1
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Farheen A, Case NT, MacAlpine J, Fu C, Robbins N, Cowen LE. The putative prenyltransferase Nus1 is required for filamentation in the human fungal pathogen Candida albicans. G3 (BETHESDA, MD.) 2024; 14:jkae124. [PMID: 38874344 PMCID: PMC11304969 DOI: 10.1093/g3journal/jkae124] [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: 04/03/2024] [Revised: 04/03/2024] [Accepted: 05/31/2024] [Indexed: 06/15/2024]
Abstract
Candida albicans is a major fungal pathogen of humans that can cause serious systemic infections in vulnerable immunocompromised populations. One of its virulence attributes is its capacity to transition between yeast and filamentous morphologies, but our understanding of this process remains incomplete. Here, we analyzed data from a functional genomic screen performed with the C. albicans Gene Replacement And Conditional Expression collection to identify genes crucial for morphogenesis in host-relevant conditions. Through manual scoring of microscopy images coupled with analysis of each image using a deep learning-based method termed Candescence, we identified 307 genes important for filamentation in tissue culture medium at 37°C with 5% CO2. One such factor was orf19.5963, which is predicted to encode the prenyltransferase Nus1 based on sequence homology to Saccharomyces cerevisiae. We further showed that Nus1 and its predicted interacting partner Rer2 are important for filamentation in multiple liquid filament-inducing conditions as well as for wrinkly colony formation on solid agar. Finally, we highlight that Nus1 and Rer2 likely govern C. albicans morphogenesis due to their importance in intracellular trafficking, as well as maintaining lipid homeostasis. Overall, this work identifies Nus1 and Rer2 as important regulators of C. albicans filamentation and highlights the power of functional genomic screens in advancing our understanding of gene function in human fungal pathogens.
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Affiliation(s)
- Aiman Farheen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Nicola T Case
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Jessie MacAlpine
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Ci Fu
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
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2
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Goo YH, Plakkal Ayyappan J, Cheeran FD, Bangru S, Saha PK, Baar P, Schulz S, Lydic TA, Spengler B, Wagner AH, Kalsotra A, Yechoor VK, Paul A. Lipid droplet-associated hydrolase mobilizes stores of liver X receptor sterol ligands and protects against atherosclerosis. Nat Commun 2024; 15:6540. [PMID: 39095402 PMCID: PMC11297204 DOI: 10.1038/s41467-024-50949-y] [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: 06/05/2023] [Accepted: 07/24/2024] [Indexed: 08/04/2024] Open
Abstract
Foam cells in atheroma are engorged with lipid droplets (LDs) that contain esters of regulatory lipids whose metabolism remains poorly understood. LD-associated hydrolase (LDAH) has a lipase structure and high affinity for LDs of foam cells. Using knockout and transgenic mice of both sexes, here we show that LDAH inhibits atherosclerosis development and promotes stable lesion architectures. Broad and targeted lipidomic analyzes of primary macrophages and comparative lipid profiling of atheroma identified a broad impact of LDAH on esterified sterols, including natural liver X receptor (LXR) sterol ligands. Transcriptomic analyzes coupled with rescue experiments show that LDAH modulates the expression of prototypical LXR targets and leads macrophages to a less inflammatory phenotype with a profibrotic gene signature. These studies underscore the role of LDs as reservoirs and metabolic hubs of bioactive lipids, and suggest that LDAH favorably modulates macrophage activation and protects against atherosclerosis via lipolytic mobilization of regulatory sterols.
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Affiliation(s)
- Young-Hwa Goo
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA.
| | | | - Francis D Cheeran
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Sushant Bangru
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA
- Cancer Center@Illinois, University of Illinois, Urbana-Champaign, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL, USA
| | - Pradip K Saha
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Paula Baar
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Sabine Schulz
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Todd A Lydic
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
- TransMIT GmbH, Center for Mass Spectrometric Developments, Giessen, Germany
| | - Andreas H Wagner
- Department of Cardiovascular Physiology, Heidelberg University, Heidelberg, Germany
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA
- Cancer Center@Illinois, University of Illinois, Urbana-Champaign, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL, USA
- Division of Nutritional Sciences, University of Illinois, Urbana-Champaign, IL, USA
| | - Vijay K Yechoor
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Antoni Paul
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA.
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3
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Garaiova M, Ding Y, Holic R, Valachovic M, Zhang C, Hapala I, Liu P. Yeast perilipin Pet10p/Pln1p interacts with Erg6p in ergosterol metabolism. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159506. [PMID: 38734059 DOI: 10.1016/j.bbalip.2024.159506] [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: 05/06/2023] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
Lipid droplets (LD) are highly dynamic organelles specialized for the regulation of energy storage and cellular homeostasis. LD consist of a neutral lipid core surrounded by a phospholipid monolayer membrane with embedded proteins, most of which are involved in lipid homeostasis. In this study, we focused on one of the major LD proteins, sterol C24-methyltransferase, encoded by ERG6. We found that the absence of Erg6p resulted in an increased accumulation of yeast perilipin Pet10p in LD, while the disruption of PET10 was accompanied by Erg6p LD over-accumulation. An observed reciprocal enrichment of Erg6p and Pet10p in pet10Δ and erg6Δ mutants in LD, respectively, was related to specific functional changes in the LD and was not due to regulation on the expression level. The involvement of Pet10p in neutral lipid homeostasis was observed in experiments that focused on the dynamics of neutral lipid mobilization as time-dependent changes in the triacylglycerols (TAG) and steryl esters (SE) content. We found that the kinetics of SE hydrolysis was reduced in erg6Δ cells and the mobilization of SE was completely lost in mutants that lacked both Erg6p and Pet10p. In addition, we observed that decreased levels of SE in erg6Δpet10Δ was linked to an overexpression of steryl ester hydrolase Yeh1p. Lipid analysis of erg6Δpet10Δ showed that PET10 deletion altered the composition of ergosterol intermediates which had accumulated in erg6Δ. In conclusion, yeast perilipin Pet10p functionally interacts with Erg6p during the metabolism of ergosterol.
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Affiliation(s)
- Martina Garaiova
- Department of Biochemistry of Biomembranes, Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 840 05, Slovakia.
| | - Yunfeng Ding
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Roman Holic
- Department of Biochemistry of Biomembranes, Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 840 05, Slovakia
| | - Martin Valachovic
- Department of Biochemistry of Biomembranes, Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 840 05, Slovakia
| | - Congyan Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ivan Hapala
- Department of Biochemistry of Biomembranes, Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 840 05, Slovakia
| | - Pingsheng Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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4
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Suri A, Hu KKY, Younas T, Dumsday G, Haritos VS. Functionalizing Yeast Lipid Droplets as Versatile Biomaterials. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308463. [PMID: 38566530 DOI: 10.1002/smll.202308463] [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: 09/23/2023] [Revised: 01/02/2024] [Indexed: 04/04/2024]
Abstract
Lipid droplets (LD) are dynamic cellular organelles of ≈1 µm diameter in yeast where a neutral lipid core is surrounded by a phospholipid monolayer and attendant proteins. Beyond the storage of lipids, opportunities for LD engineering remain underdeveloped but they show excellent potential as new biomaterials. In this research, LD from yeast Saccharomyces cerevisiae is engineered to display mCherry fluorescent protein, Halotag ligand binding protein, plasma membrane binding v-SNARE protein, and carbonic anhydrase enzyme via linkage to oleosin, an LD anchoring protein. Each protein-oleosin fusion is coded via a single gene construct. The expressed fusion proteins are specifically displayed on LD and their functions can be assessed within cells by fluorescence confocal microscopy, TEM, and as isolated materials via AFM, flow cytometry, spectrophotometry, and by enzyme activity assay. LD isolated from the cell are shown to be robust and stabilize proteins anchored into them. These engineered LD function as reporters, bind specific ligands, guide LD and their attendant proteins into union with the plasma membrane, and catalyze reactions. Here, engineered LD functions are extended well beyond traditional lipid storage toward new material applications aided by a versatile oleosin platform anchored into LD and displaying linked proteins.
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Affiliation(s)
- Ankita Suri
- Department of Chemical and Biological Engineering, Monash University, Clayton, 3800, Australia
- CSIRO Black Mountain, 2-40 Clunies Ross Street, Acton, ACT, 2601, Australia
| | - Kevin K Y Hu
- Department of Chemical and Biological Engineering, Monash University, Clayton, 3800, Australia
| | - Tayyaba Younas
- Department of Chemical and Biological Engineering, Monash University, Clayton, 3800, Australia
| | - Geoff Dumsday
- CSIRO Clayton, Research Way, Clayton, Victoria, 3168, Australia
| | - Victoria S Haritos
- Department of Chemical and Biological Engineering, Monash University, Clayton, 3800, Australia
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5
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Speer NO, Braun RJ, Reynolds EG, Brudnicka A, Swanson JM, Henne WM. Tld1 is a regulator of triglyceride lipolysis that demarcates a lipid droplet subpopulation. J Cell Biol 2024; 223:e202303026. [PMID: 37889293 PMCID: PMC10609110 DOI: 10.1083/jcb.202303026] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 09/09/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
Cells store lipids in the form of triglyceride (TG) and sterol ester (SE) in lipid droplets (LDs). Distinct pools of LDs exist, but a pervasive question is how proteins localize to and convey functions to LD subsets. Here, we show that the yeast protein YDR275W/Tld1 (for TG-associated LD protein 1) localizes to a subset of TG-containing LDs and reveal it negatively regulates lipolysis. Mechanistically, Tld1 LD targeting requires TG, and it is mediated by two distinct hydrophobic regions (HRs). Molecular dynamics simulations reveal that Tld1's HRs interact with TG on LDs and adopt specific conformations on TG-rich LDs versus SE-rich LDs in yeast and human cells. Tld1-deficient yeast display no defect in LD biogenesis but exhibit elevated TG lipolysis dependent on lipase Tgl3. Remarkably, overexpression of Tld1, but not LD protein Pln1/Pet10, promotes TG accumulation without altering SE pools. Finally, we find that Tld1-deficient cells display altered LD mobilization during extended yeast starvation. We propose that Tld1 senses TG-rich LDs and regulates lipolysis on LD subpopulations.
