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Xiao X, Le HH, Lee MT, Lamm D, Johnson EL, Brito IL. Prevotella copri variants among a single host diverge in sphingolipid production. mBio 2024; 15:e0240923. [PMID: 38236049 PMCID: PMC10865984 DOI: 10.1128/mbio.02409-23] [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: 09/05/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024] Open
Abstract
Sphingolipids serve as vital structural and signaling components of the cell membranes in both eukaryotes and prokaryotes. Within the gut microbiome, Bacteroides species have been identified as major producers of sphingolipids, and Bacteroides-produced sphingolipids have been shown to be modulators of host immune and metabolic functions. While Bacteroides species are a prominent feature of the gut microbiomes of populations living in industrialized countries, Prevotella copri, a member of the same phyla, albeit a different family, is the dominant feature across the remainder of the global population, although their sphingolipid-producing capabilities have not been as thoroughly investigated. To fill this gap, we examined the genomes of over 60 diverse isolates of P. copri and identified several key enzymes involved in sphingolipid synthesis in P. copri. Combining bioorthogonal labeling and liquid chromatography-mass spectrometry (LC-MS) based lipidomics, we functionally characterized the first step in P. copri de novo sphingolipid synthesis in addition to profiling the sphingolipidomes of P. copri strains, identifying key enzymes that may play roles in producing a diverse set of P. copri sphingolipids. Given the limited genetic engineering tools amenable for use in P. copri, our approach takes advantage of comparative genomics and phenotypic profiling to explore sphingolipid production in these understudied, yet highly prevalent, organisms.IMPORTANCESphingolipids are important signaling molecules for maintaining metabolic and immune homeostasis in the host. These lipids are also produced by gut commensals, most notably by Bacteroides species. Despite the global prevalence of Prevotella copri in gut microbiomes of individuals, little is known about the types of sphingolipids they produce and whether they are similar in composition and structure to those produced by Bacteroides. Given the varied associations of P. copri with diverse sphingolipid-related health outcomes, such as rheumatoid arthritis and glucose intolerance, it is important to first characterize the specific sphingolipids produced by individual strains of P. copri and to identify the genes involved in their pathways of production. This characterization of P. copri-derived sphingolipids provides further insight into how bacterial sphingolipid production can serve as a mechanism for microbial modulation of host phenotypes.
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Affiliation(s)
- Xieyue Xiao
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York State, USA
| | - Henry H. Le
- Division of Nutritional Sciences, Cornell University, Ithaca, New York State, USA
| | - Min-Ting Lee
- Division of Nutritional Sciences, Cornell University, Ithaca, New York State, USA
| | - Daniel Lamm
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York State, USA
| | - Elizabeth L. Johnson
- Division of Nutritional Sciences, Cornell University, Ithaca, New York State, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Ilana L. Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York State, USA
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Waidmann S, Béziat C, Ferreira Da Silva Santos J, Feraru E, Feraru MI, Sun L, Noura S, Boutté Y, Kleine-Vehn J. Endoplasmic reticulum stress controls PIN-LIKES abundance and thereby growth adaptation. Proc Natl Acad Sci U S A 2023; 120:e2218865120. [PMID: 37487064 PMCID: PMC10400986 DOI: 10.1073/pnas.2218865120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/21/2023] [Indexed: 07/26/2023] Open
Abstract
Extreme environmental conditions eventually limit plant growth [J. R. Dinneny, Annu. Rev. Cell Dev. Biol. 35, 1-19 (2019), N. Gigli-Bisceglia, C. Testerink, Curr. Opin. Plant Biol. 64, 102120 (2021)]. Here, we reveal a mechanism that enables multiple external cues to get integrated into auxin-dependent growth programs in Arabidopsis thaliana. Our forward genetics approach on dark-grown hypocotyls uncovered that an imbalance in membrane lipids enhances the protein abundance of PIN-LIKES (PILS) [E. Barbez et al., Nature 485, 119 (2012)] auxin transport facilitators at the endoplasmic reticulum (ER), which thereby limits nuclear auxin signaling and growth rates. We show that this subcellular response relates to ER stress signaling, which directly impacts PILS protein turnover in a tissue-dependent manner. This mechanism allows PILS proteins to integrate environmental input with phytohormone auxin signaling, contributing to stress-induced growth adaptation in plants.
