipids and ether neutral lipids and phospholipids. Most of the lipids are specified in terms of the carbon and double bond contents of each constituent hydrocarbon chain, and more ether lipids are specified to this degree than in any previous insect lipidomic analyses. Class-specific profiles of chain length and (un)saturation are broadly similar to those reported in D. melanogaster, although we found fewer medium-length chains in ether lipids. The high level of chain specification in our dataset also revealed widespread non-random combinations of different chain types in several ester lipid classes, including deficits of combinations involving chains of the same carbon and double bond contents among four phospholipid classes and excesses of combinations of dissimilar chains in several classes. Large differences were also found in the length and double bond profiles of the acyl vs. alkyl or alkenyl chains of the ether lipids. Work on other organisms suggests some of the differences observed will be functionally consequential and mediated, at least in part, by differences in substrate specificity among enzymes in lipid synthesis and remodelling pathways. Interrogation of the B. tryoni genome showed it has comparable levels of diversity overall in these enzymes but with some gene gain/loss differences and considerable sequence divergence from D. melanogaster.
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Affiliation(s)
- Shirleen S. Prasad
- Environment, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, Acton, ACT 2601, Australia; (S.S.P.); (M.C.T.); (V.C.); (H.L.Y.); (S.F.L.); (J.G.O.)
- Applied BioSciences, Macquarie University, North Ryde, NSW 2109, Australia;
- Australian Research Council Centre for Fruit Fly Biosecurity Innovation, Macquarie University, North Ryde, NSW 2109, Australia
| | - Matthew C. Taylor
- Environment, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, Acton, ACT 2601, Australia; (S.S.P.); (M.C.T.); (V.C.); (H.L.Y.); (S.F.L.); (J.G.O.)
| | - Valentina Colombo
- Environment, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, Acton, ACT 2601, Australia; (S.S.P.); (M.C.T.); (V.C.); (H.L.Y.); (S.F.L.); (J.G.O.)
| | - Heng Lin Yeap
- Environment, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, Acton, ACT 2601, Australia; (S.S.P.); (M.C.T.); (V.C.); (H.L.Y.); (S.F.L.); (J.G.O.)
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Parkville, VIC 3052, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3052, Australia
| | - Gunjan Pandey
- Environment, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, Acton, ACT 2601, Australia; (S.S.P.); (M.C.T.); (V.C.); (H.L.Y.); (S.F.L.); (J.G.O.)
- Applied BioSciences, Macquarie University, North Ryde, NSW 2109, Australia;
| | - Siu Fai Lee
- Environment, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, Acton, ACT 2601, Australia; (S.S.P.); (M.C.T.); (V.C.); (H.L.Y.); (S.F.L.); (J.G.O.)
- Applied BioSciences, Macquarie University, North Ryde, NSW 2109, Australia;
- Australian Research Council Centre for Fruit Fly Biosecurity Innovation, Macquarie University, North Ryde, NSW 2109, Australia
| | - Phillip W. Taylor
- Applied BioSciences, Macquarie University, North Ryde, NSW 2109, Australia;
- Australian Research Council Centre for Fruit Fly Biosecurity Innovation, Macquarie University, North Ryde, NSW 2109, Australia
| | - John G. Oakeshott
- Environment, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, Acton, ACT 2601, Australia; (S.S.P.); (M.C.T.); (V.C.); (H.L.Y.); (S.F.L.); (J.G.O.)
