1
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Sosa Ponce ML, Remedios MH, Moradi-Fard S, Cobb JA, Zaremberg V. SIR telomere silencing depends on nuclear envelope lipids and modulates sensitivity to a lysolipid. J Cell Biol 2023; 222:e202206061. [PMID: 37042812 PMCID: PMC10103788 DOI: 10.1083/jcb.202206061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/29/2022] [Accepted: 03/24/2023] [Indexed: 04/13/2023] Open
Abstract
The nuclear envelope (NE) is important in maintaining genome organization. The role of lipids in communication between the NE and telomere regulation was investigated, including how changes in lipid composition impact gene expression and overall nuclear architecture. Yeast was treated with the non-metabolizable lysophosphatidylcholine analog edelfosine, known to accumulate at the perinuclear ER. Edelfosine induced NE deformation and disrupted telomere clustering but not anchoring. Additionally, the association of Sir4 at telomeres decreased. RNA-seq analysis showed altered expression of Sir-dependent genes located at sub-telomeric (0-10 kb) regions, consistent with Sir4 dispersion. Transcriptomic analysis revealed that two lipid metabolic circuits were activated in response to edelfosine, one mediated by the membrane sensing transcription factors, Spt23/Mga2, and the other by a transcriptional repressor, Opi1. Activation of these transcriptional programs resulted in higher levels of unsaturated fatty acids and the formation of nuclear lipid droplets. Interestingly, cells lacking Sir proteins displayed resistance to unsaturated-fatty acids and edelfosine, and this phenotype was connected to Rap1.
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Affiliation(s)
| | | | - Sarah Moradi-Fard
- Departments of Biochemistry and Molecular Biology and Oncology, Cumming School of Medicine, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Calgary, Canada
| | - Jennifer A. Cobb
- Departments of Biochemistry and Molecular Biology and Oncology, Cumming School of Medicine, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Calgary, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| | - Vanina Zaremberg
- Department of Biological Sciences, University of Calgary, Calgary, Canada
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2
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Abstract
Sphingolipid biosynthesis occurs in both the endoplasmic reticulum (ER) and the Golgi apparatus. Ceramide synthesized in the ER is transported to the Golgi and incorporated into complex sphingolipids. Here, we present a step-by-step protocol to analyze sphingolipid metabolism in budding yeast. Ceramide and inositolphosphorylceramide (IPC) are classes of sphingolipids present in yeast and are metabolically labeled with radioactive precursors. This protocol for metabolic labeling can be used to investigate ceramide transport in an in vivo environment. For complete details on the use and execution of this protocol, please refer to Ikeda et al. (2020). A step-by-step procedure for analyzing sphingolipid metabolism in budding yeast Quantification and statistical analysis of sphingolipid metabolism assay data The protocol can be applied to other cells synthesizing inositol-containing sphingolipids
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Affiliation(s)
- Atsuko Ikeda
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| | - Kazuki Hanaoka
- School of Applied Biological Science, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| | - Kouichi Funato
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan.,School of Applied Biological Science, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
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3
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Okai H, Ikema R, Nakamura H, Kato M, Araki M, Mizuno A, Ikeda A, Renbaum P, Segel R, Funato K. Cold‐sensitive phenotypes of a yeast null mutant of ARV1 support its role as a GPI flippase. FEBS Lett 2020; 594:2431-2439. [DOI: 10.1002/1873-3468.13843] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/11/2020] [Accepted: 05/11/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Haruka Okai
- School of Applied Biological Science Hiroshima University Higashi‐Hiroshima Japan
| | - Ryoko Ikema
- Graduate School of Integrated Sciences for Life Hiroshima University Higashi‐Hiroshima Japan
| | - Hiroki Nakamura
- Graduate School of Biosphere Science Hiroshima University Higashi‐Hiroshima Japan
| | - Mei Kato
- Graduate School of Integrated Sciences for Life Hiroshima University Higashi‐Hiroshima Japan
| | - Misako Araki
- Graduate School of Integrated Sciences for Life Hiroshima University Higashi‐Hiroshima Japan
| | - Ayumi Mizuno