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Affiliation(s)
- Natalie Ortiz Speer
- Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - R. Jay Braun
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Emma Grace Reynolds
- Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alicja Brudnicka
- Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - W. Mike Henne
- Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
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6
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Pan H, Qin Y, Zhu J, Wang W, Liu Z, Huang X, Lam SM, Shui G, Wang Y, Jiang Y, Huang X. Centrins control chicken cone cell lipid droplet dynamics through lipid-droplet-localized SPDL1. Dev Cell 2023; 58:2528-2544.e8. [PMID: 37699389 DOI: 10.1016/j.devcel.2023.08.012] [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: 07/30/2022] [Revised: 05/10/2023] [Accepted: 08/08/2023] [Indexed: 09/14/2023]
Abstract
As evolutionarily conserved organelles, lipid droplets (LDs) carry out numerous functions and have various subcellular localizations in different cell types and species. In avian cone cells, there is a single apically localized LD. We demonstrated that CIDEA (cell death inducing DFFA like effector a) and microtubules promote the formation of the single LD in chicken cone cells. Centrins, which are well-known centriole proteins, target to the cone cell LD via their C-terminal calcium-binding domains. Centrins localize on cone cell LDs with the help of SPDL1-L (spindle apparatus coiled-coil protein 1-L), a previously uncharacterized isoform of the kinetochore-associated dynein adaptor SPDL1. The loss of CETN3 or overexpression of a truncated CETN1 abrogates the apical localization of the cone cell LD. Simulation analysis showed that multiple LDs or a single mispositioned LD reduces the light sensitivity. Collectively, our findings identify a role of centrins in the regulation of cone cell LD localization, which is important for the light sensitivity of cone cells.
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Affiliation(s)
- Huimin Pan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaqiang Qin
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinglin Zhu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhonghua Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuqiang Jiang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xun Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou 450001, China.
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7
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Al Mamun MA, Reza MA, Islam MS. Identification of novel proteins regulating lipid droplet biogenesis in filamentous fungi. Mol Microbiol 2023; 120:702-722. [PMID: 37748926 DOI: 10.1111/mmi.15170] [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: 03/02/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/27/2023]
Abstract
Lipid droplets (LDs) are storage organelles for neutral lipids which are critical for lipid homeostasis. Current knowledge of fungal LD biogenesis is largely limited to budding yeast, while LD regulation in multinucleated filamentous fungi which exhibit considerable metabolic activity remains unexplored. In this study, 19 LD-associated proteins were identified in the multinucleated species Aspergillus oryzae using a colocalization screening of a previously established enhanced green fluorescent protein (EGFP) fusion library. Functional screening identified 12 lipid droplet-regulating (LDR) proteins whose loss of function resulted in irregular LD biogenesis, particularly in terms of LD number and size. Bioinformatics analysis, targeted mutagenesis, and microscopy revealed four LDR proteins that localize to LD via the putative amphipathic helices (AHs). Further analysis revealed that LdrA with an Opi1 domain is essential for cytoplasmic and nuclear LD biogenesis involving a novel AH. Phylogenetic analysis demonstrated that the patterns of gene evolution were predominantly based on gene duplication. Our study identified a set of novel proteins involved in the regulation of LD biogenesis, providing unique molecular and evolutionary insights into fungal lipid storage.
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Affiliation(s)
- Md Abdulla Al Mamun
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - M Abu Reza
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
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8
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Speer NO, Braun RJ, Reynolds E, Brudnicka A, Swanson J, Henne WM. Tld1 is a novel regulator of triglyceride lipolysis that demarcates a lipid droplet subpopulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531595. [PMID: 36945645 PMCID: PMC10028886 DOI: 10.1101/2023.03.07.531595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Cells store lipids in the form of triglyceride (TG) and sterol-ester (SE) in lipid droplets (LDs). Distinct pools of LDs exist, but a pervasive question is how proteins localize to and convey functions to LD subsets. Here, we show the yeast protein YDR275W/Tld1 (for TG-associated LD protein 1) localizes to a subset of TG-containing LDs, and reveal it negatively regulates lipolysis. Mechanistically, Tld1 LD targeting requires TG, and is mediated by two distinct hydrophobic regions (HRs). Molecular dynamics simulations reveal Tld1 HRs interact with TG on LDs and adopt specific conformations on TG-rich LDs versus SE-rich LDs in yeast and human cells. Tld1-deficient yeast display no defect in LD biogenesis, but exhibit elevated TG lipolysis dependent on lipase Tgl3. Remarkably, over-expression of Tld1, but not LD protein Pln1/Pet10, promotes TG accumulation without altering SE pools. Finally, we find Tld1-deficient cells display altered LD mobilization during extended yeast starvation. We propose Tld1 senses TG-rich LDs and regulates lipolysis on LD subpopulations.
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9
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Bresgen N, Kovacs M, Lahnsteiner A, Felder TK, Rinnerthaler M. The Janus-Faced Role of Lipid Droplets in Aging: Insights from the Cellular Perspective. Biomolecules 2023; 13:912. [PMID: 37371492 DOI: 10.3390/biom13060912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/22/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
It is widely accepted that nine hallmarks-including mitochondrial dysfunction, epigenetic alterations, and loss of proteostasis-exist that describe the cellular aging process. Adding to this, a well-described cell organelle in the metabolic context, namely, lipid droplets, also accumulates with increasing age, which can be regarded as a further aging-associated process. Independently of their essential role as fat stores, lipid droplets are also able to control cell integrity by mitigating lipotoxic and proteotoxic insults. As we will show in this review, numerous longevity interventions (such as mTOR inhibition) also lead to strong accumulation of lipid droplets in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and mammalian cells, just to name a few examples. In mammals, due to the variety of different cell types and tissues, the role of lipid droplets during the aging process is much more complex. Using selected diseases associated with aging, such as Alzheimer's disease, Parkinson's disease, type II diabetes, and cardiovascular disease, we show that lipid droplets are "Janus"-faced. In an early phase of the disease, lipid droplets mitigate the toxicity of lipid peroxidation and protein aggregates, but in a later phase of the disease, a strong accumulation of lipid droplets can cause problems for cells and tissues.
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Affiliation(s)
- Nikolaus Bresgen
- Department of Biosciences and Medical Biology, Paris-Lodron University Salzburg, 5020 Salzburg, Austria
| | - Melanie Kovacs
- Department of Biosciences and Medical Biology, Paris-Lodron University Salzburg, 5020 Salzburg, Austria
| | - Angelika Lahnsteiner
- Department of Biosciences and Medical Biology, Paris-Lodron University Salzburg, 5020 Salzburg, Austria
| | - Thomas Klaus Felder
- Department of Laboratory Medicine, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Mark Rinnerthaler
- Department of Biosciences and Medical Biology, Paris-Lodron University Salzburg, 5020 Salzburg, Austria
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10
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Poudyal NR, Paul KS. Fatty acid uptake in Trypanosoma brucei: Host resources and possible mechanisms. Front Cell Infect Microbiol 2022; 12:949409. [PMID: 36478671 PMCID: PMC9719944 DOI: 10.3389/fcimb.2022.949409] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/24/2022] [Indexed: 11/22/2022] Open
Abstract
Trypanosoma brucei spp. causes African Sleeping Sickness in humans and nagana, a wasting disease, in cattle. As T. brucei goes through its life cycle in its mammalian and insect vector hosts, it is exposed to distinct environments that differ in their nutrient resources. One such nutrient resource is fatty acids, which T. brucei uses to build complex lipids or as a potential carbon source for oxidative metabolism. Of note, fatty acids are the membrane anchoring moiety of the glycosylphosphatidylinositol (GPI)-anchors of the major surface proteins, Variant Surface Glycoprotein (VSG) and the Procyclins, which are implicated in parasite survival in the host. While T. brucei can synthesize fatty acids de novo, it also readily acquires fatty acids from its surroundings. The relative contribution of parasite-derived vs. host-derived fatty acids to T. brucei growth and survival is not known, nor have the molecular mechanisms of fatty acid uptake been defined. To facilitate experimental inquiry into these important aspects of T. brucei biology, we addressed two questions in this review: (1) What is known about the availability of fatty acids in different host tissues where T. brucei can live? (2) What is known about the molecular mechanisms mediating fatty acid uptake in T. brucei? Finally, based on existing biochemical and genomic data, we suggest a model for T. brucei fatty acid uptake that proposes two major routes of fatty acid uptake: diffusion across membranes followed by intracellular trapping, and endocytosis of host lipoproteins.
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Affiliation(s)
- Nava Raj Poudyal
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States,Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, SC, United States
| | - Kimberly S. Paul
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States,Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, SC, United States,*Correspondence: Kimberly S. Paul,
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11
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Castro IG, Shortill SP, Dziurdzik SK, Cadou A, Ganesan S, Valenti R, David Y, Davey M, Mattes C, Thomas FB, Avraham RE, Meyer H, Fadel A, Fenech EJ, Ernst R, Zaremberg V, Levine TP, Stefan C, Conibear E, Schuldiner M. Systematic analysis of membrane contact sites in Saccharomyces cerevisiae uncovers modulators of cellular lipid distribution. eLife 2022; 11:74602. [DOI: 10.7554/elife.74602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Actively maintained close appositions between organelle membranes, also known as contact sites, enable the efficient transfer of biomolecules between cellular compartments. Several such sites have been described as well as their tethering machineries. Despite these advances we are still far from a comprehensive understanding of the function and regulation of most contact sites. To systematically characterize contact site proteomes, we established a high-throughput screening approach in Saccharomyces cerevisiae based on co-localization imaging. We imaged split fluorescence reporters for six different contact sites, several of which are poorly characterized, on the background of 1165 strains expressing a mCherry-tagged yeast protein that has a cellular punctate distribution (a hallmark of contact sites), under regulation of the strong TEF2 promoter. By scoring both co-localization events and effects on reporter size and abundance, we discovered over 100 new potential contact site residents and effectors in yeast. Focusing on several of the newly identified residents, we identified three homologs of Vps13 and Atg2 that are residents of multiple contact sites. These proteins share their lipid transport domain, thus expanding this family of lipid transporters. Analysis of another candidate, Ypr097w, which we now call Lec1 (Lipid-droplet Ergosterol Cortex 1), revealed that this previously uncharacterized protein dynamically shifts between lipid droplets and the cell cortex, and plays a role in regulation of ergosterol distribution in the cell. Overall, our analysis expands the universe of contact site residents and effectors and creates a rich database to mine for new functions, tethers, and regulators.
