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Tian F, Wainaina JM, Howard-Varona C, Domínguez-Huerta G, Bolduc B, Gazitúa MC, Smith G, Gittrich MR, Zablocki O, Cronin DR, Eveillard D, Hallam SJ, Sullivan MB. Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans. MICROBIOME 2024; 12:159. [PMID: 39198891 PMCID: PMC11360552 DOI: 10.1186/s40168-024-01876-z] [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: 03/06/2024] [Accepted: 07/16/2024] [Indexed: 09/01/2024]
Abstract
BACKGROUND Prokaryotic microbes have impacted marine biogeochemical cycles for billions of years. Viruses also impact these cycles, through lysis, horizontal gene transfer, and encoding and expressing genes that contribute to metabolic reprogramming of prokaryotic cells. While this impact is difficult to quantify in nature, we hypothesized that it can be examined by surveying virus-encoded auxiliary metabolic genes (AMGs) and assessing their ecological context. RESULTS We systematically developed a global ocean AMG catalog by integrating previously described and newly identified AMGs and then placed this catalog into ecological and metabolic contexts relevant to ocean biogeochemistry. From 7.6 terabases of Tara Oceans paired prokaryote- and virus-enriched metagenomic sequence data, we increased known ocean virus populations to 579,904 (up 16%). From these virus populations, we then conservatively identified 86,913 AMGs that grouped into 22,779 sequence-based gene clusters, 7248 (~ 32%) of which were not previously reported. Using our catalog and modeled data from mock communities, we estimate that ~ 19% of ocean virus populations carry at least one AMG. To understand AMGs in their metabolic context, we identified 340 metabolic pathways encoded by ocean microbes and showed that AMGs map to 128 of them. Furthermore, we identified metabolic "hot spots" targeted by virus AMGs, including nine pathways where most steps (≥ 0.75) were AMG-targeted (involved in carbohydrate, amino acid, fatty acid, and nucleotide metabolism), as well as other pathways where virus-encoded AMGs outnumbered cellular homologs (involved in lipid A phosphates, phosphatidylethanolamine, creatine biosynthesis, phosphoribosylamine-glycine ligase, and carbamoyl-phosphate synthase pathways). CONCLUSIONS Together, this systematically curated, global ocean AMG catalog and analyses provide a valuable resource and foundational observations to understand the role of viruses in modulating global ocean metabolisms and their biogeochemical implications. Video Abstract.
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Affiliation(s)
- Funing Tian
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - James M Wainaina
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Cristina Howard-Varona
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
| | - Guillermo Domínguez-Huerta
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
- Centro Oceanográfico de Málaga (IEO-CSIC), Puerto Pesquero S/N, 29640, Fuengirola (Málaga), Spain
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
| | | | - Garrett Smith
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
| | - Marissa R Gittrich
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
| | - Dylan R Cronin
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
| | - Damien Eveillard
- Université de Nantes, CNRS, LS2N, Nantes, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara GO-SEE, Paris, France
| | - Steven J Hallam
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Genome Science and Technology Program, University of British Columbia, 2329 West Mall, Vancouver, BC, V6T 1Z4, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA.
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA.
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA.
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH, 43210, USA.
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2
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Jordan EN, Shirali Hossein Zade R, Pillay S, van Lent P, Abeel T, Kayser O. Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol. NPJ Syst Biol Appl 2024; 10:63. [PMID: 38821949 PMCID: PMC11143246 DOI: 10.1038/s41540-024-00382-0] [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: 08/24/2023] [Accepted: 05/13/2024] [Indexed: 06/02/2024] Open
Abstract
Yeast metabolism can be engineered to produce xenobiotic compounds, such as cannabinoids, the principal isoprenoids of the plant Cannabis sativa, through heterologous metabolic pathways. However, yeast cell factories continue to have low cannabinoid production. This study employed an integrated omics approach to investigate the physiological effects of cannabidiol on S. cerevisiae CENPK2-1C yeast cultures. We treated the experimental group with 0.5 mM CBD and monitored CENPK2-1C cultures. We observed a latent-stationary phase post-diauxic shift in the experimental group and harvested samples in the inflection point of this growth phase for transcriptomic and metabolomic analysis. We compared the transcriptomes of the CBD-treated yeast and the positive control, identifying eight significantly overexpressed genes with a log fold change of at least 1.5 and a significant adjusted p-value. Three notable genes were PDR5 (an ABC-steroid and cation transporter), CIS1, and YGR035C. These genes are all regulated by pleiotropic drug resistance linked promoters. Knockout and rescue of PDR5 showed that it is a causal factor in the post-diauxic shift phenotype. Metabolomic analysis revealed 48 significant spectra associated with CBD-fed cell pellets, 20 of which were identifiable as non-CBD compounds, including fatty acids, glycerophospholipids, and phosphate-salvage indicators. Our results suggest that mitochondrial regulation and lipidomic remodeling play a role in yeast's response to CBD, which are employed in tandem with pleiotropic drug resistance (PDR). We conclude that bioengineers should account for off-target product C-flux, energy use from ABC-transport, and post-stationary phase cell growth when developing cannabinoid-biosynthetic yeast strains.
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Affiliation(s)
- Erin Noel Jordan
- Technical Biochemistry, TU Dortmund University, Emil-Figge-Straße 66, 44227, Dortmund, Germany.
| | - Ramin Shirali Hossein Zade
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Broekmanweg 6, 2628 XE, Delft, The Netherlands
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Stephanie Pillay
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Broekmanweg 6, 2628 XE, Delft, The Netherlands
| | - Paul van Lent
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Broekmanweg 6, 2628 XE, Delft, The Netherlands
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Broekmanweg 6, 2628 XE, Delft, The Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Oliver Kayser
- Technical Biochemistry, TU Dortmund University, Emil-Figge-Straße 66, 44227, Dortmund, Germany.
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Venkatraman K, Lee CT, Garcia GC, Mahapatra A, Milshteyn D, Perkins G, Kim K, Pasolli HA, Phan S, Lippincott‐Schwartz J, Ellisman MH, Rangamani P, Budin I. Cristae formation is a mechanical buckling event controlled by the inner mitochondrial membrane lipidome. EMBO J 2023; 42:e114054. [PMID: 37933600 PMCID: PMC10711667 DOI: 10.15252/embj.2023114054] [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: 03/19/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023] Open
Abstract
Cristae are high-curvature structures in the inner mitochondrial membrane (IMM) that are crucial for ATP production. While cristae-shaping proteins have been defined, analogous lipid-based mechanisms have yet to be elucidated. Here, we combine experimental lipidome dissection with multi-scale modeling to investigate how lipid interactions dictate IMM morphology and ATP generation. When modulating phospholipid (PL) saturation in engineered yeast strains, we observed a surprisingly abrupt breakpoint in IMM topology driven by a continuous loss of ATP synthase organization at cristae ridges. We found that cardiolipin (CL) specifically buffers the inner mitochondrial membrane against curvature loss, an effect that is independent of ATP synthase dimerization. To explain this interaction, we developed a continuum model for cristae tubule formation that integrates both lipid and protein-mediated curvatures. This model highlighted a snapthrough instability, which drives IMM collapse upon small changes in membrane properties. We also showed that cardiolipin is essential in low-oxygen conditions that promote PL saturation. These results demonstrate that the mechanical function of cardiolipin is dependent on the surrounding lipid and protein components of the IMM.
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Affiliation(s)
- Kailash Venkatraman
- Department of Chemistry and BiochemistryUniversity of California San DiegoLa JollaCAUSA
| | - Christopher T Lee
- Department of Mechanical and Aerospace EngineeringUniversity of California San DiegoLa JollaCAUSA
| | - Guadalupe C Garcia
- Computational Neurobiology LaboratorySalk Institute for Biological StudiesLa JollaCAUSA
| | - Arijit Mahapatra
- Department of Mechanical and Aerospace EngineeringUniversity of California San DiegoLa JollaCAUSA
- Present address:
Applied Physical SciencesUniversity of North Carolina Chapel HillChapel HillNCUSA
| | - Daniel Milshteyn
- Department of Chemistry and BiochemistryUniversity of California San DiegoLa JollaCAUSA
| | - Guy Perkins
- National Center for Microscopy and Imaging Research, Center for Research in Biological SystemsUniversity of California San DiegoLa JollaCAUSA
| | - Keun‐Young Kim
- National Center for Microscopy and Imaging Research, Center for Research in Biological SystemsUniversity of California San DiegoLa JollaCAUSA
| | - H Amalia Pasolli
- Howard Hughes Medical InstituteAshburnVAUSA
- Present address:
Electron Microscopy Resource CenterThe Rockefeller UniversityNew YorkNYUSA
| | - Sebastien Phan
- National Center for Microscopy and Imaging Research, Center for Research in Biological SystemsUniversity of California San DiegoLa JollaCAUSA
| | | | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological SystemsUniversity of California San DiegoLa JollaCAUSA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace EngineeringUniversity of California San DiegoLa JollaCAUSA
| | - Itay Budin
- Department of Chemistry and BiochemistryUniversity of California San DiegoLa JollaCAUSA
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4
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Esch BM, Walter S, Schmidt O, Fröhlich F. Identification of distinct active pools of yeast serine palmitoyltransferase in sub-compartments of the ER. J Cell Sci 2023; 136:jcs261353. [PMID: 37982431 DOI: 10.1242/jcs.261353] [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: 05/22/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023] Open
Abstract
Sphingolipids (SPs) are one of the three major lipid classes in eukaryotic cells and serve as structural components of the plasma membrane. The rate-limiting step in SP biosynthesis is catalyzed by the serine palmitoyltransferase (SPT). In budding yeast (Saccharomyces cerevisiae), SPT is negatively regulated by the two proteins, Orm1 and Orm2. Regulating SPT activity enables cells to adapt SP metabolism to changing environmental conditions. Therefore, the Orm proteins are phosphorylated by two signaling pathways originating from either the plasma membrane or the lysosome (or vacuole in yeast). Moreover, uptake of exogenous serine is necessary for the regulation of SP biosynthesis, which suggests the existence of differentially regulated SPT pools based on their intracellular localization. However, measuring lipid metabolic enzyme activity in different cellular sub-compartments has been challenging. Combining a nanobody recruitment approach with SP flux analysis, we show that the nuclear endoplasmic reticulum (ER)-localized SPT and the peripheral ER localized SPT pools are differentially active. Thus, our data add another layer to the complex network of SPT regulation. Moreover, combining lipid metabolic enzyme re-localization with flux analysis serves as versatile tool to measure lipid metabolism with subcellular resolution.
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Affiliation(s)
- Bianca M Esch
- Osnabrück University, Department of Biology-Chemistry, Bioanalytical Chemistry Section, Barbarastrasse 13, 49076 Osnabrück, Germany
- Osnabrück University, Center for Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Stefan Walter
- Osnabrück University, Center for Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Oliver Schmidt
- Institute of Cell Biology, Biocenter Innsbruck, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria
| | - Florian Fröhlich
- Osnabrück University, Department of Biology-Chemistry, Bioanalytical Chemistry Section, Barbarastrasse 13, 49076 Osnabrück, Germany
- Osnabrück University, Center for Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
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Sugahara S, Ishino Y, Sawada K, Iwata T, Shimanaka Y, Aoki J, Arai H, Kono N. Disease-related PSS1 mutant impedes the formation and function of osteoclasts. J Lipid Res 2023; 64:100443. [PMID: 37714410 PMCID: PMC10641532 DOI: 10.1016/j.jlr.2023.100443] [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: 02/06/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/17/2023] Open
Abstract
Phosphatidylserine (PS) is an acidic phospholipid that is involved in various cellular events. Heterologous dominant mutations have been identified in the gene encoding PS synthase 1 (PSS1) in patients with a congenital disease called Lenz-Majewski syndrome (LMS). Patients with LMS show various symptoms, including craniofacial/distal-limb bone dysplasia and progressive hyperostosis. The LMS-causing gain-of-function mutants of PSS1 (PSS1LMS) have been shown to synthesize PS without control, but why the uncontrolled synthesis would lead to LMS is unknown. Here we investigated the effect of PSS1LMS on osteoclasts (OCs) to elucidate the causative mechanism of LMS. PSS1LMS did not affect the expression of OC-related genes but inhibited the formation, multinucleation, and activity of OCs. Especially, OCs expressing PSS1LMS showed abnormal patterns and dynamics of actin podosome clusters, which have roles in OC migration and fusion. PSS1LMS did not affect the level of PS but changed the acyl chain compositions of PS and phosphatidylethanolamine, and decreased the level of phosphatidylinositol. The introduction of a catalytically inactive mutation into PSSLMS canceled the changes in phospholipids and the phenotypes observed in OCs expressing PSS1LMS. A gain-of-function mutant of PSS2 (PSS2 R97K) also impaired OC formation and caused changes in phospholipid composition similar to the changes caused by PSS1LMS. Our results suggest that uncontrolled PS synthesis by PSS1LMS causes changes in the quantity or fatty acid composition of certain phospholipid classes, impairing OC formation and function, which might be a cause of osteosclerosis in patients with LMS.