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Affiliation(s)
- Sascha Waidmann
- Institute of Biology II, Chair of Molecular Plant Physiology, University of Freiburg, 79104Freiburg, Germany
- Center for Integrative Biological Signalling Studies, University of Freiburg, 79104Freiburg, Germany
- Department of Applied Genetics and Cell Biology, Institute of Molecular Plant Biology, University of Natural Resources and Life Sciences,1190Vienna, Austria
| | - Chloé Béziat
- Department of Applied Genetics and Cell Biology, Institute of Molecular Plant Biology, University of Natural Resources and Life Sciences,1190Vienna, Austria
| | - Jonathan Ferreira Da Silva Santos
- Institute of Biology II, Chair of Molecular Plant Physiology, University of Freiburg, 79104Freiburg, Germany
- Department of Applied Genetics and Cell Biology, Institute of Molecular Plant Biology, University of Natural Resources and Life Sciences,1190Vienna, Austria
| | - Elena Feraru
- Department of Applied Genetics and Cell Biology, Institute of Molecular Plant Biology, University of Natural Resources and Life Sciences,1190Vienna, Austria
| | - Mugurel I. Feraru
- Department of Applied Genetics and Cell Biology, Institute of Molecular Plant Biology, University of Natural Resources and Life Sciences,1190Vienna, Austria
| | - Lin Sun
- Department of Applied Genetics and Cell Biology, Institute of Molecular Plant Biology, University of Natural Resources and Life Sciences,1190Vienna, Austria
| | - Seinab Noura
- Institute of Biology II, Chair of Molecular Plant Physiology, University of Freiburg, 79104Freiburg, Germany
- Center for Integrative Biological Signalling Studies, University of Freiburg, 79104Freiburg, Germany
| | - Yohann Boutté
- CNRS-University of Bordeaux, UMR 5200 Membrane Biogenesis Laboratory, National Research Institute for Agriculture, Food and the Environment Bordeaux Aquitaine, 33140 Bordeaux, France
| | - Jürgen Kleine-Vehn
- Institute of Biology II, Chair of Molecular Plant Physiology, University of Freiburg, 79104Freiburg, Germany
- Center for Integrative Biological Signalling Studies, University of Freiburg, 79104Freiburg, Germany
- Department of Applied Genetics and Cell Biology, Institute of Molecular Plant Biology, University of Natural Resources and Life Sciences,1190Vienna, Austria
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Xing J, Zhang L, Duan Z, Lin J. Coordination of Phospholipid-Based Signaling and Membrane Trafficking in Plant Immunity. TRENDS IN PLANT SCIENCE 2021; 26:407-420. [PMID: 33309101 DOI: 10.1016/j.tplants.2020.11.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 05/26/2023]
Abstract
In plants, defense-associated signal transduction involves key membrane-related processes, such as phospholipid-based signaling and membrane trafficking. Coordination of these processes occurs in the lipid bilayer of plasma membrane (PM) and luminal/extracellular membranes. Deciphering the spatiotemporal organization of phospholipids and lipid-protein interactions provides crucial information on the mechanisms that link phospholipid-based signaling and membrane trafficking in plant immunity. In this review, we summarize recent advances in our understanding of these connections, including deployment of key enzymes and molecules in phospholipid pathways, and roles of lipid diversity in membrane trafficking. We highlight the mechanisms that mediate feedback between phospholipid-based signaling and membrane trafficking to regulate plant immunity, including their novel roles in balancing endocytosis and exocytosis.
