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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 S. cerevisiae to glucose. J Biol Chem 2024:107665. [PMID: 39128724 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, 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 (TCA) 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, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| | - Keiko Sakuragi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| | - Atsuko Ikeda
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| | - Yujia Yang
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| | - Saku Sasaki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| | - Kazuki Hanaoka
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| | - Misako Araki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| | - Tomoko Shibata
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi, Hiroshima 739-0046, Japan
| | - Muneyoshi Kanai
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi, Hiroshima 739-0046, Japan
| | - Kouichi Funato
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan.
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Liu D, Yuan H, Chen S, Ferro-Novick S, Novick P. Different ER-plasma membrane tethers play opposing roles in autophagy of the cortical ER. Proc Natl Acad Sci U S A 2024; 121:e2321991121. [PMID: 38838012 PMCID: PMC11181077 DOI: 10.1073/pnas.2321991121] [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: 12/13/2023] [Accepted: 05/08/2024] [Indexed: 06/07/2024] Open
Abstract
The endoplasmic reticulum (ER) undergoes degradation by selective macroautophagy (ER-phagy) in response to starvation or the accumulation of misfolded proteins within its lumen. In yeast, actin assembly at sites of contact between the cortical ER (cER) and endocytic pits acts to displace elements of the ER from their association with the plasma membrane (PM) so they can interact with the autophagosome assembly machinery near the vacuole. A collection of proteins tether the cER to the PM. Of these, Scs2/22 and Ist2 are required for cER-phagy, most likely through their roles in lipid transport, while deletion of the tricalbins, TCB1/2/3, bypasses those requirements. An artificial ER-PM tether blocks cER-phagy in both the wild type (WT) and a strain lacking endogenous tethers, supporting the importance of cER displacement from the PM. Scs2 and Ist2 can be cross-linked to the selective cER-phagy receptor, Atg40. The COPII cargo adaptor subunit, Lst1, associates with Atg40 and is required for cER-phagy. This requirement is also bypassed by deletion of the ER-PM tethers, suggesting a role for Lst1 prior to the displacement of the cER from the PM during cER-phagy. Although pexophagy and mitophagy also require actin assembly, deletion of ER-PM tethers does not bypass those requirements. We propose that within the context of rapamycin-induced cER-phagy, Scs2/22, Ist2, and Lst1 promote the local displacement of an element of the cER from the cortex, while Tcb1/2/3 act in opposition, anchoring the cER to the plasma membrane.
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Affiliation(s)
- Dongmei Liu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093-0668
| | - Hua Yuan
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093-0668
| | - Shuliang Chen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093-0668
| | - Susan Ferro-Novick
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093-0668
| | - Peter Novick
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093-0668
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3
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Chen SY, Chang CK, Lan CY. Antimicrobial peptide LL-37 disrupts plasma membrane and calcium homeostasis in Candida albicans via the Rim101 pathway. Microbiol Spectr 2023; 11:e0255123. [PMID: 37888991 PMCID: PMC10715129 DOI: 10.1128/spectrum.02551-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Candida albicans is a major human fungal pathogen, and antimicrobial peptides are key components of innate immunity. Studying the interplay between C. albicans and human antimicrobial peptides would enhance a better understanding of pathogen-host interactions. Moreover, potential applications of antimicrobial peptides in antifungal therapy have aroused great interest. This work explores new mechanisms of LL-37 against C. albicans and reveals the complex connection among calcium homeostasis, oxidative stress, signaling, and possibly organelle interaction. Notably, these findings support the possible use of antimicrobial peptides to prevent and treat fungal infections.
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Affiliation(s)
- Sheng-Yuan Chen
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Che-Kang Chang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chung-Yu Lan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
- School of Medicine, National Tsing Hua University, Hsinchu, Taiwan
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Davis J, Meyer T, Smolnig M, Smethurst DG, Neuhaus L, Heyden J, Broeskamp F, Edrich ES, Knittelfelder O, Kolb D, Haar TVD, Gourlay CW, Rockenfeller P. A dynamic actin cytoskeleton is required to prevent constitutive VDAC-dependent MAPK signalling and aberrant lipid homeostasis. iScience 2023; 26:107539. [PMID: 37636069 PMCID: PMC10450525 DOI: 10.1016/j.isci.2023.107539] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/14/2023] [Accepted: 07/28/2023] [Indexed: 08/29/2023] Open
Abstract
The dynamic nature of the actin cytoskeleton is required to coordinate many cellular processes, and a loss of its plasticity has been linked to accelerated cell aging and attenuation of adaptive response mechanisms. Cofilin is an actin-binding protein that controls actin dynamics and has been linked to mitochondrial signaling pathways that control drug resistance and cell death. Here we show that cofilin-driven chronic depolarization of the actin cytoskeleton activates cell wall integrity mitogen-activated protein kinase (MAPK) signalling and disrupts lipid homeostasis in a voltage-dependent anion channel (VDAC)-dependent manner. Expression of the cof1-5 mutation, which reduces the dynamic nature of actin, triggers loss of cell wall integrity, vacuole fragmentation, disruption of lipid homeostasis, lipid droplet (LD) accumulation, and the promotion of cell death. The integrity of the actin cytoskeleton is therefore essential to maintain the fidelity of MAPK signaling, lipid homeostasis, and cell health in S. cerevisiae.