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Affiliation(s)
| | - Shawn P Shortill
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Samantha Katarzyna Dziurdzik
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Angela Cadou
- Laboratory for Molecular Cell Biology, University College London
| | | | - Rosario Valenti
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Yotam David
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
| | - Carsten Mattes
- Medical Biochemistry and Molecular Biology, PZMS, Medical Faculty, Saarland University
| | - Ffion B Thomas
- Laboratory for Molecular Cell Biology, University College London
| | | | - Hadar Meyer
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Amir Fadel
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Emma J Fenech
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Robert Ernst
- Medical Biochemistry and Molecular Biology, PZMS, Medical Faculty, Saarland University
| | | | - Tim P Levine
- UCL Institute of Ophthalmology, University College London
| | | | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science
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12
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Rogers S, Gui L, Kovalenko A, Zoni V, Carpentier M, Ramji K, Ben Mbarek K, Bacle A, Fuchs P, Campomanes P, Reetz E, Speer NO, Reynolds E, Thiam AR, Vanni S, Nicastro D, Henne WM. Triglyceride lipolysis triggers liquid crystalline phases in lipid droplets and alters the LD proteome. J Cell Biol 2022; 221:213472. [PMID: 36112368 PMCID: PMC9485706 DOI: 10.1083/jcb.202205053] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/10/2022] [Accepted: 08/22/2022] [Indexed: 01/08/2023] Open
Abstract
Lipid droplets (LDs) are reservoirs for triglycerides (TGs) and sterol-esters (SEs), but how these lipids are organized within LDs and influence their proteome remain unclear. Using in situ cryo-electron tomography, we show that glucose restriction triggers lipid phase transitions within LDs generating liquid crystalline lattices inside them. Mechanistically this requires TG lipolysis, which decreases the LD's TG:SE ratio, promoting SE transition to a liquid crystalline phase. Molecular dynamics simulations reveal TG depletion promotes spontaneous TG and SE demixing in LDs, additionally altering the lipid packing of the PL monolayer surface. Fluorescence imaging and proteomics further reveal that liquid crystalline phases are associated with selective remodeling of the LD proteome. Some canonical LD proteins, including Erg6, relocalize to the ER network, whereas others remain LD-associated. Model peptide LiveDrop also redistributes from LDs to the ER, suggesting liquid crystalline phases influence ER-LD interorganelle transport. Our data suggests glucose restriction drives TG mobilization, which alters the phase properties of LD lipids and selectively remodels the LD proteome.
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Affiliation(s)
- Sean Rogers
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Long Gui
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Anastasiia Kovalenko
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Valeria Zoni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Maxime Carpentier
- Laboratoire de Physique de l'École Normale Supérieure, École normale supérieure, Université Paris Sciences et Lettres, Centre national de la recherche scientifique, Sorbonne Université, Université de Paris, Paris, France
| | - Kamran Ramji
- Laboratoire de Physique de l'École Normale Supérieure, École normale supérieure, Université Paris Sciences et Lettres, Centre national de la recherche scientifique, Sorbonne Université, Université de Paris, Paris, France
| | - Kalthoum Ben Mbarek
- Laboratoire de Physique de l'École Normale Supérieure, École normale supérieure, Université Paris Sciences et Lettres, Centre national de la recherche scientifique, Sorbonne Université, Université de Paris, Paris, France
| | - Amelie Bacle
- Institute Jacques Monod, Centre national de la recherche scientifique, University of Paris, Paris, France
| | - Patrick Fuchs
- Laboratoire des Biomolécules, Paris, France.,Université de Paris, UFR Sciences du Vivant, Paris, France
| | - Pablo Campomanes
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Evan Reetz
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Natalie Ortiz Speer
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Emma Reynolds
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Abdou Rachid Thiam
- Laboratoire de Physique de l'École Normale Supérieure, École normale supérieure, Université Paris Sciences et Lettres, Centre national de la recherche scientifique, Sorbonne Université, Université de Paris, Paris, France
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Daniela Nicastro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - W Mike Henne
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
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13
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Bonatto D. The multiple roles of lipid metabolism in yeast physiology during beer fermentation. Genet Mol Biol 2022; 45:e20210325. [PMID: 36149459 PMCID: PMC9511687 DOI: 10.1590/1678-4685-gmb-2021-0325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 07/17/2022] [Indexed: 11/21/2022] Open
Abstract
The ability of brewing yeasts (Saccharomyces cerevisiae and Saccharomyces pastorianus) to cope with the toxic effects of ethanol during beer fermentation depends on the modulation of lipid and lipid droplets (LDs) biosynthesis, which affects membrane fluidity. However, it has been demonstrated that lipids and LDs can modulate different biological mechanisms associated to ethanol tolerance, including proteostasis and autophagy, leading to the hypothesis that lipid and LDs biosynthesis are integrative processes necessary for ethanol tolerance in yeast. Supporting this hypothesis, a transcriptome and systems biology analyses indicated the upregulation of autophagy, lipid biosynthesis, and proteostasis (ALP)-associated genes in lager yeast during beer fermentation, whose respective proteins interact in a shortest-pathway ALP network. These results indicated a cross-communication between various pathways linked to inter-organelle autophagy, lipid metabolism, and proteostasis (ALP) during lager beer fermentation, thus highlighting the importance of lipids for beer fermentation.
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Affiliation(s)
- Diego Bonatto
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia da UFRGS, Laboratório de Biologia Molecular e Computacional, Departamento de Biologia Molecular e Biotecnologia, Porto Alegre, RS, Brazil
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14
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Park JS, Hu Y, Hollingsworth NM, Miltenberger-Miltenyi G, Neiman AM. Interaction between VPS13A and the XK scramblase is important for VPS13A function in humans. J Cell Sci 2022; 135:jcs260227. [PMID: 35950506 PMCID: PMC9482346 DOI: 10.1242/jcs.260227] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/02/2022] [Indexed: 11/20/2022] Open
Abstract
VPS13 family proteins form conduits between the membranes of different organelles through which lipids are transferred. In humans, there are four VPS13 paralogs, and mutations in the genes encoding each of them are associated with different inherited disorders. VPS13 proteins contain multiple conserved domains. The Vps13 adaptor-binding (VAB) domain binds to adaptor proteins that recruit VPS13 to specific membrane contact sites. This work demonstrates the importance of a different domain in VPS13A function. The pleckstrin homology (PH) domain at the C-terminal region of VPS13A is required to form a complex with the XK scramblase and for the co-localization of VPS13A with XK within the cell. Alphafold modeling was used to predict an interaction surface between VPS13A and XK. Mutations in this region disrupt both complex formation and co-localization of the two proteins. Mutant VPS13A alleles found in patients with VPS13A disease truncate the PH domain. The phenotypic similarities between VPS13A disease and McLeod syndrome caused by mutations in VPS13A and XK, respectively, argue that loss of the VPS13A-XK complex is the basis of both diseases.
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Affiliation(s)
- Jae-Sook Park
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Yiying Hu
- Fish Core Unit, German Center for Neurodegenerative Diseases München (DZNE), 81377 Munich, Germany
- Munich Medical Research School (MMRS), 80336 Munich, Germany
| | - Nancy M. Hollingsworth
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | | | - Aaron M. Neiman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
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15
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Brands M, Dörmann P. Two AMP-Binding Domain Proteins from Rhizophagus irregularis Involved in Import of Exogenous Fatty Acids. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:464-476. [PMID: 35285673 DOI: 10.1094/mpmi-01-22-0026-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) colonize roots, where they provide nutrients in exchange for sugars and lipids. Because AMF lack genes for cytosolic fatty acid de novo synthase (FAS), they depend on host-derived fatty acids. AMF colonization is accompanied by expression of specific lipid genes and synthesis of sn-2 monoacylglycerols (MAGs). It is unknown how host-derived fatty acids are taken up by AMF. We describe the characterization of two AMP-binding domain protein genes from Rhizophagus irregularis, RiFAT1 and RiFAT2, with sequence similarity to Saccharomyces cerevisiae fatty acid transporter 1 (FAT1). Uptake of 13C-myristic acid (14:0) and, to a lesser extent, 13C-palmitic acid (16:0) was enhanced after expression of RiFAT1 or RiFAT2 in S. cerevisiae Δfat1 cells. The uptake of 2H-labeled fatty acids from 2H-myristoylglycerol or 2H-palmitoylglycerol was also increased after RiFAT1 and RiFAT2 expression in Δfat, but intact 2H-MAGs were not detected. RiFAT1 and RiFAT2 expression was induced in colonized roots compared with extraradical mycelium. 13C-label in the AMF-specific palmitvaccenic acid (16:1Δ11) and eicosatrienoic acid (20:3) were detected in colonized roots only when 13C2-acetate was supplemented but not 13C-fatty acids, demonstrating that de novo synthesized, host-derived fatty acids are rapidly taken up by R. irregularis from the roots. The results show that RiFAT1 and RiFAT2 are involved in the uptake of myristic acid (14:0) and palmitic acid (16:0), while fatty acids from MAGs are only taken up after hydrolysis. Therefore, the two proteins might be involved in fatty acid import into the fungal arbuscules in colonized roots.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Mathias Brands
- University of Bonn, Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), Karlrobert-Kreiten-Straße 13, 53115 Bonn, Germany
- University of Cologne, Botanical Institute, Cologne Biocenter, Zülpicher Straße 47b, 50674 Cologne, Germany
| | - Peter Dörmann
- University of Bonn, Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), Karlrobert-Kreiten-Straße 13, 53115 Bonn, Germany
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16
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Peng YJ, Zhang H, Feng MG, Ying SH. Steryl Acetyl Hydrolase 1 (BbSay1) Links Lipid Homeostasis to Conidiogenesis and Virulence in the Entomopathogenic Fungus Beauveria bassiana. J Fungi (Basel) 2022; 8:jof8030292. [PMID: 35330294 PMCID: PMC8953178 DOI: 10.3390/jof8030292] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 02/06/2023] Open
Abstract
Beauveria bassiana, as a well-studied entomopathogenic fungus, has a great potential for the biological control of insect pests. Lipid metabolism has been linked to the life cycle of B. bassiana; however, the underlying mechanisms remain unknown. In this study, a homolog of yeast steryl acetyl hydrolase 1 (Say1) was functionally characterized. The loss of B. bassianaSAY1 (BbSAY1) impaired the lipid homeostasis in conidia, with a significant reduction in oleic acid content. The ΔBbsay1 mutant strain displayed anelevated accumulation of lipid bodies and aweakened membrane permeability. As for phenotypic aspects, gene loss resulted in significant defects in germination, conidiation, and virulence. Our findings highlight that Say1, involved in lipid homeostasis, contributes to the cytomembrane integrity, development, and virulence in B. bassiana.
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17
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Pressly JD, Gurumani MZ, Varona Santos JT, Fornoni A, Merscher S, Al-Ali H. Adaptive and maladaptive roles of lipid droplets in health and disease. Am J Physiol Cell Physiol 2022; 322:C468-C481. [PMID: 35108119 PMCID: PMC8917915 DOI: 10.1152/ajpcell.00239.2021] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Advances in the understanding of lipid droplet biology have revealed essential roles for these organelles in mediating proper cellular homeostasis and stress response. Lipid droplets were initially thought to play a passive role in energy storage. However, recent studies demonstrate that they have substantially broader functions, including protection from reactive oxygen species, endoplasmic reticulum stress, and lipotoxicity. Dysregulation of lipid droplet homeostasis is associated with various pathologies spanning neurological, metabolic, cardiovascular, oncological, and renal diseases. This review provides an overview of the current understanding of lipid droplet biology in both health and disease.