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Affiliation(s)
- Sari Sugahara
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuki Ishino
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Koki Sawada
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Tsumugi Iwata
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuta Shimanaka
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Junken Aoki
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Arai
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Nozomu Kono
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
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6
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Lv W, Sha Y, Liu X, He Y, Hu J, Wang J, Li S, Guo X, Shao P, Zhao F, Li M. Interaction between Rumen Epithelial miRNAs-Microbiota-Metabolites in Response to Cold-Season Nutritional Stress in Tibetan Sheep. Int J Mol Sci 2023; 24:14489. [PMID: 37833936 PMCID: PMC10572940 DOI: 10.3390/ijms241914489] [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: 08/16/2023] [Revised: 09/16/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Tibetan sheep are already well adapted to cold season nutrient stress on the Tibetan Plateau. Rumen, an important nutrient for metabolism and as an absorption organ in ruminants, plays a vital role in the cold stress adaptations of Tibetan sheep. Ruminal microbiota also plays an indispensable role in rumen function. In this study, combined multiomics data were utilized to comprehensively analyze the interaction mechanism between rumen epithelial miRNAs and microbiota and their metabolites in Tibetan sheep under nutrient stress in the cold season. A total of 949 miRNAs were identified in the rumen epithelium of both cold and warm seasons. A total of 62 differentially expressed (DE) miRNAs were screened using FC > 1.5 and p value < 0.01, and a total of 20,206 targeted genes were predicted by DE miRNAs. KEGG enrichment analysis revealed that DE miRNA-targeted genes were mainly enriched in axon guidance(ko04360), tight junction(ko04530), inflammatory mediator regulation of TRP channels(ko04750) and metabolism-related pathways. Correlation analysis revealed that rumen microbiota, rumen VFAs and DE miRNAs were all correlated. Further study revealed that the targeted genes of cold and warm season rumen epithelial DE miRNAs were coenriched with differential metabolites of microbiota in glycerophospholipid metabolism (ko00564), apoptosis (ko04210), inflammatory mediator regulation of TRP channels (ko04750), small cell lung cancer (ko05222), and choline metabolism in cancer (ko05231) pathways. There are several interactions between Tibetan sheep rumen epithelial miRNAs, rumen microbiota, and microbial metabolites, mainly through maintaining rumen epithelial barrier function and host homeostasis of choline and cholesterol, improving host immunity, and promoting energy metabolism pathways, thus enabling Tibetan sheep to effectively respond to cold season nutrient stress. The results also suggest that rumen microbiota have coevolved with their hosts to improve the adaptive capacity of Tibetan sheep to cold season nutrient stress, providing a new perspective for the study of cold season nutritional stress adaptation in Tibetan sheep.
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Affiliation(s)
- Weibing Lv
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Yuzhu Sha
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
| | - Xiu Liu
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
| | - Yanyu He
- School of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand;
| | - Jiang Hu
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
| | - Jiqing Wang
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
| | - Shaobin Li
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
| | - Xinyu Guo
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
| | - Pengyang Shao
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
| | - Fangfang Zhao
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
| | - Mingna Li
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
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7
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Choi JY, Lopes L, Ben Mamoun C, Voelker DR. Maturation of the malarial phosphatidylserine decarboxylase is mediated by high affinity binding to anionic phospholipids. J Biol Chem 2023; 299:104659. [PMID: 36997087 PMCID: PMC10172927 DOI: 10.1016/j.jbc.2023.104659] [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: 01/17/2023] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
Decarboxylation of phosphatidylserine (PS) to form phosphatidylethanolamine by PS decarboxylases (PSDs) is an essential process in most eukaryotes. Processing of a malarial PSD proenzyme into its active alpha and beta subunits is by an autoendoproteolytic mechanism regulated by anionic phospholipids, with PS serving as an activator and phosphatidylglycerol (PG), phosphatidylinositol, and phosphatidic acid acting as inhibitors. The biophysical mechanism underlying this regulation remains unknown. We used solid phase lipid binding, liposome-binding assays, and surface plasmon resonance to examine the binding specificity of a processing-deficient Plasmodium PSD (PkPSDS308A) mutant enzyme and demonstrated that the PSD proenzyme binds strongly to PS and PG but not to phosphatidylethanolamine and phosphatidylcholine. The equilibrium dissociation constants (Kd) of PkPSD with PS and PG were 80.4 nM and 66.4 nM, respectively. The interaction of PSD with PS is inhibited by calcium, suggesting that the binding mechanism involves ionic interactions. In vitro processing of WT PkPSD proenzyme was also inhibited by calcium, consistent with the conclusion that PS binding to PkPSD through ionic interactions is required for the proenzyme processing. Peptide mapping identified polybasic amino acid motifs in the proenzyme responsible for binding to PS. Altogether, the data demonstrate that malarial PSD maturation is regulated through a strong physical association between PkPSD proenzyme and anionic lipids. Inhibition of the specific interaction between the proenzyme and the lipids can provide a novel mechanism to disrupt PSD enzyme activity, which has been suggested as a target for antimicrobials, and anticancer therapies.
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Affiliation(s)
- Jae-Yeon Choi
- Basic Science Section, Department of Medicine, National Jewish Health, Denver, Colorado, USA; Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - Lauren Lopes
- Basic Science Section, Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Choukri Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - Dennis R Voelker
- Basic Science Section, Department of Medicine, National Jewish Health, Denver, Colorado, USA.
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8
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Dillard LR, Glass EM, Lewis AL, Thomas-White K, Papin JA. Metabolic Network Models of the Gardnerella Pangenome Identify Key Interactions with the Vaginal Environment. mSystems 2023; 8:e0068922. [PMID: 36511689 PMCID: PMC9948698 DOI: 10.1128/msystems.00689-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/13/2022] [Indexed: 12/15/2022] Open
Abstract
Gardnerella is the primary pathogenic bacterial genus present in the polymicrobial condition known as bacterial vaginosis (BV). Despite BV's high prevalence and associated chronic and acute women's health impacts, the Gardnerella pangenome is largely uncharacterized at both the genetic and functional metabolic levels. Here, we used genome-scale metabolic models to characterize in silico the Gardnerella pangenome metabolic content. We also assessed the metabolic functional capacity in a BV-positive cervicovaginal fluid context. The metabolic capacity varied widely across the pangenome, with 38.15% of all reactions being core to the genus, compared to 49.60% of reactions identified as being unique to a smaller subset of species. We identified 57 essential genes across the pangenome via in silico gene essentiality screens within two simulated vaginal metabolic environments. Four genes, gpsA, fas, suhB, and psd, were identified as core essential genes critical for the metabolic function of all analyzed bacterial species of the Gardnerella genus. Further understanding these core essential metabolic functions could inform novel therapeutic strategies to treat BV. Machine learning applied to simulated metabolic network flux distributions showed limited clustering based on the sample isolation source, which further supports the presence of extensive core metabolic functionality across this genus. These data represent the first metabolic modeling of the Gardnerella pangenome and illustrate strain-specific interactions with the vaginal metabolic environment across the pangenome. IMPORTANCE Bacterial vaginosis (BV) is the most common vaginal infection among reproductive-age women. Despite its prevalence and associated chronic and acute women's health impacts, the diverse bacteria involved in BV infection remain poorly characterized. Gardnerella is the genus of bacteria most commonly and most abundantly represented during BV. In this paper, we use metabolic models, which are a computational representation of the possible functional metabolism of an organism, to investigate metabolic conservation, gene essentiality, and pathway utilization across 110 Gardnerella strains. These models allow us to investigate in silico how strains may differ with respect to their metabolic interactions with the vaginal-host environment.
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Affiliation(s)
- Lillian R. Dillard
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | - Emma M. Glass
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Amanda L. Lewis
- Department of Obstetrics and Gynecology, University of California—San Diego, La Jolla, California, USA
| | | | - Jason A. Papin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
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9
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Ferreira-Neto JRC, de Araújo FC, de Oliveira Silva RL, de Melo NF, Pandolfi V, Frosi G, de Lima Morais DA, da Silva MD, Rivas R, Santos MG, de Tarso Aidar S, Morgante CV, Benko-Iseppon AM. Dehydration response in Stylosanthes scabra: Transcriptional, biochemical, and physiological modulations. PHYSIOLOGIA PLANTARUM 2022; 174:e13821. [PMID: 36345266 DOI: 10.1111/ppl.13821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/22/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Stylosanthes scabra, popularly known as stylo, is native to the Brazilian Caatinga semiarid region and stands out as a drought-tolerant shrub forage crop. This work provides information about the plant response during the first 48 h of water deficit, followed by a rehydration treatment. Besides root transcriptomics data, 13 physiological or biochemical parameters were scrutinized. Additionally, RNA-Seq annotated transcripts not associated with the "Viridiplantae" clade were taxonomically categorized. It was found that S. scabra quickly perceives and recovers from the oscillations of the imposed water regime. Physiologically, mechanisms that minimize evapotranspiration or protect the photosynthetic apparatus stood out. Biochemically, it was found that the root tissue invests in synthesizing compounds that can act as osmolytes (proline and sugars), emphasizing the importance of osmoregulation to water deficit acclimation. Consistently, transcriptome and qPCR analyses showed that a set of enriched biological processes with upregulated (UR) transcripts were involved in protective functions against reactive oxygen species or encoding enzymes of important metabolic pathways, which might contribute to S. scabra response to water deficit. Additionally, several UR kinases and transcription factors were identified. Finally, in an innovative approach, some naturally occurring microbial groups (such as Schizosaccharomyces, Bradyrhizobium, etc.) were identified in the S. scabra roots. This study reveals insights into the physiological, biochemical, and molecular mechanisms underlying the S. scabra response to water deficit and provides candidate genes that may be useful in developing drought-tolerant crop varieties through biotechnological applications.
