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Papagiannidis D, Bircham PW, Lüchtenborg C, Pajonk O, Ruffini G, Brügger B, Schuck S. Ice2 promotes ER membrane biogenesis in yeast by inhibiting the conserved lipin phosphatase complex. EMBO J 2021; 40:e107958. [PMID: 34617598 PMCID: PMC8591542 DOI: 10.15252/embj.2021107958] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 11/30/2022] Open
Abstract
Cells dynamically adapt organelle size to current physiological demand. Organelle growth requires membrane biogenesis and therefore needs to be coordinated with lipid metabolism. The endoplasmic reticulum (ER) can undergo massive expansion, but the underlying regulatory mechanisms are largely unclear. Here, we describe a genetic screen for factors involved in ER membrane expansion in budding yeast and identify the ER transmembrane protein Ice2 as a strong hit. We show that Ice2 promotes ER membrane biogenesis by opposing the phosphatidic acid phosphatase Pah1, called lipin in metazoa. Specifically, Ice2 inhibits the conserved Nem1‐Spo7 complex and thus suppresses the dephosphorylation and activation of Pah1. Furthermore, Ice2 cooperates with the transcriptional regulation of lipid synthesis genes and helps to maintain cell homeostasis during ER stress. These findings establish the control of the lipin phosphatase complex as an important mechanism for regulating ER membrane biogenesis.
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Affiliation(s)
- Dimitrios Papagiannidis
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and Cell Networks Cluster of Excellence, Heidelberg, Germany.,Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Peter W Bircham
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and Cell Networks Cluster of Excellence, Heidelberg, Germany
| | | | - Oliver Pajonk
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and Cell Networks Cluster of Excellence, Heidelberg, Germany.,Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Giulia Ruffini
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and Cell Networks Cluster of Excellence, Heidelberg, Germany.,Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Sebastian Schuck
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and Cell Networks Cluster of Excellence, Heidelberg, Germany.,Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
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Schäfer JA, Schessner JP, Bircham PW, Tsuji T, Funaya C, Pajonk O, Schaeff K, Ruffini G, Papagiannidis D, Knop M, Fujimoto T, Schuck S. ESCRT machinery mediates selective microautophagy of endoplasmic reticulum in yeast. EMBO J 2019; 39:e102586. [PMID: 31802527 PMCID: PMC6960443 DOI: 10.15252/embj.2019102586] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 10/30/2019] [Accepted: 11/11/2019] [Indexed: 01/14/2023] Open
Abstract
ER‐phagy, the selective autophagy of endoplasmic reticulum (ER), safeguards organelle homeostasis by eliminating misfolded proteins and regulating ER size. ER‐phagy can occur by macroautophagic and microautophagic mechanisms. While dedicated machinery for macro‐ER‐phagy has been discovered, the molecules and mechanisms mediating micro‐ER‐phagy remain unknown. Here, we first show that micro‐ER‐phagy in yeast involves the conversion of stacked cisternal ER into multilamellar ER whorls during microautophagic uptake into lysosomes. Second, we identify the conserved Nem1‐Spo7 phosphatase complex and the ESCRT machinery as key components for micro‐ER‐phagy. Third, we demonstrate that macro‐ and micro‐ER‐phagy are parallel pathways with distinct molecular requirements. Finally, we provide evidence that the ESCRT machinery directly functions in scission of the lysosomal membrane to complete the microautophagic uptake of ER. These findings establish a framework for a mechanistic understanding of micro‐ER‐phagy and, thus, a comprehensive appreciation of the role of autophagy in ER homeostasis.
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Affiliation(s)
- Jasmin A Schäfer
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Julia P Schessner
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Peter W Bircham
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Takuma Tsuji
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Charlotta Funaya
- Electron Microscopy Core Facility, Heidelberg University, Heidelberg, Germany
| | - Oliver Pajonk
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Katharina Schaeff
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Giulia Ruffini
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Dimitrios Papagiannidis
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Michael Knop
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Toyoshi Fujimoto
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Sebastian Schuck
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
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