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Affiliation(s)
- Jeffrey D. Pressly
- 1Katz Division of Nephrology and Hypertension and Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, Florida,2Department of Medicine, University of Miami, Miller School of Medicine, Miami, Florida
| | - Margaret Z. Gurumani
- 1Katz Division of Nephrology and Hypertension and Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, Florida,2Department of Medicine, University of Miami, Miller School of Medicine, Miami, Florida
| | - Javier T. Varona Santos
- 1Katz Division of Nephrology and Hypertension and Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, Florida,2Department of Medicine, University of Miami, Miller School of Medicine, Miami, Florida
| | - Alessia Fornoni
- 1Katz Division of Nephrology and Hypertension and Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, Florida,2Department of Medicine, University of Miami, Miller School of Medicine, Miami, Florida
| | - Sandra Merscher
- 1Katz Division of Nephrology and Hypertension and Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, Florida,2Department of Medicine, University of Miami, Miller School of Medicine, Miami, Florida
| | - Hassan Al-Ali
- 1Katz Division of Nephrology and Hypertension and Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, Florida,2Department of Medicine, University of Miami, Miller School of Medicine, Miami, Florida,3Department of Neurological Surgery, University of Miami, Miller School of Medicine, Miami, Florida,4The Miami Project to Cure Paralysis, University of Miami, Miller School of Medicine, Miami, Florida,5Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, Florida
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18
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Olarte MJ, Swanson JMJ, Walther TC, Farese RV. The CYTOLD and ERTOLD pathways for lipid droplet-protein targeting. Trends Biochem Sci 2022; 47:39-51. [PMID: 34583871 PMCID: PMC8688270 DOI: 10.1016/j.tibs.2021.08.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 01/03/2023]
Abstract
Lipid droplets (LDs) are the main organelles for lipid storage, and their surfaces contain unique proteins with diverse functions, including those that facilitate the deposition and mobilization of LD lipids. Among organelles, LDs have an unusual structure with an organic, hydrophobic oil phase covered by a phospholipid monolayer. The unique properties of LD monolayer surfaces require proteins to localize to LDs by distinct mechanisms. Here we review the two pathways known to mediate direct LD protein localization: the CYTOLD pathway mediates protein targeting from the cytosol toLDs, and the ERTOLD pathway functions in protein targeting from the endoplasmic reticulum toLDs. We describe the emerging principles for each targeting pathway in animal cells and highlight open questions in the field.
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Affiliation(s)
- Maria-Jesus Olarte
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Tobias C Walther
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02124, USA.
| | - Robert V Farese
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02124, USA.
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19
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Klug YA, Deme JC, Corey RA, Renne MF, Stansfeld PJ, Lea SM, Carvalho P. Mechanism of lipid droplet formation by the yeast Sei1/Ldb16 Seipin complex. Nat Commun 2021; 12:5892. [PMID: 34625558 PMCID: PMC8501077 DOI: 10.1038/s41467-021-26162-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 09/21/2021] [Indexed: 11/09/2022] Open
Abstract
Lipid droplets (LDs) are universal lipid storage organelles with a core of neutral lipids, such as triacylglycerols, surrounded by a phospholipid monolayer. This unique architecture is generated during LD biogenesis at endoplasmic reticulum (ER) sites marked by Seipin, a conserved membrane protein mutated in lipodystrophy. Here structural, biochemical and molecular dynamics simulation approaches reveal the mechanism of LD formation by the yeast Seipin Sei1 and its membrane partner Ldb16. We show that Sei1 luminal domain assembles a homooligomeric ring, which, in contrast to other Seipins, is unable to concentrate triacylglycerol. Instead, Sei1 positions Ldb16, which concentrates triacylglycerol within the Sei1 ring through critical hydroxyl residues. Triacylglycerol recruitment to the complex is further promoted by Sei1 transmembrane segments, which also control Ldb16 stability. Thus, we propose that LD assembly by the Sei1/Ldb16 complex, and likely other Seipins, requires sequential triacylglycerol-concentrating steps via distinct elements in the ER membrane and lumen.
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Affiliation(s)
- Yoel A Klug
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Justin C Deme
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Mike F Renne
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, Oxford, UK
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
| | - Pedro Carvalho
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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20
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Renne MF, Hariri H. Lipid Droplet-Organelle Contact Sites as Hubs for Fatty Acid Metabolism, Trafficking, and Metabolic Channeling. Front Cell Dev Biol 2021; 9:726261. [PMID: 34595176 PMCID: PMC8477659 DOI: 10.3389/fcell.2021.726261] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/12/2021] [Indexed: 01/21/2023] Open
Abstract
Cells prepare for fluctuations in nutrient availability by storing energy in the form of neutral lipids in organelles called Lipid Droplets (LDs). Upon starvation, fatty acids (FAs) released from LDs are trafficked to different cellular compartments to be utilized for membrane biogenesis or as a source of energy. Despite the biochemical pathways being known in detail, the spatio-temporal regulation of FA synthesis, storage, release, and breakdown is not completely understood. Recent studies suggest that FA trafficking and metabolism are facilitated by inter-organelle contact sites that form between LDs and other cellular compartments such as the Endoplasmic Reticulum (ER), mitochondria, peroxisomes, and lysosomes. LD-LD contact sites are also sites where FAs are transferred in a directional manner to support LD growth and expansion. As the storage site of neutral lipids, LDs play a central role in FA homeostasis. In this mini review, we highlight the role of LD contact sites with other organelles in FA trafficking, channeling, and metabolism and discuss the implications for these pathways on cellular lipid and energy homeostasis.
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Affiliation(s)
- Mike F. Renne
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Hanaa Hariri
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
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21
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Abstract
Lipid droplets (LDs) are endoplasmic reticulum-derived organelles that consist of a core of neutral lipids encircled by a phospholipid monolayer decorated with proteins. As hubs of cellular lipid and energy metabolism, LDs are inherently involved in the etiology of prevalent metabolic diseases such as obesity and nonalcoholic fatty liver disease. The functions of LDs are regulated by a unique set of associated proteins, the LD proteome, which includes integral membrane and peripheral proteins. These proteins control key activities of LDs such as triacylglycerol synthesis and breakdown, nutrient sensing and signal integration, and interactions with other organelles. Here we review the mechanisms that regulate the composition of the LD proteome, such as pathways that mediate selective and bulk LD protein degradation and potential connections between LDs and cellular protein quality control.
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Affiliation(s)
- Melissa A Roberts
- Department of Molecular and Cell Biology and Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720, USA;
| | - James A Olzmann
- Department of Molecular and Cell Biology and Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720, USA; .,Chan Zuckerberg Biohub, San Francisco, California 94158, USA
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22
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Rahman MA, Kumar R, Sanchez E, Nazarko TY. Lipid Droplets and Their Autophagic Turnover via the Raft-Like Vacuolar Microdomains. Int J Mol Sci 2021; 22:8144. [PMID: 34360917 PMCID: PMC8348048 DOI: 10.3390/ijms22158144] [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: 07/01/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 01/01/2023] Open
Abstract
Although once perceived as inert structures that merely serve for lipid storage, lipid droplets (LDs) have proven to be the dynamic organelles that hold many cellular functions. The LDs' basic structure of a hydrophobic core consisting of neutral lipids and enclosed in a phospholipid monolayer allows for quick lipid accessibility for intracellular energy and membrane production. Whereas formed at the peripheral and perinuclear endoplasmic reticulum, LDs are degraded either in the cytosol by lipolysis or in the vacuoles/lysosomes by autophagy. Autophagy is a regulated breakdown of dysfunctional, damaged, or surplus cellular components. The selective autophagy of LDs is called lipophagy. Here, we review LDs and their degradation by lipophagy in yeast, which proceeds via the micrometer-scale raft-like lipid domains in the vacuolar membrane. These vacuolar microdomains form during nutrient deprivation and facilitate internalization of LDs via the vacuolar membrane invagination and scission. The resultant intra-vacuolar autophagic bodies with LDs inside are broken down by vacuolar lipases and proteases. This type of lipophagy is called microlipophagy as it resembles microautophagy, the type of autophagy when substrates are sequestered right at the surface of a lytic compartment. Yeast microlipophagy via the raft-like vacuolar microdomains is a great model system to study the role of lipid domains in microautophagic pathways.
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Affiliation(s)
- Muhammad Arifur Rahman
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (M.A.R.); (E.S.)
| | - Ravinder Kumar
- Department of Obstetrics, Gynecology and Reproductive Science, University of California, San Francisco, CA 94143, USA;
| | - Enrique Sanchez
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (M.A.R.); (E.S.)
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Taras Y. Nazarko
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (M.A.R.); (E.S.)
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23
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Athenstaedt K. Phosphatidic acid biosynthesis in the model organism yeast Saccharomyces cerevisiae - a survey. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158907. [PMID: 33610760 PMCID: PMC7613133 DOI: 10.1016/j.bbalip.2021.158907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/04/2021] [Accepted: 02/11/2021] [Indexed: 01/07/2023]
Abstract
Phosphatidic acid biosynthesis represents the initial part of de novo formation of all glycerophospholipids (membrane lipids) as well as triacylglycerols (storage lipids), and is thus the centerpiece of glycerolipid metabolism. The universal route of phosphatidic acid biosynthesis starts from the precursor glycerol-3-phosphate and comprises two consecutive acylation reactions which are catalyzed by a glycerol-3-phosphate acyltransferase and a 1-acyl glycerol-3-phosphate acyltransferase. In addition, yeast and mammals harbor a set of enzymes which can synthesize phosphatidic acid from the precursor dihydroxyacetone phosphate. In the present review our current knowledge about enzymes contributing to phosphatidic acid biosynthesis in the invaluable model organism yeast, Saccharomyces cerevisiae, is summarized. A special focus is laid upon the regulation and the localization of these enzymes. Furthermore, research needs for a deeper insight into the high complexity of phosphatidic acid biosynthesis and consequently the entire lipid metabolic network is presented.
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Affiliation(s)
- Karin Athenstaedt
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/2, 8010 Graz, Austria.
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24
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A Conserved Machinery Underlies the Synthesis of a Chitosan Layer in the Candida Chlamydospore Cell Wall. mSphere 2021; 6:6/2/e00080-21. [PMID: 33910989 PMCID: PMC8092133 DOI: 10.1128/msphere.00080-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The polysaccharide chitosan is found in the cell wall of specific cell types in a variety of fungal species where it contributes to stress resistance, or in pathogenic fungi, virulence. Under certain growth conditions, the pathogenic yeast Candida dubliniensis forms a cell type termed a chlamydospore, which has an additional internal layer in its cell wall compared to hyphal or yeast cell types. We report that this internal layer of the chlamydospore wall is rich in chitosan. The ascospore wall of Saccharomyces cerevisiae also has a distinct chitosan layer. As in S. cerevisiae, formation of the chitosan layer in the C. dubliniensis wall requires the chitin synthase CHS3 and the chitin deacetylase CDA2 In addition, three lipid droplet-localized proteins-Rrt8, Srt1, and Mum3-identified in S. cerevisiae as important for chitosan layer assembly in the ascospore wall are required for the formation of the chitosan layer of the chlamydospore wall in C. dubliniensis These results reveal that a conserved machinery is required for the synthesis of a distinct chitosan layer in the walls of these two yeasts and may be generally important for incorporation of chitosan into fungal walls.IMPORTANCE The cell wall is the interface between the fungal cell and its environment and disruption of cell wall assembly is an effective strategy for antifungal therapies. Therefore, a detailed understanding of how cell walls form is critical to identify potential drug targets and develop therapeutic strategies. This study shows that a set of genes required for the assembly of a chitosan layer in the cell wall of S. cerevisiae is also necessary for chitosan formation in a different cell type in a different yeast, C. dubliniensis Because chitosan incorporation into the cell wall can be important for virulence, the conservation of this pathway suggests possible new targets for antifungals aimed at disrupting cell wall function.