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Affiliation(s)
- José Ribamar Costa Ferreira-Neto
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Flávia Czekalski de Araújo
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Roberta Lane de Oliveira Silva
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | | | - Valesca Pandolfi
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Gabriella Frosi
- Départament de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Manassés Daniel da Silva
- Laboratório de Genética Molecular, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Rebeca Rivas
- Laboratório de Genética Molecular, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Mauro Guida Santos
- Laboratório de Fisiologia Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Saulo de Tarso Aidar
- Empresa Brasileira de Pesquisa Agropecuária (SEMIÁRIDO), Petrolina, Pernambuco, Brazil
| | | | - Ana Maria Benko-Iseppon
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
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10
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Tang X, Cao Y, Arora G, Hwang J, Sajid A, Brown CL, Mehta S, Marín-López A, Chuang YM, Wu MJ, Ma H, Pal U, Narasimhan S, Fikrig E. The Lyme disease agent co-opts adiponectin receptor-mediated signaling in its arthropod vector. eLife 2021; 10:e72568. [PMID: 34783654 PMCID: PMC8639152 DOI: 10.7554/elife.72568] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/04/2021] [Indexed: 12/24/2022] Open
Abstract
Adiponectin-mediated pathways contribute to mammalian homeostasis; however, little is known about adiponectin and adiponectin receptor signaling in arthropods. In this study, we demonstrate that Ixodes scapularis ticks have an adiponectin receptor-like protein (ISARL) but lack adiponectin, suggesting activation by alternative pathways. ISARL expression is significantly upregulated in the tick gut after Borrelia burgdorferi infection, suggesting that ISARL signaling may be co-opted by the Lyme disease agent. Consistent with this, RNA interference (RNAi)-mediated silencing of ISARL significantly reduced the B. burgdorferi burden in the tick. RNA-seq-based transcriptomics and RNAi assays demonstrate that ISARL-mediated phospholipid metabolism by phosphatidylserine synthase I is associated with B. burgdorferi survival. Furthermore, the tick complement C1q-like protein 3 interacts with ISARL, and B. burgdorferi facilitates this process. This study identifies a new tick metabolic pathway that is connected to the life cycle of the Lyme disease spirochete.
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Affiliation(s)
- Xiaotian Tang
- Section of Infectious Diseases, Department of Internal Medicine, School of Medicine, Yale UniversityNew HavenUnited States
| | - Yongguo Cao
- Section of Infectious Diseases, Department of Internal Medicine, School of Medicine, Yale UniversityNew HavenUnited States
- Department of Clinical Veterinary Medicine, and Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin UniversityChangchunChina
| | - Gunjan Arora
- Section of Infectious Diseases, Department of Internal Medicine, School of Medicine, Yale UniversityNew HavenUnited States
| | - Jesse Hwang
- Section of Infectious Diseases, Department of Internal Medicine, School of Medicine, Yale UniversityNew HavenUnited States
| | - Andaleeb Sajid
- Section of Infectious Diseases, Department of Internal Medicine, School of Medicine, Yale UniversityNew HavenUnited States
| | - Courtney L Brown
- Yale Combined Program in the Biological and Biomedical Sciences, Yale UniversityNew HavenUnited States
| | - Sameet Mehta
- Yale Center for Genome Analysis, Yale UniversityNew HavenUnited States
| | - Alejandro Marín-López
- Section of Infectious Diseases, Department of Internal Medicine, School of Medicine, Yale UniversityNew HavenUnited States
| | - Yu-Min Chuang
- Section of Infectious Diseases, Department of Internal Medicine, School of Medicine, Yale UniversityNew HavenUnited States
| | - Ming-Jie Wu
- Section of Infectious Diseases, Department of Internal Medicine, School of Medicine, Yale UniversityNew HavenUnited States
| | - Hongwei Ma
- Section of Infectious Diseases, Department of Internal Medicine, School of Medicine, Yale UniversityNew HavenUnited States
- Department of Microbiology, School of Basic Medicine, Fourth Military Medical UniversityShaanxiChina
| | - Utpal Pal
- Department of Veterinary Medicine, University of Maryland, College ParkCollege ParkUnited States
| | - Sukanya Narasimhan
- Section of Infectious Diseases, Department of Internal Medicine, School of Medicine, Yale UniversityNew HavenUnited States
| | - Erol Fikrig
- Section of Infectious Diseases, Department of Internal Medicine, School of Medicine, Yale UniversityNew HavenUnited States
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11
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Shvetsova A, Masud AJ, Schneider L, Bergmann U, Monteuuis G, Miinalainen IJ, Hiltunen JK, Kastaniotis AJ. A hunt for OM45 synthetic petite interactions in Saccharomyces cerevisiae reveals a role for Miro GTPase Gem1p in cristae structure maintenance. Microbiologyopen 2021; 10:e1238. [PMID: 34713605 PMCID: PMC8501180 DOI: 10.1002/mbo3.1238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/09/2021] [Accepted: 09/09/2021] [Indexed: 11/28/2022] Open
Abstract
Om45 is a major protein of the yeast's outer mitochondrial membrane under respiratory conditions. However, the cellular role of the protein has remained obscure. Previously, deletion mutant phenotypes have not been found, and clear amino acid sequence similarities that would allow inferring its functional role are not available. In this work, we describe synthetic petite mutants of GEM1 and UGO1 that depend on the presence of OM45 for respiratory growth, as well as the identification of several multicopy suppressors of the synthetic petite phenotypes. In the analysis of our mutants, we demonstrate that Om45p and Gem1p have a collaborative role in the maintenance of mitochondrial morphology, cristae structure, and mitochondrial DNA maintenance. A group of multicopy suppressors rescuing the synthetic lethal phenotypes of the mutants on non-fermentable carbon sources additionally supports this result. Our results imply that the synthetic petite phenotypes we observed are due to the disturbance of the inner mitochondrial membrane and point to this mitochondrial sub-compartment as the main target of action of Om45p, Ugo1p, and the yeast Miro GTPase Gem1p.
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Affiliation(s)
- Antonina Shvetsova
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
| | - Ali J. Masud
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
| | - Laura Schneider
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
| | - Ulrich Bergmann
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
| | - Geoffray Monteuuis
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
- Present address:
Department of Biochemistry and Developmental BiologyUniversity of HelsinkiHelsinkiFinland
| | - Ilkka J. Miinalainen
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
| | - J. Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
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12
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The retromer is co-opted to deliver lipid enzymes for the biogenesis of lipid-enriched tombusviral replication organelles. Proc Natl Acad Sci U S A 2021; 118:2016066118. [PMID: 33376201 DOI: 10.1073/pnas.2016066118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Biogenesis of viral replication organelles (VROs) is critical for replication of positive-strand RNA viruses. In this work, we demonstrate that tomato bushy stunt virus (TBSV) and the closely related carnation Italian ringspot virus (CIRV) hijack the retromer to facilitate building VROs in the surrogate host yeast and in plants. Depletion of retromer proteins, which are needed for biogenesis of endosomal tubular transport carriers, strongly inhibits the peroxisome-associated TBSV and the mitochondria-associated CIRV replication in yeast and in planta. In vitro reconstitution revealed the need for the retromer for the full activity of the viral replicase. The viral p33 replication protein interacts with the retromer complex, including Vps26, Vps29, and Vps35. We demonstrate that TBSV p33-driven retargeting of the retromer into VROs results in delivery of critical retromer cargoes, such as 1) Psd2 phosphatidylserine decarboxylase, 2) Vps34 phosphatidylinositol 3-kinase (PI3K), and 3) phosphatidylinositol 4-kinase (PI4Kα-like). The recruitment of these cellular enzymes by the co-opted retromer is critical for de novo production and enrichment of phosphatidylethanolamine phospholipid, phosphatidylinositol-3-phosphate [PI(3)P], and phosphatidylinositol-4-phosphate [PI(4)P] phosphoinositides within the VROs. Co-opting cellular enzymes required for lipid biosynthesis and lipid modifications suggest that tombusviruses could create an optimized lipid/membrane microenvironment for efficient VRO assembly and protection of the viral RNAs during virus replication. We propose that compartmentalization of these lipid enzymes within VROs helps tombusviruses replicate in an efficient milieu. In summary, tombusviruses target a major crossroad in the secretory and recycling pathways via coopting the retromer complex and the tubular endosomal network to build VROs in infected cells.
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13
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Dowhan W, Bogdanov M. Eugene P. Kennedy's Legacy: Defining Bacterial Phospholipid Pathways and Function. Front Mol Biosci 2021; 8:666203. [PMID: 33842554 PMCID: PMC8027125 DOI: 10.3389/fmolb.2021.666203] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/01/2021] [Indexed: 12/27/2022] Open
Abstract
In the 1950's and 1960's Eugene P. Kennedy laid out the blueprint for phospholipid biosynthesis in somatic cells and Escherichia coli, which have been coined the Kennedy Pathways for phospholipid biosynthesis. His research group continued to make seminal contributions in the area of phospholipids until his retirement in the early 1990's. During these years he mentored many young scientists that continued to build on his early discoveries and who also mentored additional scientists that continue to make important contributions in areas related to phospholipids and membrane biogenesis. This review will focus on the initial E. coli Kennedy Pathways and how his early contributions have laid the foundation for our current understanding of bacterial phospholipid genetics, biochemistry and function as carried on by his scientific progeny and others who have been inspired to study microbial phospholipids.
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Affiliation(s)
- William Dowhan
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
| | - Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
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14
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Cho G, Lee E, Kim J. Structural insights into phosphatidylethanolamine formation in bacterial membrane biogenesis. Sci Rep 2021; 11:5785. [PMID: 33707636 PMCID: PMC7952604 DOI: 10.1038/s41598-021-85195-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/26/2021] [Indexed: 01/07/2023] Open
Abstract
Phosphatidylethanolamine (PE), a major component of the cellular membrane across all domains of life, is synthesized exclusively by membrane-anchored phosphatidylserine decarboxylase (PSD) in most bacteria. The enzyme undergoes auto-cleavage for activation and utilizes the pyruvoyl moiety to form a Schiff base intermediate with PS to facilitate decarboxylation. However, the structural basis for self-maturation, PS binding, and decarboxylation processes directed by PSD remain unclear. Here, we present X-ray crystal structures of PSD from Escherichia coli, representing an apo form and a PE-bound complex, in which the phospholipid is chemically conjugated to the essential pyruvoyl residue, mimicking the Schiff base intermediate. The high-resolution structures of PE-complexed PSD clearly illustrate extensive hydrophobic interactions with the fatty acyl chains of the phospholipid, providing insights into the broad specificity of the enzyme over a wide range of cellular PS. Furthermore, these structures strongly advocate the unique topology of the enzyme in a lipid bilayer environment, where the enzyme associates with cell membranes in a monotopic fashion via the N-terminal domain composed of three amphipathic helices. Lastly, mutagenesis analyses reveal that E. coli PSD primarily employs D90/D142-H144-S254 to achieve auto-cleavage for the proenzyme maturation, where D90 and D142 act in complementary to each other.
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Affiliation(s)
- Gyuhyeok Cho
- grid.61221.360000 0001 1033 9831Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005 Republic of Korea
| | - Eunju Lee
- grid.61221.360000 0001 1033 9831Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005 Republic of Korea
| | - Jungwook Kim
- grid.61221.360000 0001 1033 9831Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005 Republic of Korea
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15
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Tang L, Chi H, Li W, Zhang L, Zhang L, Chen L, Zou S, Liu H, Liang Y, Yu J, Dong H. FgPsd2, a phosphatidylserine decarboxylase of Fusarium graminearum, regulates development and virulence. Fungal Genet Biol 2020; 146:103483. [PMID: 33176219 DOI: 10.1016/j.fgb.2020.103483] [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] [Received: 07/18/2020] [Revised: 10/21/2020] [Accepted: 11/03/2020] [Indexed: 11/25/2022]
Abstract
Phosphatidylserine decarboxylases (Psds) are enzymes regulating phosphatidylethanolamine biosynthesis in prokaryotes and eukaryotes, and have the central role in lipid metabolism. To date, the functions of Psds in plant pathogenic fungi are not fully understood. In this study, we have characterized two yeast Psd orthologues: FgPsd1 and FgPsd2, in Fusarium graminearum. Our results indicate that FgPsd1 and FgPsd2 are localized in mitochondria and Golgi, respectively. In addition, we have determined that FgPsd1 is a lethal gene and deletion of FgPsd2 resulted in a significant reduction of mycelial growth and conidiation. Futhermore, the FgPsd2 deletion mutant (ΔFgPsd2) is defective in ascospore production and virulence in wheat. Our study has also found that the ΔFgPsd2 mutant is more sensitive to osmotic and oxygen stresses. Moreover, deletion of FgPsd2 reduced the formation of lipid droplets and aggravated autophagy in F. graminearum. In summary, our findings indicate that FgPsd2 is important for mycelial growth, sexual and asexual reproduction, virulence, lipid droplet formation and autophagy in F. graminearum.