- School of Applied Biological Science Hiroshima University Higashi‐Hiroshima Japan
| | - Atsuko Ikeda
- Graduate School of Biosphere Science Hiroshima University Higashi‐Hiroshima Japan
| | - Paul Renbaum
- Medical Genetics Institute Shaare Zedek Medical Center Jerusalem Israel
| | - Reeval Segel
- Medical Genetics Institute Shaare Zedek Medical Center Jerusalem Israel
| | - Kouichi Funato
- School of Applied Biological Science Hiroshima University Higashi‐Hiroshima Japan
- Graduate School of Integrated Sciences for Life Hiroshima University Higashi‐Hiroshima Japan
- Graduate School of Biosphere Science Hiroshima University Higashi‐Hiroshima Japan
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4
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A defect in GPI synthesis as a suggested mechanism for the role of ARV1 in intellectual disability and seizures. Neurogenetics 2020; 21:259-267. [DOI: 10.1007/s10048-020-00615-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/05/2020] [Indexed: 01/05/2023]
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5
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Sosa Ponce ML, Moradi-Fard S, Zaremberg V, Cobb JA. SUNny Ways: The Role of the SUN-Domain Protein Mps3 Bridging Yeast Nuclear Organization and Lipid Homeostasis. Front Genet 2020; 11:136. [PMID: 32184804 PMCID: PMC7058695 DOI: 10.3389/fgene.2020.00136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/04/2020] [Indexed: 12/14/2022] Open
Abstract
Mps3 is a SUN (Sad1-UNC-84) domain-containing protein that is located in the inner nuclear membrane (INM). Genetic screens with multiple Mps3 mutants have suggested that distinct regions of Mps3 function in relative isolation and underscore the broad involvement of Mps3 in multiple pathways including mitotic spindle formation, telomere maintenance, and lipid metabolism. These pathways have largely been characterized in isolation, without a holistic consideration for how key regulatory events within one pathway might impinge on other aspects of biology at the nuclear membrane. Mps3 is uniquely positioned to function in these multiple pathways as its N- terminus is in the nucleoplasm, where it is important for telomere anchoring at the nuclear periphery, and its C-terminus is in the lumen, where it has links with lipid metabolic processes. Emerging work suggests that the role of Mps3 in nuclear organization and lipid homeostasis are not independent, but more connected. For example, a failure in regulating Mps3 levels through the cell cycle leads to nuclear morphological abnormalities and loss of viability, suggesting a link between the N-terminal domain of Mps3 and nuclear envelope homeostasis. We will highlight work suggesting that Mps3 is pivotal factor in communicating events between the nucleus and the lipid bilayer.
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Affiliation(s)
- Maria Laura Sosa Ponce
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, Calgary, AB, Canada.,Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Sarah Moradi-Fard
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, Calgary, AB, Canada
| | - Vanina Zaremberg
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jennifer A Cobb
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, Calgary, AB, Canada
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6
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Sphingolipid/Pkh1/2-TORC1/Sch9 Signaling Regulates Ribosome Biogenesis in Tunicamycin-Induced Stress Response in Yeast. Genetics 2019; 212:175-186. [PMID: 30824472 DOI: 10.1534/genetics.118.301874] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/26/2019] [Indexed: 12/26/2022] Open
Abstract
Reduced ribosome biogenesis in response to environmental conditions is a key feature of cell adaptation to stress. For example, ribosomal genes are transcriptionally repressed when cells are exposed to tunicamycin, a protein glycosylation inhibitor that induces endoplasmic reticulum stress and blocks vesicular trafficking in the secretory pathway. Here, we describe a novel regulatory model, in which tunicamycin-mediated stress induces the accumulation of long-chain sphingoid bases and subsequent activation of Pkh1/2 signaling, which leads to decreased expression of ribosomal protein genes via the downstream effectors Pkc1 and Sch9. Target of rapamycin complex 1 (TORC1), an upstream activator of Sch9, is also required. This pathway links ribosome biogenesis to alterations in membrane lipid composition under tunicamycin-induced stress conditions. Our results suggest that sphingolipid/Pkh1/2-TORC1/Sch9 signaling is an important determinant for adaptation to tunicamycin-induced stress.