- Applied BioSciences, Macquarie University, North Ryde, NSW 2109, Australia;
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Ju J, Zhou B, Yang G, Fu X, Wang X, Guo L, Liu W. Study on the metabolic process of phthalic acid driven proliferation of Rhizoctonia solani. FRONTIERS IN PLANT SCIENCE 2023; 14:1266916. [PMID: 37885668 PMCID: PMC10598758 DOI: 10.3389/fpls.2023.1266916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023]
Abstract
Introduction Continuous cropping obstacle seriously affects the quality and yield of Salvia miltiorrhiza, and the synergistic effect of root exudates and rhizosphere pathogenic microorganisms may be an important cause of continuous cropping obstacle. This study aimed to explore the effects of representative organic acids on the growth and metabolism of specific microorganisms in the S. miltiorrhiza rhizosphere soil under continuous cropping, and clarify its mechanism. Methods The effect of phthalic acid (PA) on the growth and metabolism of Rhizoctonia solani was evaluated by mycelial growth inhibition method. Ultra-high performance liquid chromatography and tandem mass spectrometry were used to identify the differential metabolites of R. solani induced by exogenous PA. Results PA exerted a concentration-dependent effect on mycelial growth, biomass, intracellular polysaccharides con-tent, and total protein content in R. solani. A total of 1773 metabolites and 1040 differential metabolites were identified in the blank medium (CK), Fungi (CK + fungi), and PA-Fungi (CK + fungi + acid) groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the differential metabolites were mainly involved in the sugar, lipid, and protein metabolic pathways related to stable membrane structure and cell growth. Discussion The proliferation and metabolism network of R. solani induced by PA was proposed, and the enhancement of sugar, lipid, and amino acid metabolism was presumed to be related to the active resistance of cells to organic acid stress. These results offer new in-sights into the effects of PA metabolism on promoting R. solani proliferation, and provide theoretical support for further optimizing the rhizosphere microecological environment of Salvia miltiorrhiza continuous cropping soil and reducing continuous cropping obstacle.
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Affiliation(s)
- Jidong Ju
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Key Laboratory for Natural Active Pharmaceutical Constituents Research in Universities of Shandong Province, School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Pharmaceutical Institute, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Bingqian Zhou
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Key Laboratory for Natural Active Pharmaceutical Constituents Research in Universities of Shandong Province, School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Guohong Yang
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Key Laboratory for Natural Active Pharmaceutical Constituents Research in Universities of Shandong Province, School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Xinyu Fu
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Key Laboratory for Natural Active Pharmaceutical Constituents Research in Universities of Shandong Province, School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Pharmaceutical Institute, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiao Wang
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Key Laboratory for Natural Active Pharmaceutical Constituents Research in Universities of Shandong Province, School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Lanping Guo
- Chinese Medicine Resource Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Liu
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Key Laboratory for Natural Active Pharmaceutical Constituents Research in Universities of Shandong Province, School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
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Vial T, Marti G, Missé D, Pompon J. Lipid Interactions Between Flaviviruses and Mosquito Vectors. Front Physiol 2021; 12:763195. [PMID: 34899388 PMCID: PMC8660100 DOI: 10.3389/fphys.2021.763195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/20/2021] [Indexed: 11/18/2022] Open
Abstract
Mosquito-borne flaviviruses, such as dengue (DENV), Zika (ZIKV), yellow fever (YFV), West Nile (WNV), and Japanese encephalitis (JEV) viruses, threaten a large part of the human populations. In absence of therapeutics and effective vaccines against each flaviviruses, targeting viral metabolic requirements in mosquitoes may hold the key to new intervention strategies. Development of metabolomics in the last decade opened a new field of research: mosquito metabolomics. It is now clear that flaviviruses rely on mosquito lipids, especially phospholipids, for their cellular cycle and propagation. Here, we review the biosyntheses of, biochemical properties of and flaviviral interactions with mosquito phospholipids. Phospholipids are structural lipids with a polar headgroup and apolar acyl chains, enabling the formation of lipid bilayer that form plasma- and endomembranes. Phospholipids are mostly synthesized through the de novo pathway and remodeling cycle. Variations in headgroup and acyl chains influence phospholipid physicochemical properties and consequently the membrane behavior. Flaviviruses interact with cellular membranes at every step of their cellular cycle. Recent evidence demonstrates that flaviviruses reconfigure the phospholipidome in mosquitoes by regulating phospholipid syntheses to increase virus multiplication. Identifying the phospholipids involved and understanding how flaviviruses regulate these in mosquitoes is required to design new interventions.