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Affiliation(s)
- Lin Tang
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Haowen Chi
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Weidong Li
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Li Zhang
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Liyuan Zhang
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Lei Chen
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Shenshen Zou
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Huixiang Liu
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Yuancun Liang
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Taian 271018, China.
| | - Jinfeng Yu
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Hansong Dong
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
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16
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Kaiser L, Weinschrott H, Quint I, Blaess M, Csuk R, Jung M, Kohl M, Deigner HP. Metabolite Patterns in Human Myeloid Hematopoiesis Result from Lineage-Dependent Active Metabolic Pathways. Int J Mol Sci 2020; 21:ijms21176092. [PMID: 32847028 PMCID: PMC7504406 DOI: 10.3390/ijms21176092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 12/18/2022] Open
Abstract
Assessment of hematotoxicity from environmental or xenobiotic compounds is of notable interest and is frequently assessed via the colony forming unit (CFU) assay. Identification of the mode of action of single compounds is of further interest, as this often enables transfer of results across different tissues and compounds. Metabolomics displays one promising approach for such identification, nevertheless, suitability with current protocols is restricted. Here, we combined a hematopoietic stem and progenitor cell (HSPC) expansion approach with distinct lineage differentiations, resulting in formation of erythrocytes, dendritic cells and neutrophils. We examined the unique combination of pathway activity in glycolysis, glutaminolysis, polyamine synthesis, fatty acid oxidation and synthesis, as well as glycerophospholipid and sphingolipid metabolism. We further assessed their interconnections and essentialness for each lineage formation. By this, we provide further insights into active metabolic pathways during the differentiation of HSPC into different lineages, enabling profound understanding of possible metabolic changes in each lineage caused by exogenous compounds.
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Affiliation(s)
- Lars Kaiser
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 Villingen-Schwenningen, Germany; (L.K.); (H.W.); (I.Q.); (M.B.); (M.K.)
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg i. Br., Germany;
| | - Helga Weinschrott
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 Villingen-Schwenningen, Germany; (L.K.); (H.W.); (I.Q.); (M.B.); (M.K.)
| | - Isabel Quint
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 Villingen-Schwenningen, Germany; (L.K.); (H.W.); (I.Q.); (M.B.); (M.K.)
| | - Markus Blaess
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 Villingen-Schwenningen, Germany; (L.K.); (H.W.); (I.Q.); (M.B.); (M.K.)
| | - René Csuk
- Organic Chemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany;
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg i. Br., Germany;
- CIBSS—Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Matthias Kohl
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 Villingen-Schwenningen, Germany; (L.K.); (H.W.); (I.Q.); (M.B.); (M.K.)
| | - Hans-Peter Deigner
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 Villingen-Schwenningen, Germany; (L.K.); (H.W.); (I.Q.); (M.B.); (M.K.)
- Fraunhofer Institute IZI, Leipzig, EXIM Department, Schillingallee 68, 18057 Rostock, Germany
- Associated member of Tuebingen University, Faculty of Science, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Correspondence: ; Tel.: +49-7720-307-4232
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17
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Cui K, Zhao Y, He L, Ding J, Li B, Mu W, Liu F. Comparison of Transcriptome Profiles of the Fungus Botrytis cinerea and Insect Pest Bradysia odoriphaga in Response to Benzothiazole. Front Microbiol 2020; 11:1043. [PMID: 32655508 PMCID: PMC7325989 DOI: 10.3389/fmicb.2020.01043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/27/2020] [Indexed: 12/25/2022] Open
Abstract
Benzothiazole (BT) has a strong inhibitory effect on the growth and development of a wide spectrum of fungi and insects, such as Botrytis cinerea and Bradysia odoriphaga, that cause serious losses in agriculture. To investigate the underlying antifungal and insecticidal mechanisms of BT, RNA-seq analysis was performed for B. cinerea after BT treatment for 12, 24, and 48 h and for B. odoriphaga after BT treatment for 6 and 24 h. In B. cinerea, the pectin degradation process was inhibited, suggesting a low utilization of carbohydrate sources. As the treatment time was extended, the cell walls of B. cinerea thickened, and increases in melanin synthesis and ion transport were observed. In B. odoriphaga, signaling pathways including MAPK, insulin, adipocytokine, forkhead box class O, and peroxisome proliferator-activated receptor were activated at 6 h, and phosphoenolpyruvate carboxykinase was the core gene in the signal transduction pathways that responded to BT; digestive system and melanogenesis genes were obviously altered at 24 h. In addition, we identified several insecticidal target genes, such as trypsin, aminopeptidase N, and tyrosinase. Benzothiazole significantly affected nutrient metabolism, especially carbohydrate metabolism, in both species, and the pentose and glucuronate interconversions pathway was shared by both species, although the individual genes were different in each species. Overall, our results suggested that BT was a melanogenesis disrupter for the insect but an activator for the fungus. Our findings are helpful for deeply exploring the genes targeted by BT and for developing new pesticide compounds with unique mechanisms of action.
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Affiliation(s)
- Kaidi Cui
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China.,College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Yunhe Zhao
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China.,College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Leiming He
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China.,College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Jinfeng Ding
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China.,College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Beixing Li
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China.,College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Wei Mu
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China.,College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Feng Liu
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China.,College of Plant Protection, Shandong Agricultural University, Tai'an, China
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18
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Hakobyan G, Davtyan H, Harutyunyan K, Alexanyan K, Amirkhanyan Y, Gharibyan AL, Asatryan L, Tadevosyan Y. Similarities in Blood Mononuclear Cell Membrane Phospholipid Profiles During Malignancy. Med Sci (Basel) 2018; 6:medsci6040105. [PMID: 30477187 PMCID: PMC6313534 DOI: 10.3390/medsci6040105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/15/2018] [Accepted: 11/20/2018] [Indexed: 11/16/2022] Open
Abstract
Phospholipids (PLs), key elements of cellular membranes, are regulated reciprocally with membrane proteins and can act as sensors for alterations in physiological or pathological states of cells including initiation and development of cancer. On the other hand, peripheral blood mononuclear cells (MNCs) play an important role in antitumor immune response by reacting to cancerous modifications in distant organs. In the current study, we tested the hypothesis that tumor initiation and development are reflected in the alteration pattern of the MNC PL component. We analyzed MNC membrane PL fractions in samples from healthy individuals and from patients with diverse types of cancers to reveal possible alterations induced by malignancy. Compared to healthy controls, the cancer samples demonstrated shifts in several membrane PL profiles. In particular, when analyzing cancer data pooled together, there were significantly higher levels in lysophosphatidylcholine, phosphatidylcholine, and phosphatidylethanolamine fractions, and significantly lower quantities in phosphatidylinositol, phosphatidylserine, and phosphatidic acid fractions in cancer samples compared to controls. The levels of sphingomyelins and diphosphatidylglycerols were relatively unaffected. Most of the differences in PLs were sustained during the analysis of individual cancers such as breast cancer and chronic lymphocytic leukemia. Our findings suggest the presence of a common pattern of changes in MNC PLs during malignancy.
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Affiliation(s)
- Gohar Hakobyan
- Laboratory of Regulation of Cellular Activity, Institute of Molecular Biology, National Academy of Sciences, 0014 Yerevan, Armenia.
| | - Hasmik Davtyan
- Laboratory of Regulation of Cellular Activity, Institute of Molecular Biology, National Academy of Sciences, 0014 Yerevan, Armenia.
| | - Kristine Harutyunyan
- Laboratory of Regulation of Cellular Activity, Institute of Molecular Biology, National Academy of Sciences, 0014 Yerevan, Armenia.
| | - Knarik Alexanyan
- Center of Oncology after V. Fanarjyan, Ministry of Health RA, 0052 Yerevan, Armenia.
| | | | - Anna L Gharibyan
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden.
| | - Liana Asatryan
- School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA.
| | - Yuri Tadevosyan
- Laboratory of Regulation of Cellular Activity, Institute of Molecular Biology, National Academy of Sciences, 0014 Yerevan, Armenia.
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19
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A plant-responsive bacterial-signaling system senses an ethanolamine derivative. Proc Natl Acad Sci U S A 2018; 115:9785-9790. [PMID: 30190434 DOI: 10.1073/pnas.1809611115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Certain plant-associated Proteobacteria sense their host environment by detecting an unknown plant signal recognized by a member of a LuxR subfamily of transcription factors. This interkingdom communication is important for both mutualistic and pathogenic interactions. The Populus root endophyte Pseudomonas sp. GM79 possesses such a regulator, named PipR. In a previous study we reported that PipR activates an adjacent gene (pipA) coding for a proline iminopeptidase in response to Populus leaf macerates and peptides and that this activation is dependent on a putative ABC-type transporter [Schaefer AL, et al. (2016) mBio 7:e01101-16]. In this study we identify a chemical derived from ethanolamine that induces PipR activity at picomolar concentrations, and we present evidence that this is the active inducer present in plant leaf macerates. First, a screen of more than 750 compounds indicated ethanolamine was a potent inducer for the PipR-sensing system; however, ethanolamine failed to bind to the periplasmic-binding protein (PBP) required for the signal response. This led us to discover that a specific ethanolamine derivative, N-(2-hydroxyethyl)-2-(2-hydroxyethylamino) acetamide (HEHEAA), binds to the PBP and serves as a potent PipR-dependent inducer. We also show that a compound, which coelutes with HEHEAA in HPLC and induces pipA gene expression in a PipR-dependent manner, can be found in Populus leaf macerates. This work sheds light on how plant-associated bacteria can sense their environment and on the nature of inducers for a family of plant-responsive LuxR-like transcription factors found in plant-associated bacteria.
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20
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Dawoody Nejad L, Serricchio M, Jelk J, Hemphill A, Bütikofer P. TbLpn, a key enzyme in lipid droplet formation and phospholipid metabolism, is essential for mitochondrial integrity and growth of Trypanosoma brucei. Mol Microbiol 2018; 109:105-120. [PMID: 29679486 DOI: 10.1111/mmi.13976] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2018] [Indexed: 01/02/2023]
Abstract
Mammalian phosphatidic acid phosphatases, also called lipins, show high amino acid sequence identity to Saccharomyces cerevisiae Pah1p and catalyze the dephosphorylation of phosphatidic acid (PA) to diacylglycerol. Both the substrate and product of the reaction are key precursors for the synthesis of phospholipids and triacylglycerol (TAG). We now show that expression of the Trypanosoma brucei lipin homolog TbLpn is essential for parasite survival in culture. Inducible down-regulation of TbLpn in T. brucei procyclic forms increased cellular PA content, decreased the numbers of lipid droplets, reduced TAG steady-state levels and inhibited in vivo [3 H]TAG formation after labeling trypanosomes with [3 H]glycerol. In addition, fluorescence and transmission electron microscopy revealed that depletion of TbLpn caused major alterations in mitochondrial morphology and function, i.e., the appearance of distorted mitochondrial matrix, and reduced ATP production via oxidative phosphorylation. Effects of lipin depletion on mitochondrial integrity have previously not been reported. N- and C-terminally tagged forms of TbLpn were localized in the cytosol.
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Affiliation(s)
- Ladan Dawoody Nejad
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Mauro Serricchio
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Jennifer Jelk
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Andrew Hemphill
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Peter Bütikofer
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
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21
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Renne MF, de Kroon AIPM. The role of phospholipid molecular species in determining the physical properties of yeast membranes. FEBS Lett 2017; 592:1330-1345. [PMID: 29265372 PMCID: PMC5947837 DOI: 10.1002/1873-3468.12944] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/27/2017] [Accepted: 12/11/2017] [Indexed: 12/18/2022]
Abstract
In most eukaryotes, including Saccharomyces cerevisiae, glycerophospholipids are the main membrane lipid constituents. Besides serving as general membrane ‘building blocks’, glycerophospholipids play an important role in determining the physical properties of the membrane, which are crucial for proper membrane function. To ensure optimal physical properties, membrane glycerophospholipid composition and synthesis are tightly regulated. This review will summarize our current knowledge of factors and processes determining the membrane glycerophospholipid composition of the reference eukaryote S. cerevisiae at the level of molecular species. Extrapolating from relevant model membrane data, we also discuss how modulation of the molecular species composition can regulate membrane physical properties.