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7
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He Y, Zhang W, Peng F, Lu R, Zhou H, Bao G, Wang B, Huang B, Li Z, Hu F. Metabolomic variation in wild and cultured cordyceps and mycelia of Isaria cicadae. Biomed Chromatogr 2019; 33:e4478. [PMID: 30578653 DOI: 10.1002/bmc.4478] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/27/2018] [Accepted: 12/03/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Yaqiong He
- Anhui Agricultural University; Hefei China
| | - Wancun Zhang
- Children's Hospital Affiliaten of Zhengzhou University; Zhengzhou China
| | - Fan Peng
- Anhui Agricultural University; Hefei China
| | - Ruili Lu
- Anhui Agricultural University; Hefei China
| | - Hong Zhou
- Naval Postgraduate School; Monterey CA USA
| | - Guanhu Bao
- Anhui Agricultural University; Hefei China
| | - Bin Wang
- Anhui Agricultural University; Hefei China
| | - Bo Huang
- Anhui Agricultural University; Hefei China
| | - Zengzhi Li
- Anhui Agricultural University; Hefei China
| | - Fenglin Hu
- Anhui Agricultural University; Hefei China
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8
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Villasmil ML, Francisco J, Gallo-Ebert C, Donigan M, Liu HY, Brower M, Nickels JT. Ceramide signals for initiation of yeast mating-specific cell cycle arrest. Cell Cycle 2016; 15:441-54. [PMID: 26726837 DOI: 10.1080/15384101.2015.1127475] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Sphingolipids are major constituents of membranes. A number of S. cerevisiae sphingolipid intermediates such as long chains sphingoid bases (LCBs) and ceramides act as signaling molecules regulating cell cycle progression, adaptability to heat stress, and survival in response to starvation. Here we show that S. cerevisiae haploid cells must synthesize ceramide in order to induce mating specific cell cycle arrest. Cells devoid of sphingolipid biosynthesis or defective in ceramide synthesis are sterile and harbor defects in pheromone-induced MAP kinase-dependent transcription. Analyses of G1/S cyclin levels indicate that mutant cells cannot reduce Cln1/2 levels in response to pheromone. FACS analysis indicates a lack of ability to arrest. The addition of LCBs to sphingolipid deficient cells restores MAP kinase-dependent transcription, reduces cyclin levels, and allows for mating, as does the addition of a cell permeable ceramide to cells blocked at ceramide synthesis. Pharmacological studies using the inositolphosphorylceramide synthase inhibitor aureobasidin A indicate that the ability to synthesize and accumulate ceramide alone is sufficient for cell cycle arrest and mating. Studies indicate that ceramide also has a role in PI(4,5)P2 polarization during mating, an event necessary for initiating cell cycle arrest and mating itself. Moreover, our studies suggest a third role for ceramide in localizing the mating-specific Ste5 scaffold to the plasma membrane. Thus, ceramide plays a role 1) in pheromone-induced cell cycle arrest, 2) in activation of MAP kinase-dependent transcription, and 3) in PtdIns(4,5)P2 polarization. All three events are required for differentiation during yeast mating.