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25
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Kumanski S, Viart BT, Kossida S, Moriel-Carretero M. Lipid Droplets Are a Physiological Nucleoporin Reservoir. Cells 2021; 10:472. [PMID: 33671805 PMCID: PMC7926788 DOI: 10.3390/cells10020472] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 02/09/2021] [Accepted: 02/19/2021] [Indexed: 12/13/2022] Open
Abstract
Lipid Droplets (LD) are dynamic organelles that originate in the Endoplasmic Reticulum and mostly bud off toward the cytoplasm, where they store neutral lipids for energy and protection purposes. LD also have diverse proteins on their surface, many of which are necessary for the their correct homeostasis. However, these organelles also act as reservoirs of proteins that can be made available elsewhere in the cell. In this sense, they act as sinks that titrate key regulators of many cellular processes. Among the specialized factors that reside on cytoplasmic LD are proteins destined for functions in the nucleus, but little is known about them and their impact on nuclear processes. By screening for nuclear proteins in publicly available LD proteomes, we found that they contain a subset of nucleoporins from the Nuclear Pore Complex (NPC). Exploring this, we demonstrate that LD act as a physiological reservoir, for nucleoporins, that impacts the conformation of NPCs and hence their function in nucleo-cytoplasmic transport, chromatin configuration, and genome stability. Furthermore, our in silico modeling predicts a role for LD-released fatty acids in regulating the transit of nucleoporins from LD through the cytoplasm and to nuclear pores.
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Affiliation(s)
- Sylvain Kumanski
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier CEDEX 05, France;
| | - Benjamin T. Viart
- International ImMunoGeneTics Information System (IMGT®), Institut de Génétique Humaine (IGH), Université de Montpellier, Centre National de la Recherche Scientifique, 34396 Montpellier CEDEX 05, France; (B.T.V.); (S.K.)
| | - Sofia Kossida
- International ImMunoGeneTics Information System (IMGT®), Institut de Génétique Humaine (IGH), Université de Montpellier, Centre National de la Recherche Scientifique, 34396 Montpellier CEDEX 05, France; (B.T.V.); (S.K.)
| | - María Moriel-Carretero
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier CEDEX 05, France;
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Sesham K, Manda NK. Molecular modeling, docking and dynamics analysis of lipid droplet associated enzyme Ypr147cp from Saccharomyces cerevisiae. Bioinformation 2021; 17:132-138. [PMID: 34393428 PMCID: PMC8340710 DOI: 10.6026/97320630017132] [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: 12/02/2020] [Revised: 12/31/2020] [Accepted: 01/26/2021] [Indexed: 12/02/2022] Open
Abstract
Ypr147cp of Saccharomyces cerevisiae was localized to lipid droplets. The recombinant Ypr147cp showed both triacylglycerol lipase and ester hydrolase activities. Knock out of YPR147C led to accumulation of TAG in ypr147cΔ when compared to wild type (WT). Transmission electron microscopic analysis of ypr147cΔ cells show increased lipid bodies. Moreover, the lipid profiling confirmed the accumulation of fatty acids derived from neutral and phospholipids in ypr147cΔ cells. Sequence analysis of Ypr147cp show the presence of an a/b hydrolase domain with the conserved GXSXG lipase motif. The YPR147c homology model was built and the modeled protein was analysed using RMSD and root mean square fluctuation (RMSF) for a 100 ns simulation trajectory. Docking the acetate, butyrate and palmitate ligands with the model confirmed covalent binding of ligands with the Ser207 of the GXSXG motif. Thus, Ypr147cp is a lipid droplet associated triacylglycerol lipase having short chain ester hydrolyzing capacity.
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Affiliation(s)
- Kishore Sesham
- Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Naresh Kumar Manda
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana-500046, India
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Bosch M, Parton RG, Pol A. Lipid droplets, bioenergetic fluxes, and metabolic flexibility. Semin Cell Dev Biol 2020; 108:33-46. [DOI: 10.1016/j.semcdb.2020.02.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/13/2020] [Accepted: 02/27/2020] [Indexed: 12/18/2022]
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Schittmayer M, Vujic N, Darnhofer B, Korbelius M, Honeder S, Kratky D, Birner-Gruenberger R. Spatially Resolved Activity-based Proteomic Profiles of the Murine Small Intestinal Lipases. Mol Cell Proteomics 2020; 19:2104-2115. [PMID: 33023980 PMCID: PMC7710144 DOI: 10.1074/mcp.ra120.002171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/28/2020] [Indexed: 01/05/2023] Open
Abstract
Despite the crucial function of the small intestine in nutrient uptake our understanding of the molecular events underlying the digestive function is still rudimentary. Recent studies demonstrated that enterocytes do not direct the entire dietary triacylglycerol toward immediate chylomicron synthesis. Especially after high-fat challenges, parts of the resynthesized triacylglycerol are packaged into cytosolic lipid droplets for transient storage in the endothelial layer of the small intestine. The reason for this temporary storage of triacylglycerol is not completely understood. To utilize lipids from cytosolic lipid droplets for chylomicron synthesis in the endoplasmic reticulum, stored triacylglycerol has to be hydrolyzed either by cytosolic lipolysis or lipophagy. Interestingly, triacylglycerol storage and chylomicron secretion rates are unevenly distributed along the small intestine, with the proximal jejunum exhibiting the highest intermittent storage capacity. We hypothesize that correlating hydrolytic enzyme activities with the reported distribution of triacylglycerol storage and chylomicron secretion in different sections of the small intestine is a promising strategy to determine key enzymes in triacylglycerol remobilization. We employed a serine hydrolase specific activity-based labeling approach in combination with quantitative proteomics to identify and rank hydrolases based on their relative activity in 11 sections of the small intestine. Moreover, we identified several clusters of enzymes showing similar activity distribution along the small intestine. Merging our activity-based results with substrate specificity and subcellular localization known from previous studies, carboxylesterase 2e and arylacetamide deacetylase emerge as promising candidates for triacylglycerol mobilization from cytosolic lipid droplets in enterocytes.
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Affiliation(s)
- Matthias Schittmayer
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Vienna, Austria; Diagnostic and Research Institute of Pathology, Medical University Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria.
| | - Nemanja Vujic
- Gottfried Schatz Research Center, Medical University Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Barbara Darnhofer
- Diagnostic and Research Institute of Pathology, Medical University Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Melanie Korbelius
- Gottfried Schatz Research Center, Medical University Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Sophie Honeder
- Diagnostic and Research Institute of Pathology, Medical University Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Dagmar Kratky
- Gottfried Schatz Research Center, Medical University Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria.
| | - Ruth Birner-Gruenberger
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Vienna, Austria; Diagnostic and Research Institute of Pathology, Medical University Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria.
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29
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Erdbrügger P, Fröhlich F. The role of very long chain fatty acids in yeast physiology and human diseases. Biol Chem 2020; 402:25-38. [PMID: 33544487 DOI: 10.1515/hsz-2020-0234] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/02/2020] [Indexed: 12/16/2022]
Abstract
Fatty acids (FAs) are a highly diverse class of molecules that can have variable chain length, number of double bonds and hydroxylation sites. FAs with 22 or more carbon atoms are described as very long chain fatty acids (VLCFAs). VLCFAs are synthesized in the endoplasmic reticulum (ER) through a four-step elongation cycle by membrane embedded enzymes. VLCFAs are precursors for the synthesis of sphingolipids (SLs) and glycerophospholipids. Besides their role as lipid constituents, VLCFAs are also found as precursors of lipid mediators. Mis-regulation of VLCFA metabolism can result in a variety of inherited diseases ranging from ichthyosis, to myopathies and demyelination. The enzymes for VLCFA biosynthesis are evolutionary conserved and many of the pioneering studies were performed in the model organism Saccharomyces cerevisiae. A growing body of evidence suggests that VLCFA metabolism is intricately regulated to maintain lipid homeostasis. In this review we will describe the metabolism of VLCFAs, how they are synthesized, transported and degraded and how these processes are regulated, focusing on budding yeast. We will review how lipid metabolism and membrane properties are affected by VLCFAs and which impact mutations in the biosynthetic genes have on physiology. We will also briefly describe diseases caused by mis-regulation of VLCFAs in human cells.
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Affiliation(s)
- Pia Erdbrügger
- Department of Biology/Chemistry, Molecular Membrane Biology Group, University of Osnabrück, Osnabrück, Germany
| | - Florian Fröhlich
- Department of Biology/Chemistry, Molecular Membrane Biology Group, University of Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics Osnabrück, Osnabrück, Germany
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30
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Christiano R, Arlt H, Kabatnik S, Mejhert N, Lai ZW, Farese RV, Walther TC. A Systematic Protein Turnover Map for Decoding Protein Degradation. Cell Rep 2020; 33:108378. [PMID: 33176155 DOI: 10.1016/j.celrep.2020.108378] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 09/01/2020] [Accepted: 10/21/2020] [Indexed: 01/20/2023] Open
Abstract
Protein degradation is mediated by an expansive and complex network of protein modification and degradation enzymes. Matching degradation enzymes with their targets and determining globally which proteins are degraded by the proteasome or lysosome/vacuole have been a major challenge. Furthermore, an integrated view of protein degradation for cellular pathways has been lacking. Here, we present an analytical platform that combines systematic gene deletions with quantitative measures of protein turnover to deconvolve protein degradation pathways for Saccharomyces cerevisiae. The resulting turnover map (T-MAP) reveals target candidates of nearly all E2 and E3 ubiquitin ligases and identifies the primary degradation routes for most proteins. We further mined this T-MAP to identify new substrates of ER-associated degradation (ERAD) involved in sterol biosynthesis and to uncover regulatory nodes for sphingolipid biosynthesis. The T-MAP approach should be broadly applicable to the study of other cellular processes, including mammalian systems.