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Affiliation(s)
- Mike F. Renne
- Membrane Biochemistry & BiophysicsDepartment of ChemistryBijvoet Center for Biomolecular Research & Institute of BiomembranesUtrecht Universitythe Netherlands
| | - Anton I. P. M. de Kroon
- Membrane Biochemistry & BiophysicsDepartment of ChemistryBijvoet Center for Biomolecular Research & Institute of BiomembranesUtrecht Universitythe Netherlands
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22
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Wagner A, Di Bartolomeo F, Klein I, Hrastnik C, Doan KN, Becker T, Daum G. Identification and characterization of the mitochondrial membrane sorting signals in phosphatidylserine decarboxylase 1 from Saccharomyces cerevisiae. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1863:117-125. [PMID: 29126902 DOI: 10.1016/j.bbalip.2017.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 11/03/2017] [Accepted: 11/06/2017] [Indexed: 12/20/2022]
Abstract
Phosphatidylserine decarboxylase 1 (Psd1p) catalyzes the formation of the majority of phosphatidylethanolamine (PE) in the yeast Saccharomyces cerevisiae. Psd1p is localized to mitochondria, anchored to the inner mitochondrial membrane (IMM) through membrane spanning domains and oriented towards the mitochondrial intermembrane space. We found that Psd1p harbors at least two inner membrane-associated domains, which we named IM1 and IM2. IM1 is important for proper orientation of Psd1p within the IMM (Horvath et al., J. Biol. Chem. 287 (2012) 36744-55), whereas it remained unclear whether IM2 is important for membrane-association of Psd1p. To discover the role of IM2 in Psd1p import, processing and assembly into the mitochondria, we constructed Psd1p variants with deletions in IM2. Removal of the complete IM2 led to an altered topology of the protein with the soluble domain exposed to the matrix and to decreased enzyme activity. Psd1p variants lacking portions of the N-terminal moiety of IM2 were inserted into IMM with an altered topology. Psd1p variants with deletions of C-terminal portions of IM2 accumulated at the outer mitochondrial membrane and lost their enzyme activity. In conclusion we showed that IM2 is essential for full enzymatic activity, maturation and correct integration of yeast Psd1p into the inner mitochondrial membrane.
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Affiliation(s)
- Ariane Wagner
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010 Graz, Austria
| | - Francesca Di Bartolomeo
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010 Graz, Austria
| | - Isabella Klein
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010 Graz, Austria
| | - Claudia Hrastnik
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010 Graz, Austria
| | - Kim Nguyen Doan
- Institute of Biochemistry and Molecular Biology ZBMZ, Faculty of Medicine, University of Freiburg, Germany; Faculty of Biology, University of Freiburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology ZBMZ, Faculty of Medicine, University of Freiburg, Germany; BIOSS Center for Biological Signalling Studies, University of Freiburg, Germany
| | - Günther Daum
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010 Graz, Austria.
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23
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Matsudaira T, Mukai K, Noguchi T, Hasegawa J, Hatta T, Iemura SI, Natsume T, Miyamura N, Nishina H, Nakayama J, Semba K, Tomita T, Murata S, Arai H, Taguchi T. Endosomal phosphatidylserine is critical for the YAP signalling pathway in proliferating cells. Nat Commun 2017; 8:1246. [PMID: 29093443 PMCID: PMC5665887 DOI: 10.1038/s41467-017-01255-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 09/01/2017] [Indexed: 02/07/2023] Open
Abstract
Yes-associated protein (YAP) is a recently discovered growth-promoting transcription coactivator that has been shown to regulate the malignancy of various cancers. How YAP is regulated is not fully understood. Here, we show that one of the factors regulating YAP is phosphatidylserine (PS) in recycling endosomes (REs). We use proximity biotinylation to find proteins proximal to PS. Among these proteins are YAP and multiple proteins related to YAP signalling. Knockdown of ATP8A1 (an RE PS-flippase) or evectin-2 (an RE-resident protein) and masking of PS in the cytoplasmic leaflet of membranes, all suppress nuclear localization of YAP and YAP-dependent transcription. ATP8A1 knockdown increases the phosphorylated (activated) form of Lats1 that phosphorylates and inactivates YAP, whereas evectin-2 knockdown reduces the ubiquitination and increased the level of Lats1. The proliferation of YAP-dependent metastatic cancer cells is suppressed by knockdown of ATP8A1 or evectin-2. These results suggest a link between a membrane phospholipid and cell proliferation.
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Affiliation(s)
- Tatsuyuki Matsudaira
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kojiro Mukai
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Taishin Noguchi
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Junya Hasegawa
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tomohisa Hatta
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-3-26, Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Shun-Ichiro Iemura
- Medical Industry Translational Research Center, Fukushima Medical University, 1, Hikarigaoka, Fukushima, 960-1295, Japan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-3-26, Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Norio Miyamura
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Hiroshi Nishina
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Jun Nakayama
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2, Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Kentaro Semba
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2, Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Takuya Tomita
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Shigeo Murata
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroyuki Arai
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,Pathological Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,AMED-CREST, Japan Agency for Medical Research and Development, 1-7-1, Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan.
| | - Tomohiko Taguchi
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,Pathological Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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24
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Di Bartolomeo F, Doan KN, Athenstaedt K, Becker T, Daum G. Involvement of a putative substrate binding site in the biogenesis and assembly of phosphatidylserine decarboxylase 1 from Saccharomyces cerevisiae. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:716-725. [PMID: 28473294 DOI: 10.1016/j.bbalip.2017.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 04/20/2017] [Accepted: 04/28/2017] [Indexed: 11/20/2022]
Abstract
In the yeast Saccharomyces cerevisiae, the mitochondrial phosphatidylserine decarboxylase 1 (Psd1p) produces the largest amount of cellular phosphatidylethanolamine (PE). Psd1p is synthesized as a larger precursor on cytosolic ribosomes and then imported into mitochondria in a three-step processing event leading to the formation of an α-subunit and a β-subunit. The α-subunit harbors a highly conserved motif, which was proposed to be involved in phosphatidylserine (PS) binding. Here, we present a molecular analysis of this consensus motif for the function of Psd1p by using Psd1p variants bearing either deletions or point mutations in this region. Our data show that mutations in this motif affect processing and stability of Psd1p, and consequently the enzyme's activity. Thus, we conclude that this consensus motif is essential for structural integrity and processing of Psd1p.
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Affiliation(s)
| | - Kim Nguyen Doan
- Institute of Biochemistry and Molecular Biology ZBMZ, Faculty of Medicine, University of Freiburg, Germany; Faculty of Biology, University of Freiburg, Germany
| | - Karin Athenstaedt
- Institute of Biochemistry, Graz University of Technology, NaWi Graz, Austria; Institute of Molecular Biosciences, University of Graz, NaWi Graz, Austria.
| | - Thomas Becker
- BIOSS Center for Biological Signalling Studies, University of Freiburg, Germany; Institute of Biochemistry and Molecular Biology ZBMZ, Faculty of Medicine, University of Freiburg, Germany.
| | - Günther Daum
- Institute of Biochemistry, Graz University of Technology, NaWi Graz, Austria.
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25
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Farine L, Jelk J, Choi J, Voelker DR, Nunes J, Smith TK, Bütikofer P. Phosphatidylserine synthase 2 and phosphatidylserine decarboxylase are essential for aminophospholipid synthesis in Trypanosoma brucei. Mol Microbiol 2017; 104:412-427. [PMID: 28142188 PMCID: PMC5413845 DOI: 10.1111/mmi.13637] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2017] [Indexed: 01/09/2023]
Abstract
Phosphatidylethanolamine (PE) and phosphatidylserine (PS) are ubiquitously expressed and metabolically interconnected glycerophospholipids in eukaryotes and prokaryotes. In Trypanosoma brucei, PE synthesis has been shown to occur mainly via the Kennedy pathway, one of the three routes leading to PE synthesis in eukaryotes, while PS synthesis has not been studied experimentally. We now reveal the importance of T. brucei PS synthase 2 (TbPSS2) and T. brucei PS decarboxylase (TbPSD), two key enzymes involved in aminophospholipid synthesis, for trypanosome viability. By using tetracycline-inducible down-regulation of gene expression and in vivo and in vitro metabolic labeling, we found that TbPSS2 (i) is necessary for normal growth of procyclic trypanosomes, (ii) localizes to the endoplasmic reticulum and (iii) represents the unique route for PS formation in T. brucei. In addition, we identified TbPSD as type I PS decarboxylase in the mitochondrion and found that it is processed proteolytically at a WGSS cleavage site into a heterodimer. Down-regulation of TbPSD expression affected mitochondrial integrity in both procyclic and bloodstream form trypanosomes, decreased ATP production via oxidative phosphorylation in procyclic form and affected parasite growth.
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Affiliation(s)
- Luce Farine
- Institute of Biochemistry and Molecular MedicineUniversity of BernBern3012Switzerland
| | - Jennifer Jelk
- Institute of Biochemistry and Molecular MedicineUniversity of BernBern3012Switzerland
| | - Jae‐Yeon Choi
- Department of MedicineNational Jewish HealthDenverCO80206USA
| | | | - Jon Nunes
- Biomedical Sciences Research ComplexUniversity of St. AndrewsSt. AndrewsScotland
| | - Terry K. Smith
- Biomedical Sciences Research ComplexUniversity of St. AndrewsSt. AndrewsScotland
| | - Peter Bütikofer
- Institute of Biochemistry and Molecular MedicineUniversity of BernBern3012Switzerland
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26
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Abstract
Mitochondria have to import the vast majority of their proteins, which are synthesized as precursors on cytosolic ribosomes. The translocase of the outer membrane (TOM complex) forms the general entry gate for the precursor proteins, which are subsequently sorted by protein machineries into the mitochondrial subcompartments: the outer and inner membrane, the intermembrane space and the mitochondrial matrix. The transport across and into the inner membrane is driven by the membrane potential, which is generated by the respiratory chain. Recent studies revealed that the lipid composition of mitochondrial membranes is important for the biogenesis of mitochondrial proteins. Cardiolipin and phosphatidylethanolamine exhibit unexpectedly specific functions for the activity of distinct protein translocases. Both phospholipids are required for full activity of respiratory chain complexes and thus to maintain the membrane potential for protein import. In addition, cardiolipin is required to maintain structural integrity of mitochondrial protein translocases. Finally, the low sterol content in the mitochondrial outer membrane may contribute to the targeting of some outer membrane proteins with a single α-helical membrane anchor. Altogether, mitochondrial lipids modulate protein import on various levels involving precursor targeting, membrane potential generation, stability and activity of protein translocases.
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27
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Di Bartolomeo F, Wagner A, Daum G. Cell biology, physiology and enzymology of phosphatidylserine decarboxylase. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:25-38. [PMID: 27650064 DOI: 10.1016/j.bbalip.2016.09.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/02/2016] [Accepted: 09/10/2016] [Indexed: 12/17/2022]
Abstract
Phosphatidylethanolamine is one of the most abundant phospholipids whose major amounts are formed by phosphatidylserine decarboxylases (PSD). Here we provide a comprehensive description of different types of PSDs in the different kingdoms of life. In eukaryotes, type I PSDs are mitochondrial enzymes, whereas other PSDs are localized to other cellular compartments. We describe the role of mitochondrial Psd1 proteins, their function, enzymology, biogenesis, assembly into mitochondria and their contribution to phospholipid homeostasis in much detail. We also discuss briefly the cellular physiology and the enzymology of Psd2. This article is part of a Special Issue entitled: Lipids of Mitochondria edited by Guenther Daum.
