1
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Schlarmann P, Sakuragi K, Ikeda A, Yang Y, Sasaki S, Hanaoka K, Araki M, Shibata T, Kanai M, Funato K. The tricalbin family of membrane contact site tethers is involved in the transcriptional responses of Saccharomyces cerevisiae to glucose. J Biol Chem 2024; 300:107665. [PMID: 39128724 PMCID: PMC11408865 DOI: 10.1016/j.jbc.2024.107665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/24/2024] [Accepted: 08/05/2024] [Indexed: 08/13/2024] Open
Abstract
Cellular organelles maintain areas of close apposition with other organelles at which the cytosolic gap in between them is reduced to a minimum. These membrane contact sites (MCS) are vital for organelle communication and are formed by molecular tethers that physically connect opposing membranes. Although many regulatory pathways are known to converge at MCS, a link between MCS and transcriptional regulation-the primary mechanism through which cells adapt their metabolism to environmental cues-remains largely elusive. In this study, we performed RNA-sequencing on Saccharomyces cerevisiae cells lacking tricalbin proteins (Tcb1, Tcb2, and Tcb3), a family of tethering proteins that connect the endoplasmic reticulum with the plasma membrane and Golgi, to investigate if gene expression is altered when MCS are disrupted. Our results indicate that in the tcb1Δ2Δ3Δ strain, pathways responsive to a high-glucose environment, including glycolysis, fermentation, amino acid synthesis, and low-affinity glucose uptake, are upregulated. Conversely, pathways crucial during glucose depletion, such as the tricarboxylic acid cycle, respiration, high-affinity glucose uptake, and amino acid uptake are downregulated. In addition, we demonstrate that the altered gene expression of tcb1Δ2Δ3Δ in glucose metabolism correlates with increased growth, glucose consumption, CO2 production, and ethanol generation. In conclusion, our findings reveal that tricalbin protein deletion induces a shift in gene expression patterns mimicking cellular responses to a high-glucose environment. This suggests that MCS play a role in sensing and signaling pathways that modulate gene transcription in response to glucose availability.
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Affiliation(s)
- Philipp Schlarmann
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Keiko Sakuragi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Atsuko Ikeda
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yujia Yang
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Saku Sasaki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kazuki Hanaoka
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Misako Araki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Tomoko Shibata
- National Research Institute of Brewing, Higashi-Hiroshima, Japan
| | - Muneyoshi Kanai
- National Research Institute of Brewing, Higashi-Hiroshima, Japan
| | - Kouichi Funato
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.
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2
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Bandyopadhyay S, Adebayo D, Obaseki E, Hariri H. Lysosomal membrane contact sites: Integrative hubs for cellular communication and homeostasis. CURRENT TOPICS IN MEMBRANES 2024; 93:85-116. [PMID: 39181579 DOI: 10.1016/bs.ctm.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Lysosomes are more than just cellular recycling bins; they play a crucial role in regulating key cellular functions. Proper lysosomal function is essential for growth pathway regulation, cell proliferation, and metabolic homeostasis. Impaired lysosomal function is associated with lipid storage disorders and neurodegenerative diseases. Lysosomes form extensive and dynamic close contacts with the membranes of other organelles, including the endoplasmic reticulum, mitochondria, peroxisomes, and lipid droplets. These membrane contacts sites (MCSs) are vital for many lysosomal functions. In this chapter, we will explore lysosomal MCSs focusing on the machinery that mediates these contacts, how they are regulated, and their functional implications on physiology and pathology.
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Affiliation(s)
- Sumit Bandyopadhyay
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Daniel Adebayo
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Eseiwi Obaseki
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Hanaa Hariri
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States.