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Affiliation(s)
- Thomas Vial
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.,UMR 152 PHARMADEV-IRD, Université Paul Sabatier, Toulouse, France
| | - Guillaume Marti
- LRSV (UMR 5546), CNRS, Université de Toulouse, Toulouse, France.,MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Dorothée Missé
- MIVEGEC, Université Montpellier, IRD, CNRS, Montpellier, France
| | - Julien Pompon
- MIVEGEC, Université Montpellier, IRD, CNRS, Montpellier, France
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Lipid Droplets, Phospholipase A 2, Arachidonic Acid, and Atherosclerosis. Biomedicines 2021; 9:biomedicines9121891. [PMID: 34944707 PMCID: PMC8699036 DOI: 10.3390/biomedicines9121891] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/01/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023] Open
Abstract
Lipid droplets, classically regarded as static storage organelles, are currently considered as dynamic structures involved in key processes of lipid metabolism, cellular homeostasis and signaling. Studies on the inflammatory state of atherosclerotic plaques suggest that circulating monocytes interact with products released by endothelial cells and may acquire a foamy phenotype before crossing the endothelial barrier and differentiating into macrophages. One such compound released in significant amounts into the bloodstream is arachidonic acid, the common precursor of eicosanoids, and a potent inducer of neutral lipid synthesis and lipid droplet formation in circulating monocytes. Members of the family of phospholipase A2, which hydrolyze the fatty acid present at the sn-2 position of phospholipids, have recently emerged as key controllers of lipid droplet homeostasis, regulating their formation and the availability of fatty acids for lipid mediator production. In this paper we discuss recent findings related to lipid droplet dynamics in immune cells and the ways these organelles are involved in regulating arachidonic acid availability and metabolism in the context of atherosclerosis.
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Chan MZA, Lau H, Lim SY, Li SFY, Liu SQ. Untargeted LC-QTOF-MS/MS based metabolomics approach for revealing bioactive components in probiotic fermented coffee brews. Food Res Int 2021; 149:110656. [PMID: 34600658 DOI: 10.1016/j.foodres.2021.110656] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Amidst trends in non-dairy probiotic foods and functional coffees, we recently developed a fermented coffee brew containing high live counts of the probiotics Lacticaseibacillus rhamnosus GG and Saccharomyces boulardii CNCM-I745. However, probiotic fermentation did not alter levels of principal coffee bioactive components based on targeted analyses. Here, to provide therapeutic justification compared to other non-fermented coffee brews, we aimed to discover postbiotics in coffee brews fermented with L. rhamnosus GG and/or S. boulardii CNCM-I745. By using an untargeted LC-QTOF-MS/MS based metabolomics approach coupled with validated multivariate analyses, 37 differential metabolites between fermentation treatments were putatively annotated. These include the production of postbiotics such as 2-isopropylmalate by S. boulardii CNCM-I745, and aromatic amino acid catabolites (indole-3-lactate, p-hydroxyphenyllactate, 3-phenyllactate), and hydroxydodecanoic acid by L. rhamnosus GG. Overall, LC-QTOF based untargeted metabolomics can be an effective approach to uncover postbiotics, which may substantiate additional potential functionalities of probiotic fermented foods compared to their non-fermented counterparts.
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Affiliation(s)
- Mei Zhi Alcine Chan
- Department of Food Science & Technology, National University of Singapore, Science Drive 2, Singapore 117542, Singapore
| | - Hazel Lau
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore; Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A∗STAR), 2 Fusionopolis Way, Innovis, #08-03, Singapore 138634, Singapore
| | - Si Ying Lim
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
| | - Sam Fong Yau Li
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore; NUS Environmental Research Institute (NERI), #02-01, T-Lab Building (TL), 5A Engineering Drive 1, Singapore 117411, Singapore
| | - Shao-Quan Liu
- Department of Food Science & Technology, National University of Singapore, Science Drive 2, Singapore 117542, Singapore; National University of Singapore (Suzhou) Research Institute, No. 377 Linquan Street, Suzhou Industrial Park, Suzhou 215123, Jiangsu, China.