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Affiliation(s)
- Francesca Di Bartolomeo
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, A-8010 Graz, Austria
| | - Ariane Wagner
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, A-8010 Graz, Austria
| | - Günther Daum
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, A-8010 Graz, Austria.
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28
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Forbes CD, Toth JG, Ozbal CC, Lamarr WA, Pendleton JA, Rocks S, Gedrich RW, Osterman DG, Landro JA, Lumb KJ. High-Throughput Mass Spectrometry Screening for Inhibitors of Phosphatidylserine Decarboxylase. ACTA ACUST UNITED AC 2016; 12:628-34. [PMID: 17478478 DOI: 10.1177/1087057107301320] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A high-throughput mass spectrometry assay to measure the catalytic activity of phosphatidylserine decarboxylase (PISD) is described. PISD converts phosphatidylserine to phosphatidylethanolamine during lipid synthesis. Traditional methods of measuring PISD activity are low throughput and unsuitable for the high-throughput screening of large compound libraries. The high-throughput mass spectrometry assay directly measures phosphatidylserine and phosphatidylethanolamine using the RapidFire™ platform at a rate of 1 sample every 7.5 s. The assay is robust, with an average Z′ value of 0.79 from a screen of 9920 compounds. Of 60 compounds selected for confirmation, 54 are active in dose-response studies. The application of high-throughput mass spectrometry permitted a high-quality screen to be performed for an otherwise intractable target. ( Journal of Biomolecular Screening 2007:628-634)
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Affiliation(s)
- Chris D Forbes
- Department of Research Technologies, Bayer Pharmaceuticals Corporation, West Haven, CT 06516, USA
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29
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Vevea JD, Garcia EJ, Chan RB, Zhou B, Schultz M, Di Paolo G, McCaffery JM, Pon LA. Role for Lipid Droplet Biogenesis and Microlipophagy in Adaptation to Lipid Imbalance in Yeast. Dev Cell 2016; 35:584-599. [PMID: 26651293 DOI: 10.1016/j.devcel.2015.11.010] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 08/14/2015] [Accepted: 11/09/2015] [Indexed: 12/22/2022]
Abstract
The immediate responses to inhibition of phosphatidylcholine (PC) biosynthesis in yeast are altered phospholipid levels, slow growth, and defects in the morphology and localization of ER and mitochondria. With chronic lipid imbalance, yeast adapt. Lipid droplet (LD) biogenesis and conversion of phospholipids to triacylglycerol are required for restoring some phospholipids to near-wild-type levels. We confirmed that the unfolded protein response is activated by this lipid stress and find that Hsp104p is recruited to ER aggregates. We also find that LDs form at ER aggregates, contain polyubiquitinated proteins and an ER chaperone, and are degraded in the vacuole by a process resembling microautophagy. This process, microlipophagy, is required for restoration of organelle morphology and cell growth during adaptation to lipid stress. Microlipophagy does not require ATG7 but does requires ESCRT components and a newly identified class E VPS protein that localizes to ER and is upregulated by lipid imbalance.
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Affiliation(s)
- Jason D Vevea
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 West 168(th) Street, New York, NY 10032, USA
| | - Enrique J Garcia
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 West 168(th) Street, New York, NY 10032, USA
| | - Robin B Chan
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 West 168(th) Street, New York, NY 10032, USA
| | - Bowen Zhou
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 West 168(th) Street, New York, NY 10032, USA
| | - Mei Schultz
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 West 168(th) Street, New York, NY 10032, USA
| | - Gilbert Di Paolo
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 West 168(th) Street, New York, NY 10032, USA
| | - J Michael McCaffery
- Integrated Imaging Center, Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Liza A Pon
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 West 168(th) Street, New York, NY 10032, USA.
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30
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Balasubramanian K, Maeda A, Lee JS, Mohammadyani D, Dar HH, Jiang JF, St Croix CM, Watkins S, Tyurin VA, Tyurina YY, Klöditz K, Polimova A, Kapralova VI, Xiong Z, Ray P, Klein-Seetharaman J, Mallampalli RK, Bayir H, Fadeel B, Kagan VE. Dichotomous roles for externalized cardiolipin in extracellular signaling: Promotion of phagocytosis and attenuation of innate immunity. Sci Signal 2015; 8:ra95. [PMID: 26396268 PMCID: PMC4760701 DOI: 10.1126/scisignal.aaa6179] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Among the distinct molecular signatures present in the mitochondrion is the tetra-acylated anionic phospholipid cardiolipin, a lipid also present in primordial, single-cell bacterial ancestors of mitochondria and multiple bacterial species today. Cardiolipin is normally localized to the inner mitochondrial membrane; however, when cardiolipin becomes externalized to the surface of dysregulated mitochondria, it promotes inflammasome activation and stimulates the elimination of damaged or nonfunctional mitochondria by mitophagy. Given the immunogenicity of mitochondrial and bacterial membranes that are released during sterile and pathogen-induced trauma, we hypothesized that cardiolipins might function as "eat me" signals for professional phagocytes. In experiments with macrophage cell lines and primary macrophages, we found that membranes with mitochondrial or bacterial cardiolipins on their surface were engulfed through phagocytosis, which depended on the scavenger receptor CD36. Distinct from this process, the copresentation of cardiolipin with the Toll-like receptor 4 (TLR4) agonist lipopolysaccharide dampened TLR4-stimulated production of cytokines. These data suggest that externalized, extracellular cardiolipins play a dual role in host-host and host-pathogen interactions by promoting phagocytosis and attenuating inflammatory immune responses.
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Affiliation(s)
- Krishnakumar Balasubramanian
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA.
| | - Akihiro Maeda
- Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Janet S Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Dariush Mohammadyani
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Haider Hussain Dar
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Jian Fei Jiang
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Claudette M St Croix
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Simon Watkins
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Vladimir A Tyurin
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Yulia Y Tyurina
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Katharina Klöditz
- Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Anastassia Polimova
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Valentyna I Kapralova
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Zeyu Xiong
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Prabir Ray
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | | | - Rama K Mallampalli
- Department of Internal Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, PA 15213, USA. Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, PA 15215, USA
| | - Hülya Bayir
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA. Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Bengt Fadeel
- Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden.
| | - Valerian E Kagan
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA.
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Choi JY, Duraisingh MT, Marti M, Ben Mamoun C, Voelker DR. From Protease to Decarboxylase: THE MOLECULAR METAMORPHOSIS OF PHOSPHATIDYLSERINE DECARBOXYLASE. J Biol Chem 2015; 290:10972-80. [PMID: 25724650 DOI: 10.1074/jbc.m115.642413] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Indexed: 12/26/2022] Open
Abstract
Phosphatidylserine decarboxylase (PSDs) play a central role in the synthesis of phosphatidylethanolamine in numerous species of prokaryotes and eukaryotes. PSDs are unusual decarboxylase containing a pyruvoyl prosthetic group within the active site. The covalently attached pyruvoyl moiety is formed in a concerted reaction when the PSD proenzyme undergoes an endoproteolytic cleavage into a large β-subunit, and a smaller α-subunit, which harbors the prosthetic group at its N terminus. The mechanism of PSD proenzyme cleavage has long been unclear. Using a coupled in vitro transcription/translation system with the soluble Plasmodium knowlesi enzyme (PkPSD), we demonstrate that the post-translational processing is inhibited by the serine protease inhibitor, phenylmethylsulfonyl fluoride. Comparison of PSD sequences across multiple phyla reveals a uniquely conserved aspartic acid within an FFXRX6RX12PXD motif, two uniquely conserved histidine residues within a PXXYHXXHXP motif, and a uniquely conserved serine residue within a GS(S/T) motif, suggesting that PSDs belong to the D-H-S serine protease family. The function of the conserved D-H-S residues was probed using site-directed mutagenesis of PkPSD. The results from these mutagenesis experiments reveal that Asp-139, His-198, and Ser-308 are all essential for endoproteolytic processing of PkPSD, which occurs in cis. In addition, within the GS(S/T) motif found in all PSDs, the Gly-307 residue is also essential, but the Ser/Thr-309 is non-essential. These results define the mechanism whereby PSDs begin their biochemical existence as proteases that execute one autoendoproteolytic cleavage reaction to give rise to a mature PSD harboring a pyruvoyl prosthetic group.
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Affiliation(s)
- Jae-Yeon Choi
- From the Department of Medicine, Basic Science Section, National Jewish Health, Denver, Colorado 80206
| | - Manoj T Duraisingh
- the Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Matthias Marti
- the Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Choukri Ben Mamoun
- the Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut 06520, and
| | - Dennis R Voelker
- From the Department of Medicine, Basic Science Section, National Jewish Health, Denver, Colorado 80206,
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32
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Kannan M, Riekhof WR, Voelker DR. Transport of Phosphatidylserine from the Endoplasmic Reticulum to the Site of Phosphatidylserine Decarboxylase2 in Yeast. Traffic 2014; 16:123-34. [DOI: 10.1111/tra.12236] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 10/17/2014] [Accepted: 10/28/2014] [Indexed: 02/03/2023]
Affiliation(s)
- Muthukumar Kannan
- Department of Medicine and Program in Cell Biology; National Jewish Health; Denver CO 80206 USA
| | - Wayne R. Riekhof
- School of Biological Sciences; University of Nebraska; Lincoln NE 68588 USA
| | - Dennis R. Voelker
- Department of Medicine and Program in Cell Biology; National Jewish Health; Denver CO 80206 USA
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33
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Paul S, Moye-Rowley WS. Multidrug resistance in fungi: regulation of transporter-encoding gene expression. Front Physiol 2014; 5:143. [PMID: 24795641 PMCID: PMC3997011 DOI: 10.3389/fphys.2014.00143] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 03/25/2014] [Indexed: 11/24/2022] Open
Abstract
A critical risk to the continued success of antifungal chemotherapy is the acquisition of resistance; a risk exacerbated by the few classes of effective antifungal drugs. Predictably, as the use of these drugs increases in the clinic, more resistant organisms can be isolated from patients. A particularly problematic form of drug resistance that routinely emerges in the major fungal pathogens is known as multidrug resistance. Multidrug resistance refers to the simultaneous acquisition of tolerance to a range of drugs via a limited or even single genetic change. This review will focus on recent progress in understanding pathways of multidrug resistance in fungi including those of most medical relevance. Analyses of multidrug resistance in Saccharomyces cerevisiae have provided the most detailed outline of multidrug resistance in a eukaryotic microorganism. Multidrug resistant isolates of S. cerevisiae typically result from changes in the activity of a pair of related transcription factors that in turn elicit overproduction of several target genes. Chief among these is the ATP-binding cassette (ABC)-encoding gene PDR5. Interestingly, in the medically important Candida species, very similar pathways are involved in acquisition of multidrug resistance. In both C. albicans and C. glabrata, changes in the activity of transcriptional activator proteins elicits overproduction of a protein closely related to S. cerevisiae Pdr5 called Cdr1. The major filamentous fungal pathogen, Aspergillus fumigatus, was previously thought to acquire resistance to azole compounds (the principal antifungal drug class) via alterations in the azole drug target-encoding gene cyp51A. More recent data indicate that pathways in addition to changes in the cyp51A gene are important determinants in A. fumigatus azole resistance. We will discuss findings that suggest azole resistance in A. fumigatus and Candida species may share more mechanistic similarities than previously thought.