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3
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Prokisch S, Büttner S. Partitioning into ER membrane microdomains impacts autophagic protein turnover during cellular aging. Sci Rep 2024; 14:13653. [PMID: 38871812 DOI: 10.1038/s41598-024-64493-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 06/09/2024] [Indexed: 06/15/2024] Open
Abstract
Eukaryotic membranes are compartmentalized into distinct micro- and nanodomains that rearrange dynamically in response to external and internal cues. This lateral heterogeneity of the lipid bilayer and associated clustering of distinct membrane proteins contribute to the spatial organization of numerous cellular processes. Here, we show that membrane microdomains within the endoplasmic reticulum (ER) of yeast cells are reorganized during metabolic reprogramming and aging. Using biosensors with varying transmembrane domain length to map lipid bilayer thickness, we demonstrate that in young cells, microdomains of increased thickness mainly exist within the nuclear ER, while progressing cellular age drives the formation of numerous microdomains specifically in the cortical ER. Partitioning of biosensors with long transmembrane domains into these microdomains increased protein stability and prevented autophagic removal. In contrast, reporters with short transmembrane domains progressively accumulated at the membrane contact site between the nuclear ER and the vacuole, the so-called nucleus-vacuole junction (NVJ), and were subjected to turnover via selective microautophagy occurring specifically at these sites. Reporters with long transmembrane domains were excluded from the NVJ. Our data reveal age-dependent rearrangement of the lateral organization of the ER and establish transmembrane domain length as a determinant of membrane contact site localization and autophagic degradation.
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Affiliation(s)
- Simon Prokisch
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden.
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4
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Álvarez-Guerra I, Block E, Broeskamp F, Gabrijelčič S, Infant T, de Ory A, Habernig L, Andréasson C, Levine TP, Höög JL, Büttner S. LDO proteins and Vac8 form a vacuole-lipid droplet contact site to enable starvation-induced lipophagy in yeast. Dev Cell 2024; 59:759-775.e5. [PMID: 38354739 DOI: 10.1016/j.devcel.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 11/15/2023] [Accepted: 01/18/2024] [Indexed: 02/16/2024]
Abstract
Lipid droplets (LDs) are fat storage organelles critical for energy and lipid metabolism. Upon nutrient exhaustion, cells consume LDs via gradual lipolysis or via lipophagy, the en bloc uptake of LDs into the vacuole. Here, we show that LDs dock to the vacuolar membrane via a contact site that is required for lipophagy in yeast. The LD-localized LDO proteins carry an intrinsically disordered region that directly binds vacuolar Vac8 to form vCLIP, the vacuolar-LD contact site. Nutrient limitation drives vCLIP formation, and its inactivation blocks lipophagy, resulting in impaired caloric restriction-induced longevity. We establish a functional link between lipophagy and microautophagy of the nucleus, both requiring Vac8 to form respective contact sites upon metabolic stress. In sum, we identify the tethering machinery of vCLIP and find that Vac8 provides a platform for multiple and competing contact sites associated with autophagy.
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Affiliation(s)
- Irene Álvarez-Guerra
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Emma Block
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Filomena Broeskamp
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Sonja Gabrijelčič
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Terence Infant
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Ana de Ory
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Lukas Habernig
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Tim P Levine
- UCL Institute of Ophthalmology, Bath Street, London EC1V 9EL, UK
| | - Johanna L Höög
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden.
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5
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Bâcle J, Groizard L, Kumanski S, Moriel-Carretero M. Nuclear envelope-remodeling events as models to assess the potential role of membranes on genome stability. FEBS Lett 2023; 597:1946-1956. [PMID: 37339935 DOI: 10.1002/1873-3468.14688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/31/2023] [Accepted: 05/31/2023] [Indexed: 06/22/2023]
Abstract
The nuclear envelope (NE) encloses the genetic material and functions in chromatin organization and stability. In Saccharomyces cerevisiae, the NE is bound to the ribosomal DNA (rDNA), highly repeated and transcribed, thus prone to genetic instability. While tethering limits instability, it simultaneously triggers notable NE remodeling. We posit here that NE remodeling may contribute to genome integrity maintenance. The NE importance in genome expression, structure, and integrity is well recognized, yet studies mostly focus on peripheral proteins and nuclear pores, not on the membrane itself. We recently characterized a NE invagination drastically obliterating the rDNA, which we propose here as a model to probe if and how membranes play an active role in genome stability preservation.