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10
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Li Y, Liu Y, Yi J, Li Y, Yang B, Shang P, Mehmood K, Bilal RM, Zhang H, Chang YF, Tang Z, Wang Y, Li Y. The potential risks of chronic fluoride exposure on nephrotoxic via altering glucolipid metabolism and activating autophagy and apoptosis in ducks. Toxicology 2021; 461:152906. [PMID: 34450209 DOI: 10.1016/j.tox.2021.152906] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 12/20/2022]
Abstract
Fluoride is one of the most widely distributed elements in nature, while some fluorine-containing compounds are toxic to several vertebrates at certain levels. The current study was performed to evaluate the nephrotoxic effects of fluoride exposure in ducks. The results showed that the renal index was decreased in NaF group, and fluoride exposure significantly decreased the levels of serum Albumin, Glucose, Total cholesterol, Urea, protein and Triglycerides, confirming that NaF exhibited adverse effects on the kidney. The overall structure of renal cells showed damage with the signs of nuclelytic, vacuolar degeneration, atrophy, renal cystic cavity widening after fluoride induction. Renal vascular growth was impaired as the expression of VEGF and HIF-1α decreased (p > 0.05). More importantly, autophagy and apoptosis levels of CYT C, LC3, p62, Beclin, M-TOR, Bax and Caspase-3 were increased (p < 0.05) in the NaF treated group. Interestingly, our results showed that Phosphatidylethanolamine (PE) and Phosphatidylcholine (PC) activated the M-TOR autophagy pathway. Meanwhile, the PE acted on Atg5/ LC3 autophagy factor, followed by the auto-phagosome generation and activation of cell autophagy. These results indicate that NaF exposure to duck induced nephron-toxicity by activating autophagy, apoptosis and glucolipid metabolism pathways, which suggest that fluorine exposure poses a risk of poisoning.
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Affiliation(s)
- Yangwei Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yingwei Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jiangnan Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yuanliang Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Bijing Yang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Peng Shang
- Animal Science College, Tibet Agriculture & Animal Husbandry University, Linzhi, Tibet, China.
| | - Khalid Mehmood
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Rana Muhammad Bilal
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Hui Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Zhaoxin Tang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yajing Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
| | - Ying Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
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11
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Backman APE, Mattjus P. Who moves the sphinx? An overview of intracellular sphingolipid transport. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:159021. [PMID: 34339859 DOI: 10.1016/j.bbalip.2021.159021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 11/28/2022]
Abstract
Lipid bilayers function as boundaries that enclose their content from the surrounding media, and the composition of different membrane types is accurately and dynamically tailored so that they can perform their function. To achieve this balance, lipid biosynthetic machinery and lipid trafficking events are intertwined into an elegant network. In this review, we focus on the intracellular movement of sphingolipids mediated by sphingolipid transfer proteins. Additionally, we will focus on the best characterized and understood mammalian sphingolipid transfer proteins and provide an overview of how they are hypothesized to function. Some are already well understood, while others remain enigmatic. A few are actual lipid transfer proteins, moving lipids from membrane to membrane, while others may have more of a sensor role, possibly reacting to changes in the concentrations of their ligands. Considering the substrates available for cytosolic sphingolipid transfer proteins, one open question that is discussed is whether galactosylceramide is a target. Another question is the exact mechanics by which sphingolipid transfer proteins are targeted to different organelles, such as how four phosphate adapter protein-2, FAPP2 is targeted to the endoplasmic reticulum. The aim of this review is to discuss what is known within the field today and to provide a basic understanding of how these proteins may work.
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Affiliation(s)
- Anders P E Backman
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Peter Mattjus
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland.
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12
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Wang C, Gong Y, Deng F, Ding E, Tang J, Codling G, Challis JK, Green D, Wang J, Chen Q, Xie Y, Su S, Yang Z, Raine J, Jones PD, Tang S, Giesy JP. Remodeling of Arctic char (Salvelinus alpinus) lipidome under a stimulated scenario of Arctic warming. GLOBAL CHANGE BIOLOGY 2021; 27:3282-3298. [PMID: 33837644 DOI: 10.1111/gcb.15638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/14/2021] [Indexed: 06/12/2023]
Abstract
Arctic warming associated with global climate change poses a significant threat to populations of wildlife in the Arctic. Since lipids play a vital role in adaptation of organisms to variations in temperature, high-resolution mass-spectrometry-based lipidomics can provide insights into adaptive responses of organisms to a warmer environment in the Arctic and help to illustrate potential novel roles of lipids in the process of thermal adaption. In this study, we studied an ecologically and economically important species-Arctic char (Salvelinus alpinus)-with a detailed multi-tissue analysis of the lipidome in response to chronic shifts in temperature using a validated lipidomics workflow. In addition, dynamic alterations in the hepatic lipidome during the time course of shifts in temperature were also characterized. Our results showed that early life stages of Arctic char were more susceptible to variations in temperature. One-year-old Arctic char responded to chronic increases in temperature with coordinated regulation of lipids, including headgroup-specific remodeling of acyl chains in glycerophospholipids (GP) and extensive alterations in composition of lipids in membranes, such as less lyso-GPs, and more ether-GPs and sphingomyelin. Glycerolipids (e.g., triacylglycerol, TG) also participated in adaptive responses of the lipidome of Arctic char. Eight-week-old Arctic char exhibited rapid adaptive alterations of the hepatic lipidome to stepwise decreases in temperature while showing blunted responses to gradual increases in temperature, implying an inability to adapt rapidly to warmer environments. Three common phosphatidylethanolamines (PEs) (PE 36:6|PE 16:1_20:5, PE 38:7|PE 16:1_22:6, and PE 40:7|PE 18:1_22:6) were finally identified as candidate lipid biomarkers for temperature shifts via machine learning approach. Overall, this work provides additional information to a better understanding of underlying regulatory mechanisms of the lipidome of Arctic organisms in the face of near-future warming.