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Affiliation(s)
- Jack Davis
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Thorsten Meyer
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
| | - Martin Smolnig
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
| | | | - Lisa Neuhaus
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
| | - Jonas Heyden
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
| | - Filomena Broeskamp
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
| | | | - Oskar Knittelfelder
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Dagmar Kolb
- Medical University of Graz, Core Facility Ultrastructure Analysis, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria
| | - Tobias von der Haar
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Campbell W. Gourlay
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Patrick Rockenfeller
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
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Nenadic A, Zaman MF, Johansen J, Volpiana MW, Beh CT. Increased Phospholipid Flux Bypasses Overlapping Essential Requirements for the Yeast Sac1p Phosphoinositide Phosphatase and ER-PM Membrane Contact Sites. J Biol Chem 2023; 299:105092. [PMID: 37507017 PMCID: PMC10470028 DOI: 10.1016/j.jbc.2023.105092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
In budding yeast cells, much of the inner surface of the plasma membrane (PM) is covered with the endoplasmic reticulum (ER). This association is mediated by seven ER membrane proteins that confer cortical ER-PM association at membrane contact sites (MCSs). Several of these membrane "tether" proteins are known to physically interact with the phosphoinositide phosphatase Sac1p. However, it is unclear how or if these interactions are necessary for their interdependent functions. We find that SAC1 inactivation in cells lacking the homologous synaptojanin-like genes INP52 and INP53 results in a significant increase in cortical ER-PM MCSs. We show in sac1Δ, sac1tsinp52Δ inp53Δ, or Δ-super-tether (Δ-s-tether) cells lacking all seven ER-PM tethering genes that phospholipid biosynthesis is disrupted and phosphoinositide distribution is altered. Furthermore, SAC1 deletion in Δ-s-tether cells results in lethality, indicating a functional overlap between SAC1 and ER-PM tethering genes. Transcriptomic profiling indicates that SAC1 inactivation in either Δ-s-tether or inp52Δ inp53Δ cells induces an ER membrane stress response and elicits phosphoinositide-dependent changes in expression of autophagy genes. In addition, by isolating high-copy suppressors that rescue sac1Δ Δ-s-tether lethality, we find that key phospholipid biosynthesis genes bypass the overlapping function of SAC1 and ER-PM tethers and that overexpression of the phosphatidylserine/phosphatidylinositol-4-phosphate transfer protein Osh6 also provides limited suppression. Combined with lipidomic analysis and determinations of intracellular phospholipid distributions, these results suggest that Sac1p and ER phospholipid flux controls lipid distribution to drive Osh6p-dependent phosphatidylserine/phosphatidylinositol-4-phosphate counter-exchange at ER-PM MCSs.
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Affiliation(s)
- Aleksa Nenadic
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Mohammad F Zaman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jesper Johansen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Matthew W Volpiana
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Christopher T Beh
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada; Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, British Columbia, Canada.
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6
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Poorinmohammad N, Fu J, Wabeke B, Kerkhoven EJ. Validated Growth Rate-Dependent Regulation of Lipid Metabolism in Yarrowia lipolytica. Int J Mol Sci 2022; 23:ijms23158517. [PMID: 35955650 PMCID: PMC9369070 DOI: 10.3390/ijms23158517] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 02/06/2023] Open
Abstract
Given the strong potential of Yarrowia lipolytica to produce lipids for use as renewable fuels and oleochemicals, it is important to gain in-depth understanding of the molecular mechanism underlying its lipid accumulation. As cellular growth rate affects biomass lipid content, we performed a comparative proteomic analysis of Y. lipolytica grown in nitrogen-limited chemostat cultures at different dilution rates. After confirming the correlation between growth rate and lipid accumulation, we were able to identify various cellular functions and biological mechanisms involved in oleaginousness. Inspection of significantly up- and downregulated proteins revealed nonintuitive processes associated with lipid accumulation in this yeast. This included proteins related to endoplasmic reticulum (ER) stress, ER–plasma membrane tether proteins, and arginase. Genetic engineering of selected targets validated that some genes indeed affected lipid accumulation. They were able to increase lipid content and were complementary to other genetic engineering strategies to optimize lipid yield.
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Affiliation(s)
- Naghmeh Poorinmohammad
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; (N.P.); (J.F.); (B.W.)
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Jing Fu
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; (N.P.); (J.F.); (B.W.)
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Bob Wabeke
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; (N.P.); (J.F.); (B.W.)
| | - Eduard J. Kerkhoven
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; (N.P.); (J.F.); (B.W.)
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- Correspondence:
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