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Affiliation(s)
- Janélie Bâcle
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Centre National de la Recherche Scientifique, Université de Montpellier, France
| | - Léa Groizard
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Centre National de la Recherche Scientifique, Université de Montpellier, France
| | - Sylvain Kumanski
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Centre National de la Recherche Scientifique, Université de Montpellier, France
| | - María Moriel-Carretero
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Centre National de la Recherche Scientifique, Université de Montpellier, France
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6
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Zhang Y, Zhou Y, Fang W, Zhu H, Ye C, Zhang D, Lee HJ. Spatial sterol metabolism unveiled by stimulated Raman imaging. Front Chem 2023; 11:1166313. [PMID: 37065823 PMCID: PMC10090450 DOI: 10.3389/fchem.2023.1166313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Graphical AbstractHigh-resolution stimulated Raman scattering (SRS) imaging of a genetically engineered model (GEM) enables metabolite imaging in a yeast model and uncovers an unexpected regulatory mechanism of sterol metabolism, providing new insights underpinning the distributional and functional importance of sterol in cells. SRS-GEM demonstrates a promising platform to explore unknown metabolic mechanisms beyond the reach of conventional approaches.
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Affiliation(s)
- Yongqing Zhang
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Interdisciplinary Centre for Quantum Information, Zhejiang University, Hangzhou, China
| | - Yihui Zhou
- Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Wen Fang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Hanlin Zhu
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Interdisciplinary Centre for Quantum Information, Zhejiang University, Hangzhou, China
| | - Cunqi Ye
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- *Correspondence: Cunqi Ye, ; Delong Zhang, ; Hyeon Jeong Lee,
| | - Delong Zhang
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Interdisciplinary Centre for Quantum Information, Zhejiang University, Hangzhou, China
- *Correspondence: Cunqi Ye, ; Delong Zhang, ; Hyeon Jeong Lee,
| | - Hyeon Jeong Lee
- Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
- *Correspondence: Cunqi Ye, ; Delong Zhang, ; Hyeon Jeong Lee,
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7
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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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8
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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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9
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Windham IA, Cohen S. Lipid droplets go through a (liquid crystalline) phase. J Cell Biol 2022; 221:e202210008. [PMID: 36264229 PMCID: PMC9587377 DOI: 10.1083/jcb.202210008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Lipid droplets (LDs) are key organelles for fat storage and trafficking. In this issue, Rogers et al. (2022. J. Cell Biol.https://doi.org/10.1083/jcb.202205053) show that glucose restriction triggers liquid crystalline lattice formation within LDs, which in turn alters the recruitment of proteins to the LD surface.