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Affiliation(s)
- Chao Wang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yufeng Gong
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Fuchang Deng
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Enmin Ding
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jie Tang
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
- School of Resources and Environment, Anhui Agricultural University, Hefei, Anhui, China
| | - Garry Codling
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
- Research Centre for Contaminants in the Environment, Masaryk University, Brno, Czech Republic
| | | | - Derek Green
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jing Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qiliang Chen
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Yuwei Xie
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Shu Su
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Zilin Yang
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jason Raine
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Paul D Jones
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Song Tang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Environmental Sciences, Baylor University, Waco, TX, USA
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
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13
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Yu L, Zhou C, Fan J, Shanklin J, Xu C. Mechanisms and functions of membrane lipid remodeling in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:37-53. [PMID: 33853198 DOI: 10.1111/tpj.15273] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 05/20/2023]
Abstract
Lipid remodeling, defined herein as post-synthetic structural modifications of membrane lipids, play crucial roles in regulating the physicochemical properties of cellular membranes and hence their many functions. Processes affected by lipid remodeling include lipid metabolism, membrane repair, cellular homeostasis, fatty acid trafficking, cellular signaling and stress tolerance. Glycerolipids are the major structural components of cellular membranes and their composition can be adjusted by modifying their head groups, their acyl chain lengths and the number and position of double bonds. This review summarizes recent advances in our understanding of mechanisms of membrane lipid remodeling with emphasis on the lipases and acyltransferases involved in the modification of phosphatidylcholine and monogalactosyldiacylglycerol, the major membrane lipids of extraplastidic and photosynthetic membranes, respectively. We also discuss the role of triacylglycerol metabolism in membrane acyl chain remodeling. Finally, we discuss emerging data concerning the functional roles of glycerolipid remodeling in plant stress responses. Illustrating the molecular basis of lipid remodeling may lead to novel strategies for crop improvement and other biotechnological applications such as bioenergy production.
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Affiliation(s)
- Linhui Yu
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Chao Zhou
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Jilian Fan
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Changcheng Xu
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
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14
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Woodall BM, Harp JR, Brewer WT, Tague ED, Campagna SR, Fozo EM. Enterococcus faecalis Readily Adapts Membrane Phospholipid Composition to Environmental and Genetic Perturbation. Front Microbiol 2021; 12:616045. [PMID: 34093456 PMCID: PMC8177052 DOI: 10.3389/fmicb.2021.616045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 04/15/2021] [Indexed: 11/22/2022] Open
Abstract
The bacterial lipid membrane, consisting both of fatty acid (acyl) tails and polar head groups, responds to changing conditions through alteration of either the acyl tails and/or head groups. This plasticity is critical for cell survival as it allows maintenance of both the protective nature of the membrane as well as functioning membrane protein complexes. Bacteria that live in fatty-acid rich environments, such as those found in the human host, can exploit host fatty acids to synthesize their own membranes, in turn, altering their physiology. Enterococcus faecalis is such an organism: it is a commensal of the mammalian intestine where it is exposed to fatty-acid rich bile, as well as a major cause of hospital infections during which it is exposed to fatty acid containing-serum. Within, we employed an untargeted approach to detect the most common phospholipid species of E. faecalis OG1RF via ultra-high performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS). We examined not only how the composition responds upon exposure to host fatty acids but also how deletion of genes predicted to synthesize major polar head groups impact lipid composition. Regardless of genetic background and differing basal lipid composition, all strains were able to alter their lipid composition upon exposure to individual host fatty acids. Specific gene deletion strains, however, had altered survival to membrane damaging agents. Combined, the enterococcal lipidome is highly resilient in response to both genetic and environmental perturbation, likely contributing to stress survival.