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Affiliation(s)
- Michelle L Villasmil
- a The Institute of Metabolic Disorders, Genesis Biotechnology Group , Hamilton , NJ , USA.,b Cato Research Ltd. , Durham , NC , USA
| | - Jamie Francisco
- a The Institute of Metabolic Disorders, Genesis Biotechnology Group , Hamilton , NJ , USA
| | - Christina Gallo-Ebert
- a The Institute of Metabolic Disorders, Genesis Biotechnology Group , Hamilton , NJ , USA
| | - Melissa Donigan
- a The Institute of Metabolic Disorders, Genesis Biotechnology Group , Hamilton , NJ , USA
| | - Hsing-Yin Liu
- a The Institute of Metabolic Disorders, Genesis Biotechnology Group , Hamilton , NJ , USA
| | - Melody Brower
- a The Institute of Metabolic Disorders, Genesis Biotechnology Group , Hamilton , NJ , USA.,c Synthes, Inc , Paoli , PA , USA
| | - Joseph T Nickels
- a The Institute of Metabolic Disorders, Genesis Biotechnology Group , Hamilton , NJ , USA
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9
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Murakami S, Shimamoto T, Nagano H, Tsuruno M, Okuhara H, Hatanaka H, Tojo H, Kodama Y, Funato K. Producing human ceramide-NS by metabolic engineering using yeast Saccharomyces cerevisiae. Sci Rep 2015; 5:16319. [PMID: 26573460 PMCID: PMC4647206 DOI: 10.1038/srep16319] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/12/2015] [Indexed: 12/24/2022] Open
Abstract
Ceramide is one of the most important intercellular components responsible for the barrier and moisture retention functions of the skin. Because of the risks involved with using products of animal origin and the low productivity of plants, the availability of ceramides is currently limited. In this study, we successfully developed a system that produces sphingosine-containing human ceramide-NS in the yeast Saccharomyces cerevisiae by eliminating the genes for yeast sphingolipid hydroxylases (encoded by SUR2 and SCS7) and introducing the gene for a human sphingolipid desaturase (encoded by DES1). The inactivation of the ceramidase gene YDC1, overexpression of the inositol phosphosphingolipid phospholipase C gene ISC1, and endoplasmic reticulum localization of the DES1 gene product resulted in enhanced production of ceramide-NS. The engineered yeast strains can serve as hosts not only for providing a sustainable source of ceramide-NS but also for developing further systems to produce sphingosine-containing sphingolipids.
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Affiliation(s)
- Suguru Murakami
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima, 739-8528, Japan
| | - Toshi Shimamoto
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima, 739-8528, Japan
| | | | - Masahiro Tsuruno
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima, 739-8528, Japan
| | | | | | - Hiromasa Tojo
- Department of Biophysics and Biochemistry, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Yukiko Kodama
- Suntory World Research Center, Kyoto 619-0284, Japan
| | - Kouichi Funato
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima, 739-8528, Japan
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10
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Ikeda A, Kajiwara K, Iwamoto K, Makino A, Kobayashi T, Mizuta K, Funato K. Complementation analysis reveals a potential role of human ARV1 in GPI anchor biosynthesis. Yeast 2015; 33:37-42. [PMID: 26460143 DOI: 10.1002/yea.3138] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/01/2015] [Accepted: 10/02/2015] [Indexed: 01/20/2023] Open
Abstract
ARV1 is involved in regulating lipid homeostasis but also in the biosynthesis of glycosylphosphatidylinositol (GPI) in Saccharomyces cerevisiae. Here, we examined whether human ARV1 can complement the role of yeast ARV1 in GPI biosynthesis. Overexpression of human ARV1 could rescue the phenotypes associated with GPI anchor synthesis defect in the yeast arv1Δ mutant. The results suggest that Arv1 function in GPI biosynthesis may be conserved in all eukaryotes, from yeast to humans.
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Affiliation(s)
- Atsuko Ikeda
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Japan
| | - Kentaro Kajiwara
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Japan
| | | | - Asami Makino
- Lipid Biology Laboratory and RIKEN, Saitama, Japan
| | | | - Keiko Mizuta
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Japan
| | - Kouichi Funato
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Japan
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