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Affiliation(s)
- Ian A. Windham
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sarah Cohen
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
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10
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Recent advances of integrated microfluidic systems for fungal and bacterial analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Peselj C, Ebrahimi M, Broeskamp F, Prokisch S, Habernig L, Alvarez-Guerra I, Kohler V, Vögtle FN, Büttner S. Sterol Metabolism Differentially Contributes to Maintenance and Exit of Quiescence. Front Cell Dev Biol 2022; 10:788472. [PMID: 35237594 PMCID: PMC8882848 DOI: 10.3389/fcell.2022.788472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 01/20/2022] [Indexed: 01/01/2023] Open
Abstract
Nutrient starvation initiates cell cycle exit and entry into quiescence, a reversible, non-proliferative state characterized by stress tolerance, longevity and large-scale remodeling of subcellular structures. Depending on the nature of the depleted nutrient, yeast cells are assumed to enter heterogeneous quiescent states with unique but mostly unexplored characteristics. Here, we show that storage and consumption of neutral lipids in lipid droplets (LDs) differentially impacts the regulation of quiescence driven by glucose or phosphate starvation. Upon prolonged glucose exhaustion, LDs were degraded in the vacuole via Atg1-dependent lipophagy. In contrast, yeast cells entering quiescence due to phosphate exhaustion massively over-accumulated LDs that clustered at the vacuolar surface but were not engulfed via lipophagy. Excessive LD biogenesis required contact formation between the endoplasmic reticulum and the vacuole at nucleus-vacuole junctions and was accompanied by a shift of the cellular lipid profile from membrane towards storage lipids, driven by a transcriptional upregulation of enzymes generating neutral lipids, in particular sterol esters. Importantly, sterol ester biogenesis was critical for long-term survival of phosphate-exhausted cells and supported rapid quiescence exit upon nutrient replenishment, but was dispensable for survival and regrowth of glucose-exhausted cells. Instead, these cells relied on de novo synthesis of sterols and fatty acids for quiescence exit and regrowth. Phosphate-exhausted cells efficiently mobilized storage lipids to support several rounds of cell division even in presence of inhibitors of fatty acid and sterol biosynthesis. In sum, our results show that neutral lipid biosynthesis and mobilization to support quiescence maintenance and exit is tailored to the respective nutrient scarcity.
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Affiliation(s)
- Carlotta Peselj
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Mahsa Ebrahimi
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Filomena Broeskamp
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Simon Prokisch
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Lukas Habernig
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Irene Alvarez-Guerra
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Verena Kohler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - F.-Nora Vögtle
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
- Network Aging Research, Heidelberg University, Heidelberg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
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12
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Kern AF, Yang GX, Khosla NM, Ang RML, Snyder MP, Fraser HB. Divergent patterns of selection on metabolite levels and gene expression. BMC Ecol Evol 2021; 21:185. [PMID: 34587900 PMCID: PMC8482673 DOI: 10.1186/s12862-021-01915-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/06/2021] [Indexed: 11/19/2022] Open
Abstract
Background Natural selection can act on multiple genes in the same pathway, leading to polygenic adaptation. For example, adaptive changes were found to down-regulate six genes involved in ergosterol biosynthesis—an essential pathway targeted by many antifungal drugs—in some strains of the yeast Saccharomyces cerevisiae. However, the impact of this polygenic adaptation on metabolite levels was unknown. Here, we performed targeted mass spectrometry to measure the levels of eight metabolites in this pathway in 74 yeast strains from a genetic cross. Results Through quantitative trait locus (QTL) mapping we identified 19 loci affecting ergosterol pathway metabolite levels, many of which overlap loci that also impact gene expression within the pathway. We then used the recently developed v-test, which identified selection acting upon three metabolite levels within the pathway, none of which were predictable from the gene expression adaptation. Conclusions These data showed that effects of selection on metabolite levels were complex and not predictable from gene expression data. This suggests that a deeper understanding of metabolism is necessary before we can understand the impacts of even relatively straightforward gene expression adaptations on metabolic pathways. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01915-5.
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Affiliation(s)
| | | | - Neil M Khosla
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Roy Moh Lik Ang
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Hunter B Fraser
- Department of Biology, Stanford University, Stanford, CA, USA.
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13
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Fausten RM, Bohnert M. A move in response to starvation. eLife 2021; 10:69680. [PMID: 34061033 PMCID: PMC8169105 DOI: 10.7554/elife.69680] [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: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
When a yeast cell runs out of fuel, it can increase the flux through a central metabolic pathway by simply changing the location of an enzyme.
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Affiliation(s)
- Rebecca Martina Fausten
- Institute of Cell Dynamics and Imaging, and the Cells in Motion Interfaculty Centre, University of Münster, Münster, Germany
| | - Maria Bohnert
- Institute of Cell Dynamics and Imaging, and the Cells in Motion Interfaculty Centre, University of Münster, Münster, Germany
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