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Affiliation(s)
- Jingjing Xing
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Liang Zhang
- College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Zhikun Duan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Qi W, Lu H, Zhang Y, Cheng J, Huang B, Lu X, Sheteiwy MSA, Kuang S, Shao H. Oil crop genetic modification for producing added value lipids. Crit Rev Biotechnol 2020; 40:777-786. [PMID: 32605455 DOI: 10.1080/07388551.2020.1785384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Plant lipids, mainly stored in seeds and other plant parts, are not only a crucial resource for food and fodder but are also a promising alternative to fossil oils as a chemical industry feedstock. Oil crop cultivation and processing are always important parts of agriculture worldwide. Vegetable oils containing polyunsaturated fatty acids, very long chain fatty acids, conjugated fatty acids, hydroxy fatty acids and wax esters, have outstanding nutritional, lubricating, surfactant, and artificial-fibre-synthesis properties, amongst others. Enhancing the production of such specific lipid components is of economic interest. There has been a considerable amount of information reported about plant lipid biosynthesis, including identification of the pathway map of carbon flux, key enzymes (and the coding genes), and substrate affinities. Plant lipid biosynthesis engineering to produce special oil compounds has become feasible, although until now, only limited progress has been made in the laboratory. It is relatively easy to achieve the experimental objectives, for example, accumulating novel lipid compounds in given plant tissues facilitated by genetic modification. Applying such technologies to agricultural production is difficult, and the challenge is to make engineered crops economically attractive, which is impeded by only moderate success. To achieve this goal, more complicated and systematic strategies should be developed and discussed based on the relevant results currently available.
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Affiliation(s)
- Weicong Qi
- Salt-soil Agricultural Center, Key Laboratory of Agricultural Environment in the Lower Reaches of Yangtze River Plain, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences(JAAS), Nanjing, PR China.,Key Laboratory of Oil Crops in Huanghuaihai Plain, Ministry of Agriculture, PR China,Henan Provincial Key Laboratory for Oil Crops Improvement, Zheng Zhou, PR China
| | - Haiying Lu
- Salt-soil Agricultural Center, Key Laboratory of Agricultural Environment in the Lower Reaches of Yangtze River Plain, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences(JAAS), Nanjing, PR China
| | - Yang Zhang
- Key Laboratory of Oil Crops in Huanghuaihai Plain, Ministry of Agriculture, PR China,Henan Provincial Key Laboratory for Oil Crops Improvement, Zheng Zhou, PR China
| | - Jihua Cheng
- Yuan Longping High-tech Agriculture Co., LTD, Changsha, PR China
| | - Bangquan Huang
- College of Life Sciences, Hubei University, Wuhan, PR China
| | - Xin Lu
- Salt-soil Agricultural Center, Key Laboratory of Agricultural Environment in the Lower Reaches of Yangtze River Plain, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences(JAAS), Nanjing, PR China
| | - Mohamed Salah Amr Sheteiwy
- Salt-soil Agricultural Center, Key Laboratory of Agricultural Environment in the Lower Reaches of Yangtze River Plain, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences(JAAS), Nanjing, PR China.,Department of Agronomy, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - Shaoping Kuang
- College of Environment and Safety Engineering, Qingdao University of Science & Technology, Qingdao, PR China
| | - Hongbo Shao
- Salt-soil Agricultural Center, Key Laboratory of Agricultural Environment in the Lower Reaches of Yangtze River Plain, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences(JAAS), Nanjing, PR China.,College of Environment and Safety Engineering, Qingdao University of Science & Technology, Qingdao, PR China.,Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, PR China
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Cai G, Wang Y, Yan W, Luan S, Lan W. Choline transporter-like 1 (CTL1) positively regulates apical hook development in etiolated Arabidopsis seedlings. Biochem Biophys Res Commun 2020; 525:491-497. [PMID: 32111354 DOI: 10.1016/j.bbrc.2020.02.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 11/30/2022]
Abstract
Ethylene is a gaseous phytohormone that is perceived by two-component histidine kinase-type receptors. Recent studies identified choline transporter-like 1 (CTL1) essential for Arabidopsis growth and development, including apical hook development in the etiolated seedlings. Here, we report that CTL1 contributes to apical hook development by enhancing ethylene response. The expression of CTL1 was highly correlated with the intensity of ethylene response and was enriched in the apical hook, cotyledon tip and hypocotyl. Genetic analysis showed that the dark-grown ctl1 mutant displayed a defect in ethylene-induced apical hook development as compared with the wild type. Accordingly, the expression of ethylene signaling reporter EBS::GUS in ctl1 mutant was greatly reduced in leaves, apical hook, hypocotyl and root, suggesting that the disruption of CTL1 impairs the ethylene signaling. Furthermore, protein-protein interaction assays demonstrated that CTL1 may interact with ethylene receptors, including ETR1, ETR2, ERS1, ERS2. Importantly, the abundance of CTL1 was diminished when ETR1 was disrupted upon ethylene response. Taken together, our results suggest that CTL1 functions as a positive regulator in ethylene signaling which in turn contributes to apical hook development of etiolated plant seedlings.