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Affiliation(s)
- Sanjoy Paul
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa Iowa City, IA, USA
| | - W Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa Iowa City, IA, USA
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34
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Klug L, Daum G. Yeast lipid metabolism at a glance. FEMS Yeast Res 2014; 14:369-88. [DOI: 10.1111/1567-1364.12141] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/23/2014] [Accepted: 02/02/2014] [Indexed: 01/07/2023] Open
Affiliation(s)
- Lisa Klug
- Institute of Biochemistry; Graz University of Technology; Graz Austria
| | - Günther Daum
- Institute of Biochemistry; Graz University of Technology; Graz Austria
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35
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Horvath SE, Daum G. Lipids of mitochondria. Prog Lipid Res 2013; 52:590-614. [PMID: 24007978 DOI: 10.1016/j.plipres.2013.07.002] [Citation(s) in RCA: 613] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 07/31/2013] [Indexed: 01/06/2023]
Abstract
A unique organelle for studying membrane biochemistry is the mitochondrion whose functionality depends on a coordinated supply of proteins and lipids. Mitochondria are capable of synthesizing several lipids autonomously such as phosphatidylglycerol, cardiolipin and in part phosphatidylethanolamine, phosphatidic acid and CDP-diacylglycerol. Other mitochondrial membrane lipids such as phosphatidylcholine, phosphatidylserine, phosphatidylinositol, sterols and sphingolipids have to be imported. The mitochondrial lipid composition, the biosynthesis and the import of mitochondrial lipids as well as the regulation of these processes will be main issues of this review article. Furthermore, interactions of lipids and mitochondrial proteins which are highly important for various mitochondrial processes will be discussed. Malfunction or loss of enzymes involved in mitochondrial phospholipid biosynthesis lead to dysfunction of cell respiration, affect the assembly and stability of the mitochondrial protein import machinery and cause abnormal mitochondrial morphology or even lethality. Molecular aspects of these processes as well as diseases related to defects in the formation of mitochondrial membranes will be described.
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Affiliation(s)
- Susanne E Horvath
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, A-8010 Graz, Austria
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36
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Dowhan W. A retrospective: use of Escherichia coli as a vehicle to study phospholipid synthesis and function. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1831:471-94. [PMID: 22925633 PMCID: PMC3513495 DOI: 10.1016/j.bbalip.2012.08.007] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 08/07/2012] [Accepted: 08/07/2012] [Indexed: 12/11/2022]
Abstract
Although the study of individual phospholipids and their synthesis began in the 1920s first in plants and then mammals, it was not until the early 1960s that Eugene Kennedy using Escherichia coli initiated studies of bacterial phospholipid metabolism. With the base of information already available from studies of mammalian tissue, the basic blueprint of phospholipid biosynthesis in E. coli was worked out by the late 1960s. In 1970s and 1980s most of the enzymes responsible for phospholipid biosynthesis were purified and many of the genes encoding these enzymes were identified. By the late 1990s conditional and null mutants were available along with clones of the genes for every step of phospholipid biosynthesis. Most of these genes had been sequenced before the complete E. coli genome sequence was available. Strains of E. coli were developed in which phospholipid composition could be changed in a systematic manner while maintaining cell viability. Null mutants, strains in which phospholipid metabolism was artificially regulated, and strains synthesizing foreign lipids not found in E. coli have been used to this day to define specific roles for individual phospholipid. This review will trace the findings that have led to the development of E. coli as an excellent model system to study mechanisms underlying the synthesis and function of phospholipids that are widely applicable to other prokaryotic and eukaryotic systems. This article is part of a Special Issue entitled Phospholipids and Phospholipid Metabolism.
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Affiliation(s)
- William Dowhan
- Department of Biochemistry and Molecular Biology, University of Texas Medical School-Houston, Houston, TX 77030, USA.
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37
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Kainu V, Hermansson M, Hänninen S, Hokynar K, Somerharju P. Import of phosphatidylserine to and export of phosphatidylethanolamine molecular species from mitochondria. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1831:429-37. [DOI: 10.1016/j.bbalip.2012.11.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 10/24/2012] [Accepted: 11/08/2012] [Indexed: 12/16/2022]
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38
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Horvath SE, Böttinger L, Vögtle FN, Wiedemann N, Meisinger C, Becker T, Daum G. Processing and topology of the yeast mitochondrial phosphatidylserine decarboxylase 1. J Biol Chem 2012; 287:36744-55. [PMID: 22984266 PMCID: PMC3481278 DOI: 10.1074/jbc.m112.398107] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 09/04/2012] [Indexed: 11/06/2022] Open
Abstract
The inner mitochondrial membrane plays a crucial role in cellular lipid homeostasis through biosynthesis of the non-bilayer-forming lipids phosphatidylethanolamine and cardiolipin. In the yeast Saccharomyces cerevisiae, the majority of cellular phosphatidylethanolamine is synthesized by the mitochondrial phosphatidylserine decarboxylase 1 (Psd1). The biogenesis of Psd1 involves several processing steps. It was speculated that the Psd1 precursor is sorted into the inner membrane and is subsequently released into the intermembrane space by proteolytic removal of a hydrophobic sorting signal. However, components involved in the maturation of the Psd1 precursor have not been identified. We show that processing of Psd1 involves the action of the mitochondrial processing peptidase and Oct1 and an autocatalytic cleavage at a highly conserved LGST motif yielding the α- and β-subunit of the enzyme. The Psd1 β-subunit (Psd1β) forms the membrane anchor, which binds the intermembrane space-localized α-subunit (Psd1α). Deletion of a transmembrane segment in the β-subunit results in mislocalization of Psd1 and reduced enzymatic activity. Surprisingly, autocatalytic cleavage does not depend on proper localization to the inner mitochondrial membrane. In summary, membrane integration of Psd1 is crucial for its functionality and for maintenance of mitochondrial lipid homeostasis.
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Affiliation(s)
- Susanne E. Horvath
- From the Institut für Biochemie, Technische Universität Graz, Petersgasse 12/2, A-8010 Graz, Austria
- the Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, D-79104 Freiburg, Germany
| | - Lena Böttinger
- the Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, D-79104 Freiburg, Germany
- the Fakultät für Biologie, Universität Freiburg, D-79104 Freiburg, Germany, and
| | - F.-Nora Vögtle
- the Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, D-79104 Freiburg, Germany
- the BIOSS Centre for Biological Signalling Studies, Universität Freiburg, D-79104 Freiburg, Germany
| | - Nils Wiedemann
- the Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, D-79104 Freiburg, Germany
- the BIOSS Centre for Biological Signalling Studies, Universität Freiburg, D-79104 Freiburg, Germany
| | - Chris Meisinger
- the Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, D-79104 Freiburg, Germany
- the BIOSS Centre for Biological Signalling Studies, Universität Freiburg, D-79104 Freiburg, Germany
| | - Thomas Becker
- the Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, D-79104 Freiburg, Germany
- the BIOSS Centre for Biological Signalling Studies, Universität Freiburg, D-79104 Freiburg, Germany
| | - Günther Daum
- From the Institut für Biochemie, Technische Universität Graz, Petersgasse 12/2, A-8010 Graz, Austria
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39
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Vance JE, Tasseva G. Formation and function of phosphatidylserine and phosphatidylethanolamine in mammalian cells. Biochim Biophys Acta Mol Cell Biol Lipids 2012; 1831:543-54. [PMID: 22960354 DOI: 10.1016/j.bbalip.2012.08.016] [Citation(s) in RCA: 382] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 08/20/2012] [Accepted: 08/21/2012] [Indexed: 12/16/2022]
Abstract
Phosphatidylserine (PS) and phosphatidylethanolamine (PE) are metabolically related membrane aminophospholipids. In mammalian cells, PS is required for targeting and function of several intracellular signaling proteins. Moreover, PS is asymmetrically distributed in the plasma membrane. Although PS is highly enriched in the cytoplasmic leaflet of plasma membranes, PS exposure on the cell surface initiates blood clotting and removal of apoptotic cells. PS is synthesized in mammalian cells by two distinct PS synthases that exchange serine for choline or ethanolamine in phosphatidylcholine (PC) or PE, respectively. Targeted disruption of each PS synthase individually in mice demonstrated that neither enzyme is required for viability whereas elimination of both synthases was embryonic lethal. Thus, mammalian cells require a threshold amount of PS. PE is synthesized in mammalian cells by four different pathways, the quantitatively most important of which are the CDP-ethanolamine pathway that produces PE in the ER, and PS decarboxylation that occurs in mitochondria. PS is made in ER membranes and is imported into mitochondria for decarboxylation to PE via a domain of the ER [mitochondria-associated membranes (MAM)] that transiently associates with mitochondria. Elimination of PS decarboxylase in mice caused mitochondrial defects and embryonic lethality. Global elimination of the CDP-ethanolamine pathway was also incompatible with mouse survival. Thus, PE made by each of these pathways has independent and necessary functions. In mammals PE is a substrate for methylation to PC in the liver, a substrate for anandamide synthesis, and supplies ethanolamine for glycosylphosphatidylinositol anchors of cell-surface signaling proteins. Thus, PS and PE participate in many previously unanticipated facets of mammalian cell biology. This article is part of a Special Issue entitled Phospholipids and Phospholipid Metabolism.
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Affiliation(s)
- Jean E Vance
- Group on the Molecular and Cell Biology of Lipids and the Department of Medicine, University of Alberta, Edmonton, Canada AB T6G 2S2.
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40
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Gupta N, Hartmann A, Lucius R, Voelker DR. The obligate intracellular parasite Toxoplasma gondii secretes a soluble phosphatidylserine decarboxylase. J Biol Chem 2012; 287:22938-47. [PMID: 22563079 DOI: 10.1074/jbc.m112.373639] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Toxoplasma gondii is an obligate intracellular parasite capable of causing fatal infections in immunocompromised individuals and neonates. Examination of the phosphatidylserine (PtdSer) metabolism of T. gondii reveals that the parasite secretes a soluble form of PtdSer decarboxylase (TgPSD1), which preferentially decarboxylates liposomal PtdSer with an apparent K(m) of 67 μM. The specific enzyme activity increases by 3-fold during the replication of T. gondii, and soluble phosphatidylserine decarboxylase (PSD) accounts for ∼20% of the total PSD, prior to the parasite egress from the host cells. Extracellular T. gondii secreted ∼20% of its total PSD activity at 37 °C, and the intracellular Ca(2+) chelator 1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid tetrakis (acetoxymethyl ester) inhibited the process by 50%. Cycloheximide, brefeldin A, ionic composition of the medium, and exogenous PtdSer did not modulate the enzyme secretion, which suggests a constitutive discharge of a presynthesized pool of PSD in axenic T. gondii. TgPSD1 consists of 968 amino acids with a 26-amino acid hydrophobic peptide at the N terminus and no predicted membrane domains. Parasites overexpressing TgPSD1-HA secreted 10-fold more activity compared with the parental strain. Exposure of apoptotic Jurkat cells to transgenic parasites demonstrated interfacial catalysis by secreted TgPSD1 that reduced host cell surface exposure of PtdSer. Immunolocalization experiments revealed that TgPSD1 resides in the dense granules of T. gondii and is also found in the parasitophorous vacuole of replicating parasites. Together, these findings demonstrate novel features of the parasite enzyme because a secreted, soluble, and interfacially active form of PSD has not been previously described for any organism.
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Affiliation(s)
- Nishith Gupta
- Department of Medicine, National Jewish Health, Denver, Colorado 80206, USA.
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41
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Michel S, Wanet A, De Pauw A, Rommelaere G, Arnould T, Renard P. Crosstalk between mitochondrial (dys)function and mitochondrial abundance. J Cell Physiol 2012; 227:2297-310. [PMID: 21928343 DOI: 10.1002/jcp.23021] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A controlled regulation of mitochondrial mass through either the production (biogenesis) or the degradation (mitochondrial quality control) of the organelle represents a crucial step for proper mitochondrial and cell function. Key steps of mitochondrial biogenesis and quality control are overviewed, with an emphasis on the role of mitochondrial chaperones and proteases that keep mitochondria fully functional, provided the mitochondrial activity impairment is not excessive. In this case, the whole organelle is degraded by mitochondrial autophagy or "mitophagy." Beside the maintenance of adequate mitochondrial abundance and functions for cell homeostasis, mitochondrial biogenesis might be enhanced, through discussed signaling pathways, in response to various physiological stimuli, like contractile activity, exposure to low temperatures, caloric restriction, and stem cells differentiation. In addition, mitochondrial dysfunction might also initiate a retrograde response, enabling cell adaptation through increased mitochondrial biogenesis.