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Affiliation(s)
- Romain Christiano
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Henning Arlt
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Sonja Kabatnik
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Niklas Mejhert
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Zon Weng Lai
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Harvard T.H. Chan Advanced Multi-Omics Platform, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Robert V Farese
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02124, USA.
| | - Tobias C Walther
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02124, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA; Harvard T.H. Chan Advanced Multi-Omics Platform, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
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31
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Garcia EJ, Liao PC, Tan G, Vevea JD, Sing CN, Tsang CA, McCaffery JM, Boldogh IR, Pon LA. Membrane dynamics and protein targets of lipid droplet microautophagy during ER stress-induced proteostasis in the budding yeast, Saccharomyces cerevisiae. Autophagy 2020. [PMID: 33021864 DOI: 10.1080/15548627.2020.1826691.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022] Open
Abstract
Our previous studies reveal a mechanism for lipid droplet (LD)-mediated proteostasis in the endoplasmic reticulum (ER) whereby unfolded proteins that accumulate in the ER in response to lipid imbalance-induced ER stress are removed by LDs and degraded by microlipophagy (µLP), autophagosome-independent LD uptake into the vacuole (the yeast lysosome). Here, we show that dithiothreitol- or tunicamycin-induced ER stress also induces µLP and identify an unexpected role for vacuolar membrane dynamics in this process. All stressors studied induce vacuolar fragmentation prior to µLP. Moreover, during µLP, fragmented vacuoles fuse to form cup-shaped structures that encapsulate and ultimately take up LDs. Our studies also indicate that proteins of the endosome sorting complexes required for transport (ESCRT) are upregulated, required for µLP, and recruited to LDs, vacuolar membranes, and sites of vacuolar membrane scission during µLP. We identify possible target proteins for LD-mediated ER proteostasis. Our live-cell imaging studies reveal that one potential target (Nup159) localizes to punctate structures that colocalizes with LDs 1) during movement from ER membranes to the cytosol, 2) during microautophagic uptake into vacuoles, and 3) within the vacuolar lumen. Finally, we find that mutations that inhibit LD biogenesis, homotypic vacuolar membrane fusion or ESCRT function inhibit stress-induced autophagy of Nup159 and other ER proteins. Thus, we have obtained the first direct evidence that LDs and µLP can mediate ER stress-induced ER proteostasis, and identified direct roles for ESCRT and vacuolar membrane fusion in that process.
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Affiliation(s)
- Enrique J Garcia
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Pin-Chao Liao
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Gary Tan
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Jason D Vevea
- HHMI and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin, USA
| | - Cierra N Sing
- Institute of Human Nutrition, Columbia University, New York, NY, USA
| | - Catherine A Tsang
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - J Michael McCaffery
- Integrated Imaging Center, Department of Biology, The Johns Hopkins University, Baltimore, MD, USA
| | - Istvan R Boldogh
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Liza A Pon
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
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32
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Garcia EJ, Liao PC, Tan G, Vevea JD, Sing CN, Tsang CA, McCaffery JM, Boldogh IR, Pon LA. Membrane dynamics and protein targets of lipid droplet microautophagy during ER stress-induced proteostasis in the budding yeast, Saccharomyces cerevisiae. Autophagy 2020; 17:2363-2383. [PMID: 33021864 PMCID: PMC8496710 DOI: 10.1080/15548627.2020.1826691] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Our previous studies reveal a mechanism for lipid droplet (LD)-mediated proteostasis in the endoplasmic reticulum (ER) whereby unfolded proteins that accumulate in the ER in response to lipid imbalance-induced ER stress are removed by LDs and degraded by microlipophagy (µLP), autophagosome-independent LD uptake into the vacuole (the yeast lysosome). Here, we show that dithiothreitol- or tunicamycin-induced ER stress also induces µLP and identify an unexpected role for vacuolar membrane dynamics in this process. All stressors studied induce vacuolar fragmentation prior to µLP. Moreover, during µLP, fragmented vacuoles fuse to form cup-shaped structures that encapsulate and ultimately take up LDs. Our studies also indicate that proteins of the endosome sorting complexes required for transport (ESCRT) are upregulated, required for µLP, and recruited to LDs, vacuolar membranes, and sites of vacuolar membrane scission during µLP. We identify possible target proteins for LD-mediated ER proteostasis. Our live-cell imaging studies reveal that one potential target (Nup159) localizes to punctate structures that colocalizes with LDs 1) during movement from ER membranes to the cytosol, 2) during microautophagic uptake into vacuoles, and 3) within the vacuolar lumen. Finally, we find that mutations that inhibit LD biogenesis, homotypic vacuolar membrane fusion or ESCRT function inhibit stress-induced autophagy of Nup159 and other ER proteins. Thus, we have obtained the first direct evidence that LDs and µLP can mediate ER stress-induced ER proteostasis, and identified direct roles for ESCRT and vacuolar membrane fusion in that process.
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Affiliation(s)
- Enrique J Garcia
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Pin-Chao Liao
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Gary Tan
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Jason D Vevea
- HHMI and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin, USA
| | - Cierra N Sing
- Institute of Human Nutrition, Columbia University, New York, NY, USA
| | - Catherine A Tsang
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - J Michael McCaffery
- Integrated Imaging Center, Department of Biology, The Johns Hopkins University, Baltimore, MD, USA
| | - Istvan R Boldogh
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Liza A Pon
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
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Hapala I, Griac P, Holic R. Metabolism of Storage Lipids and the Role of Lipid Droplets in the Yeast Schizosaccharomyces pombe. Lipids 2020; 55:513-535. [PMID: 32930427 DOI: 10.1002/lipd.12275] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/14/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022]
Abstract
Storage lipids, triacylglycerols (TAG), and steryl esters (SE), are predominant constituents of lipid droplets (LD) in fungi. In several yeast species, metabolism of TAG and SE is linked to various cellular processes, including cell division, sporulation, apoptosis, response to stress, and lipotoxicity. In addition, TAG are an important source for the generation of value-added lipids for industrial and biomedical applications. The fission yeast Schizosaccharomyces pombe is a widely used unicellular eukaryotic model organism. It is a powerful tractable system used to study various aspects of eukaryotic cellular and molecular biology. However, the knowledge of S. pombe neutral lipids metabolism is quite limited. In this review, we summarize and discuss the current knowledge of the homeostasis of storage lipids and of the role of LD in the fission yeast S. pombe with the aim to stimulate research of lipid metabolism and its connection with other essential cellular processes. We also discuss the advantages and disadvantages of fission yeast in lipid biotechnology and recent achievements in the use of S. pombe in the biotechnological production of valuable lipid compounds.
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Affiliation(s)
- Ivan Hapala
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Dúbravská cesta 9, 840 05 Bratislava, Slovakia
| | - Peter Griac
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Dúbravská cesta 9, 840 05 Bratislava, Slovakia
| | - Roman Holic
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Dúbravská cesta 9, 840 05 Bratislava, Slovakia
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The phosphatidylethanolamine-binding protein DTH1 mediates degradation of lipid droplets in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 2020; 117:23131-23139. [PMID: 32868427 DOI: 10.1073/pnas.2005600117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lipid droplets (LDs) are intracellular organelles found in a wide range of organisms and play important roles in stress tolerance. During nitrogen (N) starvation, Chlamydomonas reinhardtii stores large amounts of triacylglycerols (TAGs) inside LDs. When N is resupplied, the LDs disappear and the TAGs are degraded, presumably providing carbon and energy for regrowth. The mechanism by which cells degrade LDs is poorly understood. Here, we isolated a mutant (dth1-1, Delayed in TAG Hydrolysis 1) in which TAG degradation during recovery from N starvation was compromised. Consequently, the dth1-1 mutant grew poorly compared to its parental line during N recovery. Two additional independent loss-of-function mutants (dth1-2 and dth1-3) also exhibited delayed TAG remobilization. DTH1 transcript levels increased sevenfold upon N resupply, and DTH1 protein was localized to LDs. DTH1 contains a putative lipid-binding domain (DTH1LBD) with alpha helices predicted to be structurally similar to those in apolipoproteins E and A-I. Recombinant DTH1LBD bound specifically to phosphatidylethanolamine (PE), a major phospholipid coating the LD surface. Overexpression of DTH1LBD in Chlamydomonas phenocopied the dth1 mutant's defective TAG degradation, suggesting that the function of DTH1 depends on its ability to bind PE. Together, our results demonstrate that the lipid-binding DTH1 plays an essential role in LD degradation and provide insight into the molecular mechanism of protein anchorage to LDs at the LD surface in photosynthetic cells.
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Metabolomics profiling reveals new aspects of dolichol biosynthesis in Plasmodium falciparum. Sci Rep 2020; 10:13264. [PMID: 32764679 PMCID: PMC7414040 DOI: 10.1038/s41598-020-70246-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 07/24/2020] [Indexed: 01/27/2023] Open
Abstract
The cis-polyisoprenoid lipids namely polyprenols, dolichols and their derivatives are linear polymers of several isoprene units. In eukaryotes, polyprenols and dolichols are synthesized as a mixture of four or more homologues of different length with one or two predominant species with sizes varying among organisms. Interestingly, co-occurrence of polyprenols and dolichols, i.e. detection of a dolichol along with significant levels of its precursor polyprenol, are unusual in eukaryotic cells. Our metabolomics studies revealed that cis-polyisoprenoids are more diverse in the malaria parasite Plasmodium falciparum than previously postulated as we uncovered active de novo biosynthesis and substantial levels of accumulation of polyprenols and dolichols of 15 to 19 isoprene units. A distinctive polyprenol and dolichol profile both within the intraerythrocytic asexual cycle and between asexual and gametocyte stages was observed suggesting that cis-polyisoprenoid biosynthesis changes throughout parasite’s development. Moreover, we confirmed the presence of an active cis-prenyltransferase (PfCPT) and that dolichol biosynthesis occurs via reduction of the polyprenol to dolichol by an active polyprenol reductase (PfPPRD) in the malaria parasite.
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36
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Determinants of Endoplasmic Reticulum-to-Lipid Droplet Protein Targeting. Dev Cell 2020; 54:471-487.e7. [PMID: 32730754 DOI: 10.1016/j.devcel.2020.07.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 05/11/2020] [Accepted: 07/07/2020] [Indexed: 02/06/2023]
Abstract
Lipid droplet (LD) formation from the endoplasmic reticulum (ER) is accompanied by the targeting and accumulation of specific hydrophobic, membrane-embedded proteins on LDs. The determinants of this process are unknown. Here, we study the hydrophobic membrane motifs of two Drosophila melanogaster proteins, GPAT4 and ALG14, that utilize this pathway, and we identify crucial sequence features that mediate LD accumulation. Molecular dynamics simulations and studies in cells reveal that LD targeting of these motifs requires deeply inserted tryptophans that have lower free energy in the LD oil phase and positively charged residues near predicted hairpin hinges that become less constrained in the LD environment. Analyzing hydrophobic motifs from similar LD-targeting proteins, it appears that the distribution of tryptophan and positively charged residues distinguishes them from non-LD-targeting membrane motifs. Our studies identify specific sequence features and principles of hydrophobic membrane motifs that mediate their accumulation on LDs.