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Affiliation(s)
- Guohua Cai
- State Key Laboratory for Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210093, PR China
| | - Yuan Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai, 201602, PR China
| | - Wenwen Yan
- State Key Laboratory for Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210093, PR China
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
| | - Wenzhi Lan
- State Key Laboratory for Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210093, PR China.
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The dynamic response of the Arabidopsis root metabolome to auxin and ethylene is not predicted by changes in the transcriptome. Sci Rep 2020; 10:679. [PMID: 31959762 PMCID: PMC6971091 DOI: 10.1038/s41598-019-57161-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/19/2019] [Indexed: 12/27/2022] Open
Abstract
While the effects of phytohormones on plant gene expression have been well characterized, comparatively little is known about how hormones influence metabolite profiles. This study examined the effects of elevated auxin and ethylene on the metabolome of Arabidopsis roots using a high-resolution 24 h time course, conducted in parallel to time-matched transcriptomic analyses. Mass spectrometry using orthogonal UPLC separation strategies (reversed phase and HILIC) in both positive and negative ionization modes was used to maximize identification of metabolites with altered levels. The findings show that the root metabolome responds rapidly to hormone stimulus and that compounds belonging to the same class of metabolites exhibit similar changes. The responses were dominated by changes in phenylpropanoid, glucosinolate, and fatty acid metabolism, although the nature and timing of the response was unique for each hormone. These alterations in the metabolome were not directly predicted by the corresponding transcriptome data, suggesting that post-transcriptional events such as changes in enzyme activity and/or transport processes drove the observed changes in the metabolome. These findings underscore the need to better understand the biochemical mechanisms underlying the temporal reconfiguration of plant metabolism, especially in relation to the hormone-metabolome interface and its subsequent physiological and morphological effects.
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D'Angelo G, Clarke CJ, Silva LC. Meeting Report - The 2019 FEBS special meeting on sphingolipid biology: sphingolipids in physiology and pathology. J Cell Sci 2019; 132:132/15/jcs235705. [PMID: 31371572 DOI: 10.1242/jcs.235705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sphingolipids are a fundamental class of molecules that are involved in structural, organizational and signaling properties of eukaryotic membranes. Defects in their production or disposal lead to acquired and inherited human diseases. A growing community of scientists has embraced the challenge to dissect different aspects of sphingolipid biology using a variety of approaches, and a substantial part of this community met last May in the beautiful town of Cascais in Portugal. Over 200 scientists from 26 countries animated the conference, held in a 15th century citadel, sharing their data and opinions on the current understanding and future challenges in sphingolipid research. Here, we report some of their contributions to provide the readers with a bird's-eye view of the themes discussed at the meeting.
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Affiliation(s)
- Giovanni D'Angelo
- Interfaculty Institute of Bioengineering, Ecole polytechnique fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Christopher J Clarke
- Department of Medicine and the Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA
| | - Liana C Silva
- iMed.ULisboa-Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
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Sinclair R, Rosquete MR, Drakakaki G. Post-Golgi Trafficking and Transport of Cell Wall Components. FRONTIERS IN PLANT SCIENCE 2018; 9:1784. [PMID: 30581448 PMCID: PMC6292943 DOI: 10.3389/fpls.2018.01784] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/16/2018] [Indexed: 05/13/2023]
Abstract
The cell wall, a complex macromolecular composite structure surrounding and protecting plant cells, is essential for development, signal transduction, and disease resistance. This structure is also integral to cell expansion, as its tensile resistance is the primary balancing mechanism against internal turgor pressure. Throughout these processes, the biosynthesis, transport, deposition, and assembly of cell wall polymers are tightly regulated. The plant endomembrane system facilitates transport of polysaccharides, polysaccharide biosynthetic and modifying enzymes and glycoproteins through vesicle trafficking pathways. Although a number of enzymes involved in cell wall biosynthesis have been identified, comparatively little is known about the transport of cell wall polysaccharides and glycoproteins by the endomembrane system. This review summarizes our current understanding of trafficking of cell wall components during cell growth and cell division. Emerging technologies, such as vesicle glycomics, are also discussed as promising avenues to gain insights into the trafficking of structural polysaccharides to the apoplast.
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