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Affiliation(s)
- Sébastien Michel
- Laboratory of Biochemistry and Cell Biology (URBC), NARILIS (Namur Research Institute for Life Sciences), University of Namur (FUNDP), Namur, Belgium
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42
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Nguyen TT, Lewandowska A, Choi JY, Markgraf DF, Junker M, Bilgin M, Ejsing CS, Voelker DR, Rapoport TA, Shaw JM. Gem1 and ERMES do not directly affect phosphatidylserine transport from ER to mitochondria or mitochondrial inheritance. Traffic 2012; 13:880-90. [PMID: 22409400 PMCID: PMC3648210 DOI: 10.1111/j.1600-0854.2012.01352.x] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 03/08/2012] [Accepted: 03/12/2012] [Indexed: 11/27/2022]
Abstract
In yeast, a protein complex termed the ER-Mitochondria Encounter Structure (ERMES) tethers mitochondria to the endoplasmic reticulum. ERMES proteins are implicated in a variety of cellular functions including phospholipid synthesis, mitochondrial protein import, mitochondrial attachment to actin, polarized mitochondrial movement into daughter cells during division, and maintenance of mitochondrial DNA (mtDNA). The mitochondrial-anchored Gem1 GTPase has been proposed to regulate ERMES functions. Here, we show that ERMES and Gem1 have no direct role in the transport of phosphatidylserine (PS) from the ER to mitochondria during the synthesis of phosphatidylethanolamine (PE), as PS to PE conversion is not affected in ERMES or gem1 mutants. In addition, we report that mitochondrial inheritance defects in ERMES mutants are a secondary consequence of mitochondrial morphology defects, arguing against a primary role for ERMES in mitochondrial association with actin and mitochondrial movement. Finally, we show that ERMES complexes are long-lived, and do not depend on the presence of Gem1. Our findings suggest that the ERMES complex may have primarily a structural role in maintaining mitochondrial morphology.
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Affiliation(s)
- Tammy T Nguyen
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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43
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Arabidopsis serine decarboxylase mutants implicate the roles of ethanolamine in plant growth and development. Int J Mol Sci 2012; 13:3176-3188. [PMID: 22489147 PMCID: PMC3317708 DOI: 10.3390/ijms13033176] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 02/20/2012] [Accepted: 03/01/2012] [Indexed: 02/02/2023] Open
Abstract
Ethanolamine is important for synthesis of choline, phosphatidylethanolamine (PE) and phosphatidylcholine (PC) in plants. The latter two phospholipids are the major phospholipids in eukaryotic membranes. In plants, ethanolamine is mainly synthesized directly from serine by serine decarboxylase. Serine decarboxylase is unique to plants and was previously shown to have highly specific activity to l-serine. While serine decarboxylase was biochemically characterized, its functions and importance in plants were not biologically elucidated due to the lack of serine decarboxylase mutants. Here we characterized an Arabidopsis mutant defective in serine decarboxylase, named atsdc-1 (Arabidopsis thaliana serine decarboxylase-1). The atsdc-1 mutants showed necrotic lesions in leaves, multiple inflorescences, sterility in flower, and early flowering in short day conditions. These defects were rescued by ethanolamine application to atsdc-1, suggesting the roles of ethanolamine as well as serine decarboxylase in plant development. In addition, molecular analysis of serine decarboxylase suggests that Arabidopsis serine decarboxylase is cytosol-localized and expressed in all tissue.
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44
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Pereira L, Girardi JP, Bakovic M. Forms, crosstalks, and the role of phospholipid biosynthesis in autophagy. Int J Cell Biol 2012; 2012:931956. [PMID: 22291708 PMCID: PMC3265067 DOI: 10.1155/2012/931956] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 10/04/2011] [Accepted: 10/13/2011] [Indexed: 12/30/2022] Open
Abstract
Autophagy is a highly conserved cellular process occurring during periods of stress to ensure a cell's survival by recycling cytosolic constituents and making products that can be used in energy generation and other essential processes. Three major forms of autophagy exist according to the specific mechanism through which cytoplasmic material is transported to a lysosome. Chaperone-mediated autophagy is a highly selective form of autophagy that delivers specific proteins for lysosomal degradation. Microautophagy is a less selective form of autophagy that occurs through lysosomal membrane invaginations, forming tubes and directly engulfing cytoplasm. Finally, macroautophagy involves formation of new membrane bilayers (autophagosomes) that engulf cytosolic material and deliver it to lysosomes. This review provides new insights on the crosstalks between different forms of autophagy and the significance of bilayer-forming phospholipid synthesis in autophagosomal membrane formation.
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Affiliation(s)
- Leanne Pereira
- Department of Human Health and Nutritional Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
| | - John Paul Girardi
- Department of Human Health and Nutritional Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
| | - Marica Bakovic
- Department of Human Health and Nutritional Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
- Department of Human Health and Nutritional Sciences, University of Guelph, Animal Science and Nutrition Building, Room 346, Guelph, ON, Canada N1G 2W1
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Dresler J, Klimentova J, Stulik J. Francisella tularensis membrane complexome by blue native/SDS-PAGE. J Proteomics 2011; 75:257-69. [DOI: 10.1016/j.jprot.2011.05.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 03/09/2011] [Accepted: 05/03/2011] [Indexed: 12/11/2022]
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Choi JY, Augagneur Y, Mamoun CB, Voelker DR. Identification of gene encoding Plasmodium knowlesi phosphatidylserine decarboxylase by genetic complementation in yeast and characterization of in vitro maturation of encoded enzyme. J Biol Chem 2011; 287:222-232. [PMID: 22057268 DOI: 10.1074/jbc.m111.313676] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 23-megabase genome of Plasmodium falciparum, the causative agent of severe human malaria, contains ∼5300 genes, most of unknown function or lacking homologs in other organisms. Identification of these gene functions will help in the discovery of novel targets for the development of antimalarial drugs and vaccines. The P. falciparum genome is unusually A+T-rich, which hampers cloning and expressing these genes in heterologous systems for functional analysis. The large repertoire of genetic tools available for Saccharomyces cerevisiae makes this yeast an ideal system for large scale functional complementation analyses of parasite genes. Here, we report the construction of a cDNA library from P. knowlesi, which has a lower A+T content compared with P. falciparum. This library was applied in a yeast complementation assay to identify malaria genes involved in the decarboxylation of phosphatidylserine. Transformation of a psd1Δpsd2Δdpl1Δ yeast strain, defective in phosphatidylethanolamine synthesis, with the P. knowlesi library led to identification of a new parasite phosphatidylserine decarboxylase (PkPSD). Unlike phosphatidylserine decarboxylase enzymes from other eukaryotes that are tightly associated with membranes, the PkPSD enzyme expressed in yeast was equally distributed between membrane and soluble fractions. In vitro studies reveal that truncated forms of PkPSD are soluble and undergo auto-endoproteolytic maturation in a phosphatidylserine-dependent reaction that is inhibited by other anionic phospholipids. This study defines a new system for probing the function of Plasmodium genes by library-based genetic complementation and its usefulness in revealing new biochemical properties of encoded proteins.
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Affiliation(s)
- Jae-Yeon Choi
- Basic Science Section, Department of Medicine, National Jewish Health, Denver, Colorado 80206
| | - Yoann Augagneur
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Choukri Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Dennis R Voelker
- Basic Science Section, Department of Medicine, National Jewish Health, Denver, Colorado 80206.
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Xia J, Jones AD, Lau MW, Yuan YJ, Dale BE, Balan V. Comparative lipidomic profiling of xylose-metabolizing S. cerevisiae and its parental strain in different media reveals correlations between membrane lipids and fermentation capacity. Biotechnol Bioeng 2010; 108:12-21. [DOI: 10.1002/bit.22910] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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48
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Lipid metabolism in Trypanosoma brucei. Mol Biochem Parasitol 2010; 172:66-79. [PMID: 20382188 DOI: 10.1016/j.molbiopara.2010.04.001] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Revised: 03/31/2010] [Accepted: 04/01/2010] [Indexed: 11/28/2022]
Abstract
Trypanosoma brucei membranes consist of all major eukaryotic glycerophospholipid and sphingolipid classes. These are de novo synthesized from precursors obtained either from the host or from catabolised endocytosed lipids. In recent years, substantial progress has been made in the molecular and biochemical characterisation of several of these lipid biosynthetic pathways, using gene knockout or RNA interference strategies or by enzymatic characterization of individual reactions. Together with the completed genome, these studies have highlighted several possible differences between mammalian and trypanosome lipid biosynthesis that could be exploited for the development of drugs against the diseases caused by these parasites.
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Kim HY, Akbar M, Kim YS. Phosphatidylserine-dependent neuroprotective signaling promoted by docosahexaenoic acid. Prostaglandins Leukot Essent Fatty Acids 2010; 82:165-72. [PMID: 20207120 PMCID: PMC3383770 DOI: 10.1016/j.plefa.2010.02.025] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Enrichment of polyunsaturated fatty acids, particularly docosahexaenoic acid (DHA, 22:6n-3), in the brain is known to be critical for optimal brain development and function. Mechanisms for DHA's beneficial effects in the nervous system are not clearly understood at present. DHA is incorporated into the phospholipids in neuronal membranes, which in turn can influence not only the membrane chemical and physical properties but also the cell signaling involved in neuronal survival, proliferation and differentiation. Our studies have indicated that DHA supplementation promotes phosphatidylserine (PS) accumulation and inhibits neuronal cell death under challenged conditions, supporting a notion that DHA is an important neuroprotective agent. This article summarizes our findings on the DHA-mediated membrane-related signaling mechanisms that might explain some of the beneficial effects of DHA, particularly on neuronal survival.
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Affiliation(s)
- Hee-Yong Kim
- Laboratory of Molecular Signaling, NIAAA, NIH, Bethesda, MD 20892-9410, USA.
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Chen YL, Montedonico AE, Kauffman S, Dunlap JR, Menn FM, Reynolds TB. Phosphatidylserine synthase and phosphatidylserine decarboxylase are essential for cell wall integrity and virulence in Candida albicans. Mol Microbiol 2010; 75:1112-32. [PMID: 20132453 DOI: 10.1111/j.1365-2958.2009.07018.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phospholipid biosynthetic pathways play crucial roles in the virulence of several pathogens; however, little is known about how phospholipid synthesis affects pathogenesis in fungi such as Candida albicans. A C. albicans phosphatidylserine (PS) synthase mutant, cho1 Delta/Delta, lacks PS, has decreased phosphatidylethanolamine (PE), and is avirulent in a mouse model of systemic candidiasis. The cho1 Delta/Delta mutant exhibits defects in cell wall integrity, mitochondrial function, filamentous growth, and is auxotrophic for ethanolamine. PS is a precursor for de novo PE biosynthesis. A psd1 Delta/Delta psd2 Delta/Delta double mutant, which lacks the PS decarboxylase enzymes that convert PS to PE in the de novo pathway, has diminished PE levels like those of the cho1 Delta/Delta mutant. The psd1 Delta/Delta psd2 Delta/Delta mutant exhibits phenotypes similar to those of the cho1 Delta/Delta mutant; however, it is slightly more virulent and has less of a cell wall defect. The virulence losses exhibited by the cho1 Delta/Delta and psd1 Delta/Delta psd2 Delta/Delta mutants appear to be related to their cell wall defects which are due to loss of de novo PE biosynthesis, but are exacerbated by loss of PS itself. Cho1p is conserved in fungi, but not mammals, so fungal PS synthase is a potential novel antifungal drug target.
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Affiliation(s)
- Ying-Lien Chen
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
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