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Kubalová D, Káňovičová P, Veselá P, Awadová T, Džugasová V, Daum G, Malínský J, Balážová M. The lipid droplet protein Pgc1 controls the subcellular distribution of phosphatidylglycerol. FEMS Yeast Res 2020; 19:5524364. [PMID: 31247640 DOI: 10.1093/femsyr/foz045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/26/2019] [Indexed: 12/12/2022] Open
Abstract
The biosynthesis of yeast phosphatidylglycerol (PG) takes place in the inner mitochondrial membrane. Outside mitochondria, the abundance of PG is low. Here, we present evidence that the subcellular distribution of PG is maintained by the locally controlled enzymatic activity of the PG-specific phospholipase, Pgc1. A fluorescently labeled Pgc1 protein accumulates on the surface of lipid droplets (LD). We show, however, that LD are not only dispensable for Pgc1-mediated PG degradation, but do not even host any phospholipase activity of Pgc1. Our in vitro assays document the capability of LD-accumulated Pgc1 to degrade PG upon entry to the membranes of the endoplasmic reticulum, mitochondria and even of artificial phospholipid vesicles. Fluorescence recovery after photobleaching analysis confirms the continuous exchange of GFP-Pgc1 within the individual LD in situ, suggesting that a steady-state equilibrium exists between LD and membranes to regulate the immediate phospholipase activity of Pgc1. In this model, LD serve as a storage place and shelter Pgc1, preventing its untimely degradation, while both phospholipase activity and degradation of the enzyme occur in the membranes.
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Affiliation(s)
- Dominika Kubalová
- Department of Membrane Biochemistry, Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 84005 Bratislava, Slovakia
| | - Paulína Káňovičová
- Department of Membrane Biochemistry, Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 84005 Bratislava, Slovakia
| | - Petra Veselá
- Department of Microscopy, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic,14220 Prague, Czech Republic
| | - Thuraya Awadová
- Department of Microscopy, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic,14220 Prague, Czech Republic
| | - Vladimíra Džugasová
- Department of Genetics, Faculty of Natural Sciences, Comenius University, 84215 Bratislava, Slovakia
| | - Günther Daum
- Institute of Biochemistry, Graz University of Technology, 8010 Graz, Austria
| | - Jan Malínský
- Department of Microscopy, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic,14220 Prague, Czech Republic
| | - Mária Balážová
- Department of Membrane Biochemistry, Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 84005 Bratislava, Slovakia
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Abstract
Natural rubber (NR), principally comprising cis-1,4-polyisoprene, is an industrially important natural hydrocarbon polymer because of its unique physical properties, which render it suitable for manufacturing items such as tires. Presently, industrial NR production depends solely on latex obtained from the Pará rubber tree, Hevea brasiliensis. In latex, NR is enclosed in rubber particles, which are specialized organelles comprising a hydrophobic NR core surrounded by a lipid monolayer and membrane-bound proteins. The similarity of the basic carbon skeleton structure between NR and dolichols and polyprenols, which are found in most organisms, suggests that the NR biosynthetic pathway is related to the polyisoprenoid biosynthetic pathway and that rubber transferase, which is the key enzyme in NR biosynthesis, belongs to the cis-prenyltransferase family. Here, we review recent progress in the elucidation of molecular mechanisms underlying NR biosynthesis through the identification of the enzymes that are responsible for the formation of the NR backbone structure.
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Affiliation(s)
- Satoshi Yamashita
- Department of Material Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan;
| | - Seiji Takahashi
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan;
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39
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Chen CC, Zhang L, Yu X, Ma L, Ko TP, Guo RT. Versatile cis-isoprenyl Diphosphate Synthase Superfamily Members in Catalyzing Carbon–Carbon Bond Formation. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lilan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xuejing Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
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40
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Kiegerl B, Tavassoli M, Smart H, Shabits BN, Zaremberg V, Athenstaedt K. Phosphorylation of the lipid droplet localized glycerol‑3‑phosphate acyltransferase Gpt2 prevents a futile triacylglycerol cycle in yeast. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:158509. [DOI: 10.1016/j.bbalip.2019.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 11/30/2022]
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41
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Geltinger F, Tevini J, Briza P, Geiser A, Bischof J, Richter K, Felder T, Rinnerthaler M. The transfer of specific mitochondrial lipids and proteins to lipid droplets contributes to proteostasis upon stress and aging in the eukaryotic model system Saccharomyces cerevisiae. GeroScience 2019; 42:19-38. [PMID: 31676965 PMCID: PMC7031196 DOI: 10.1007/s11357-019-00103-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 09/11/2019] [Indexed: 01/12/2023] Open
Abstract
Originally Lipid droplets (LDs) were considered as being droplets for lipid storage only. Increasing evidence, however, demonstrates that LDs fulfill a pleiotropy of additional functions. Among them is the modulation of protein as well as lipid homeostasis. Under unfavorable pro-oxidative conditions, proteins can form aggregates which may exceed the overall proteolytic capacity of the proteasome. After stress termination LDs can adjust and support the removal of these aggregates. Additionally, LDs interact with mitochondria, specifically take over certain proteins and thus prevent apoptosis. LDs, which are loaded with these harmful proteins, are subsequently eliminated via lipophagy. Recently it was demonstrated that this autophagic process is a modulator of longevity. LDs do not only eliminate potentially dangerous proteins, but they are also able to prevent lipotoxicity by storing specific lipids. In the present study we used the model organism Saccharomyces cerevisiae to compare the proteome as well as lipidome of mitochondria and LDs under different conditions: replicative aging, stress and apoptosis. In this context we found an accumulation of proteins at LDs, supporting the role of LDs in proteostasis. Additionally, the composition of main lipid classes such as phosphatidylcholines, phosphatidylethanolamines, phosphatidylinositols, phosphatidylglycerols, triacylglycerols, ceramides, phosphatidic acids and ergosterol of LDs and mitochondria changed during stress conditions and aging.
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Affiliation(s)
- Florian Geltinger
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Julia Tevini
- Department of Laboratory Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Peter Briza
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Amrito Geiser
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Johannes Bischof
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Klaus Richter
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Thomas Felder
- Department of Laboratory Medicine, Paracelsus Medical University, Salzburg, Austria.
- Obesity Research Unit, Paracelsus Medical University, Salzburg, Austria.
| | - Mark Rinnerthaler
- Department of Biosciences, University of Salzburg, Salzburg, Austria.
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42
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Su WC, Lin YH, Pagac M, Wang CW. Seipin negatively regulates sphingolipid production at the ER-LD contact site. J Cell Biol 2019; 218:3663-3680. [PMID: 31594806 PMCID: PMC6829658 DOI: 10.1083/jcb.201902072] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/23/2019] [Accepted: 08/08/2019] [Indexed: 01/06/2023] Open
Abstract
Su et al. show that seipin negatively regulates the production of sphingoid intermediates by binding the enzymes serine palmitoyltransferase and fatty acid elongase at discrete regions of the ER in close vicinity to lipid droplets, thereby mediating the synthesis of two major building blocks for sphingolipids. Seipin is known for its critical role in controlling lipid droplet (LD) assembly at the LD-forming subdomain of the endoplasmic reticulum (ER). Here, we identified a new function of seipin as a negative regulator for sphingolipid production. We show that yeast cells lacking seipin displayed altered sensitivity to sphingolipid inhibitors, accumulated sphingoid precursors and intermediates, and increased serine palmitoyltransferase (SPT) and fatty acid (FA) elongase activities. Seipin associated with SPT and FA elongase, and the interaction was reduced by inhibitors for sphingolipid synthesis in a concentration-dependent manner. We further show that the interactions of seipin with SPT and FA elongase occurred at ER–LD contacts and were likely regulated differentially. Further evidence indicated that LD biogenesis was intact when SPT activity was blocked, whereas excess sphingoid intermediates may affect LD morphology. Expression of human seipin rescued the altered sphingolipids in yeast seipin mutants, suggesting that the negative regulation of sphingolipid synthesis by seipin is likely an evolutionarily conserved process.
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Affiliation(s)
- Wei-Cheng Su
- Institute of Plant and Microbial Biology, Academia Sinica, Nangang, Taipei, Taiwan
| | - Yi-Hsiu Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Nangang, Taipei, Taiwan
| | - Martin Pagac
- Institute of Plant and Microbial Biology, Academia Sinica, Nangang, Taipei, Taiwan
| | - Chao-Wen Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Nangang, Taipei, Taiwan
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43
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Pevalová Z, Pevala V, Blunsom NJ, Tahotná D, Kotrasová V, Holič R, Pokorná L, Bauer JA, Kutejová E, Cockcroft S, Griač P. Yeast phosphatidylinositol transfer protein Pdr17 does not require high affinity phosphatidylinositol binding for its cellular function. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:1412-1421. [DOI: 10.1016/j.bbalip.2019.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 07/09/2019] [Indexed: 11/28/2022]
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史 琳, 王 柯, 邓 玉, 王 莹, 朱 双, 杨 旭, 廖 文. [Role of lipophagy in the regulation of lipid metabolism and the molecular mechanism]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2019; 39:867-874. [PMID: 31340923 PMCID: PMC6765557 DOI: 10.12122/j.issn.1673-4254.2019.07.19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Indexed: 01/02/2023]
Abstract
Recent studies have discovered a selective autophagy-lipophagy, which can selectively identify and degrade lipids and plays an important role in regulating cellular lipid metabolism and maintaining intracellular lipid homeostasis. The process of lipophagy can be directly or indirectly regulated by genes, enzymes, transcriptional regulators and other factors. This review examines the role of lipophagy in reducing liver lipid content, regulating pancreatic lipid metabolism, and regulating adipose tissue differentiation, and summarizes the findings of the molecules (Rab GTPase, enzymes, ion channels, transcription factors, small molecular substances) involved in the regulation of lipophagy, which points to new directions for the treatment of diseases caused by lipid accumulation.
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Affiliation(s)
- 琳娜 史
- 南方医科大学 南方医院营养科,广东 广州 510515Department of Nutrition, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - 柯 王
- 华南理工大学食品科学与工程学院,广东 广 州 510640College of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510640, China
| | - 玉娣 邓
- 南方医科大学公共卫生学院,广东 广州 510515School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - 莹娜 王
- 广州市三兴生物技术有限公司,广东 广州 510000Guangzhou Sanxing Biotechnology Co., Ltd., Guangzhou 510000, China
| | - 双玲 朱
- 中山大学附属第一医院,广东 广州 510080First Affiliated Hospital, Sun Yat- sen University, Guangzhou 510080, China
| | - 旭珊 杨
- 南方医科大学公共卫生学院,广东 广州 510515School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - 文镇 廖
- 南方医科大学公共卫生学院,广东 广州 510515School of Public Health, Southern Medical University, Guangzhou 510515, China
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45
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Tunicamycin Sensitivity-Suppression by High Gene Dosage Reveals New Functions of the Yeast Hog1 MAP Kinase. Cells 2019; 8:cells8070710. [PMID: 31336877 PMCID: PMC6678945 DOI: 10.3390/cells8070710] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/03/2019] [Accepted: 07/09/2019] [Indexed: 01/10/2023] Open
Abstract
In the yeast Saccharomyces cerevisiae, components of the High Osmolarity Glycerol (HOG) pathway are important for the response to diverse stresses including response to endoplasmic reticulum stress (ER stress), which is produced by the accumulation of unfolded proteins in the lumen of this organelle. Accumulation of unfolded proteins may be due to the inhibition of protein N-glycosylation, which can be achieved by treatment with the antibiotic tunicamycin (Tn). In this work we were interested in finding proteins involved in the ER stress response regulated by Hog1, the mitogen activated protein kinase (MAPK) of the HOG pathway. A high gene dosage suppression screening allowed us to identify genes that suppressed the sensitivity to Tn shown by a hog1Δ mutant. The suppressors participate in a limited number of cellular processes, including lipid/carbohydrate biosynthesis and protein glycosylation, vesicle-mediated transport and exocytosis, cell wall organization and biogenesis, and cell detoxification processes. The finding of suppressors Rer2 and Srt1, which participate in the dolichol biosynthesis pathway revealed that the hog1Δ strain has a defective polyprenol metabolism. This work uncovers new genetic and functional interactors of Hog1 and contributes to a better understanding of the participation of this MAPK in the ER stress response.