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Affiliation(s)
- Brittni M. Woodall
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - John R. Harp
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - William T. Brewer
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Eric D. Tague
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Shawn R. Campagna
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN, United States
- Biological and Small Molecule Mass Spectrometry Core, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Elizabeth M. Fozo
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
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15
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Reinhard J, Mattes C, Väth K, Radanović T, Surma MA, Klose C, Ernst R. A Quantitative Analysis of Cellular Lipid Compositions During Acute Proteotoxic ER Stress Reveals Specificity in the Production of Asymmetric Lipids. Front Cell Dev Biol 2020; 8:756. [PMID: 32850859 PMCID: PMC7417482 DOI: 10.3389/fcell.2020.00756] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022] Open
Abstract
The unfolded protein response (UPR) is central to endoplasmic reticulum (ER) homeostasis by controlling its size and protein folding capacity. When activated by unfolded proteins in the ER-lumen or aberrant lipid compositions, the UPR adjusts the expression of hundreds of target genes to counteract ER stress. The proteotoxic drugs dithiothreitol (DTT) and tunicamycin (TM) are commonly used to induce misfolding of proteins in the ER and to study the UPR. However, their potential impact on the cellular lipid composition has never been systematically addressed. Here, we report the quantitative, cellular lipid composition of Saccharomyces cerevisiae during acute, proteotoxic stress in both rich and synthetic media. We show that DTT causes rapid remodeling of the lipidome when used in rich medium at growth-inhibitory concentrations, while TM has only a marginal impact on the lipidome under our conditions of cultivation. We formulate recommendations on how to study UPR activation by proteotoxic stress without interferences from a perturbed lipid metabolism. Furthermore, our data suggest an intricate connection between the cellular growth rate, the abundance of the ER, and the metabolism of fatty acids. We show that Saccharomyces cerevisiae can produce asymmetric lipids with two saturated fatty acyl chains differing substantially in length. These observations indicate that the pairing of saturated fatty acyl chains is tightly controlled and suggest an evolutionary conservation of asymmetric lipids and their biosynthetic machineries.
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Affiliation(s)
- John Reinhard
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany.,PZMS, Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany
| | - Carsten Mattes
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany.,PZMS, Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany
| | - Kristina Väth
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany.,PZMS, Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany
| | - Toni Radanović
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany.,PZMS, Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany
| | | | | | - Robert Ernst
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany.,PZMS, Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany
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16
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A mechanism-aware and multiomic machine-learning pipeline characterizes yeast cell growth. Proc Natl Acad Sci U S A 2020; 117:18869-18879. [PMID: 32675233 DOI: 10.1073/pnas.2002959117] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Metabolic modeling and machine learning are key components in the emerging next generation of systems and synthetic biology tools, targeting the genotype-phenotype-environment relationship. Rather than being used in isolation, it is becoming clear that their value is maximized when they are combined. However, the potential of integrating these two frameworks for omic data augmentation and integration is largely unexplored. We propose, rigorously assess, and compare machine-learning-based data integration techniques, combining gene expression profiles with computationally generated metabolic flux data to predict yeast cell growth. To this end, we create strain-specific metabolic models for 1,143 Saccharomyces cerevisiae mutants and we test 27 machine-learning methods, incorporating state-of-the-art feature selection and multiview learning approaches. We propose a multiview neural network using fluxomic and transcriptomic data, showing that the former increases the predictive accuracy of the latter and reveals functional patterns that are not directly deducible from gene expression alone. We test the proposed neural network on a further 86 strains generated in a different experiment, therefore verifying its robustness to an additional independent dataset. Finally, we show that introducing mechanistic flux features improves the predictions also for knockout strains whose genes were not modeled in the metabolic reconstruction. Our results thus demonstrate that fusing experimental cues with in silico models, based on known biochemistry, can contribute with disjoint information toward biologically informed and interpretable machine learning. Overall, this study provides tools for understanding and manipulating complex phenotypes, increasing both the prediction accuracy and the extent of discernible mechanistic biological insights.
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