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46
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Abstract
Lipid droplets (LDs), important organelles for energy storage and involved in the development of metabolic disorders, are extremely dynamic and interact with many other cellular compartments to orchestrate lipid metabolism. Little is known about how these organelle contacts are changed according to cellular needs and functions under different metabolic and pathological conditions and which proteins regulate this. Here, we summarize recent exciting discoveries about the reorganization of organelle contacts in steatotic liver, including the identification of novel LD contact site proteins in cell lines and in animals. We also discuss state of the art proteomics workflows that enable the characterization of LD-organelle contacts and tethering proteins and give an outlook how this can inform obesity research.
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Affiliation(s)
- Natalie Krahmer
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Munich-Neuherberg, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,Faculty of Health Sciences, NNF Center for Protein Research, University of Copenhagen, Denmark
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47
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Abstract
Lipid droplets are storage organelles at the centre of lipid and energy homeostasis. They have a unique architecture consisting of a hydrophobic core of neutral lipids, which is enclosed by a phospholipid monolayer that is decorated by a specific set of proteins. Originating from the endoplasmic reticulum, lipid droplets can associate with most other cellular organelles through membrane contact sites. It is becoming apparent that these contacts between lipid droplets and other organelles are highly dynamic and coupled to the cycles of lipid droplet expansion and shrinkage. Importantly, lipid droplet biogenesis and degradation, as well as their interactions with other organelles, are tightly coupled to cellular metabolism and are critical to buffer the levels of toxic lipid species. Thus, lipid droplets facilitate the coordination and communication between different organelles and act as vital hubs of cellular metabolism.
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Affiliation(s)
- James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California-Berkeley, Berkeley, CA, USA.
| | - Pedro Carvalho
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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48
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Hariri H, Speer N, Bowerman J, Rogers S, Fu G, Reetz E, Datta S, Feathers JR, Ugrankar R, Nicastro D, Henne WM. Mdm1 maintains endoplasmic reticulum homeostasis by spatially regulating lipid droplet biogenesis. J Cell Biol 2019; 218:1319-1334. [PMID: 30808705 PMCID: PMC6446837 DOI: 10.1083/jcb.201808119] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/10/2019] [Accepted: 01/22/2019] [Indexed: 12/13/2022] Open
Abstract
Excess fatty acids are toxic to cells but can be sequestered as triacylglycerides in lipid droplets. Hariri et al. show that the tethering protein Mdm1 spatially regulates this process at the junction between the endoplasmic reticulum and the yeast vacuole. These findings suggest that Mdm1 can drive spatially defined lipid droplet production to maintain cell homeostasis and protect against lipotoxicity. Lipid droplets (LDs) serve as cytoplasmic reservoirs for energy-rich fatty acids (FAs) stored in the form of triacylglycerides (TAGs). During nutrient stress, yeast LDs cluster adjacent to the vacuole/lysosome, but how this LD accumulation is coordinated remains poorly understood. The ER protein Mdm1 is a molecular tether that plays a role in clustering LDs during nutrient depletion, but its mechanism of function remains unknown. Here, we show that Mdm1 associates with LDs through its hydrophobic N-terminal region, which is sufficient to demarcate sites for LD budding. Mdm1 binds FAs via its Phox-associated domain and coenriches with fatty acyl–coenzyme A ligase Faa1 at LD bud sites. Consistent with this, loss of MDM1 perturbs free FA activation and Dga1-dependent synthesis of TAGs, elevating the cellular FA level, which perturbs ER morphology and sensitizes yeast to FA-induced lipotoxicity. We propose that Mdm1 coordinates FA activation adjacent to the vacuole to promote LD production in response to stress, thus maintaining ER homeostasis.
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Affiliation(s)
- Hanaa Hariri
- Department of Cell Biology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Natalie Speer
- Department of Cell Biology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jade Bowerman
- Department of Cell Biology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Sean Rogers
- Department of Cell Biology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Gang Fu
- Department of Cell Biology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Evan Reetz
- Department of Cell Biology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Sanchari Datta
- Department of Cell Biology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | - J Ryan Feathers
- Department of Cell Biology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Rupali Ugrankar
- Department of Cell Biology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Daniela Nicastro
- Department of Cell Biology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | - W Mike Henne
- Department of Cell Biology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
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49
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Kim Y, Jung JP, Pack CG, Huh WK. Global analysis of protein homomerization in Saccharomyces cerevisiae. Genome Res 2018; 29:135-145. [PMID: 30567710 PMCID: PMC6314163 DOI: 10.1101/gr.231860.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 11/26/2018] [Indexed: 11/24/2022]
Abstract
In vivo analyses of the occurrence, subcellular localization, and dynamics of protein–protein interactions (PPIs) are important issues in functional proteomic studies. The bimolecular fluorescence complementation (BiFC) assay has many advantages in that it provides a reliable way to detect PPIs in living cells with minimal perturbation of the structure and function of the target proteins. Previously, to facilitate the application of the BiFC assay to genome-wide analysis of PPIs, we generated a collection of yeast strains expressing full-length proteins tagged with the N-terminal fragment of Venus (VN), a yellow fluorescent protein variant, from their own native promoters. In the present study, we constructed a VC (the C-terminal fragment of Venus) fusion library consisting of 5671 MATα strains expressing C-terminally VC-tagged proteins (representing ∼91% of the yeast proteome). For genome-wide analysis of protein homomer formation, we mated each strain in the VC fusion library with its cognate strain in the VN fusion library and performed the BiFC assay. From this analysis, we identified 186 homomer candidates. We further investigated the functional relevance of the homomerization of Pln1, a yeast perilipin. Our data set provides a useful resource for understanding the physiological roles of protein homomerization. Furthermore, the VC fusion library together with the VN fusion library will provide a valuable platform to systematically analyze PPIs in the natural cellular context.
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Affiliation(s)
- Yeonsoo Kim
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jong Pil Jung
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Chan-Gi Pack
- ASAN Institute for Life Sciences, ASAN Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Won-Ki Huh
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.,Institute of Microbiology, Seoul National University, Seoul 08826, Republic of Korea
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50
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Gemmink A, Daemen S, Kuijpers HJH, Schaart G, Duimel H, López-Iglesias C, van Zandvoort MAMJ, Knoops K, Hesselink MKC. Super-resolution microscopy localizes perilipin 5 at lipid droplet-mitochondria interaction sites and at lipid droplets juxtaposing to perilipin 2. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:1423-1432. [PMID: 30591149 DOI: 10.1016/j.bbalip.2018.08.016] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/06/2018] [Accepted: 08/29/2018] [Indexed: 01/26/2023]
Abstract
OBJECTIVE Intramyocellular lipid droplets (LD) and their coat proteins PLIN2 and PLIN5 are involved in lipolysis, with a putative role for PLIN5 in mitochondrial tethering. Reportedly, these proteins co-localize and cover the surface of the LD. To provide the spatial basis for understanding how these proteins possess their distinct roles, we examined the precise location of PLIN2 and PLIN5 and explored PLIN5 presence at LD-mitochondria contact sites using Stimulated emission depletion (STED) microscopy and correlative light-electron microscopy (CLEM) in human skeletal muscle sections. METHODS LDs were stained by MDH together with combinations of mitochondrial proteins and PLINs. Subcellular distribution and co-localization of PLIN proteins and mitochondria was imaged by STED microscopy (Leica TCS SP8) and quantified using Pearson's correlation coefficients and intensity profile plots. CLEM was employed to examine the presence of PLIN5 on mitochondria-LD contact sites. RESULTS Both PLIN2 and PLIN5 localized to the LD in a dot-like, juxtaposed fashion rather than colocalizing and covering the entire LD. Both STED and CLEM revealed a high fraction of PLIN5 at the LD-mitochondria interface, but not at mitochondrial cristae, as suggested previously. CONCLUSION Using two super-resolution imaging approaches, this is the first study to show that in sections of human skeletal muscle PLIN2 and PLIN5 localize to the LD at distinct sites, with abundance of PLIN5 at LD-mitochondria tethering sites. This novel spatial information uncovers that PLIN proteins do not serve as lipolytic barriers but rather are docking sites for proteins facilitating selective lipase access under a variety of lipolytic conditions.
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Affiliation(s)
- Anne Gemmink
- Department of Nutrition and Movement Sciences, Maastricht University Medical Centre+, 6200 MD Maastricht, the Netherlands; NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht, the Netherlands
| | - Sabine Daemen
- Department of Nutrition and Movement Sciences, Maastricht University Medical Centre+, 6200 MD Maastricht, the Netherlands; NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht, the Netherlands
| | - Helma J H Kuijpers
- Microscopy Core Lab, FHML and M4I Maastricht Multimodal Molecular Imaging Institute, Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Gert Schaart
- Department of Nutrition and Movement Sciences, Maastricht University Medical Centre+, 6200 MD Maastricht, the Netherlands; NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht, the Netherlands
| | - Hans Duimel
- Microscopy Core Lab, FHML and M4I Maastricht Multimodal Molecular Imaging Institute, Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Carmen López-Iglesias
- Microscopy Core Lab, FHML and M4I Maastricht Multimodal Molecular Imaging Institute, Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Marc A M J van Zandvoort
- Department of Genetics & Cell Biology - Molecular Cell Biology, Maastricht University Medical Centre+, 6200 MD Maastricht, the Netherlands; CARIM - Cardiovascular Research Institute Maastricht, Maastricht, the Netherlands; Institute for Molecular Cardiovascular Research IMCAR, Universitätsklinikum, Aachen, Pauwelstrasse 30, Aachen, Germany
| | - Kèvin Knoops
- Microscopy Core Lab, FHML and M4I Maastricht Multimodal Molecular Imaging Institute, Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Matthijs K C Hesselink
- Department of Nutrition and Movement Sciences, Maastricht University Medical Centre+, 6200 MD Maastricht, the Netherlands; NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht, the Netherlands.
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