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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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2
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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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Abstract
Beer would not exist without microbes. During fermentation, yeast cells convert cereal‐derived sugars into ethanol and CO2. Yeast also produces a wide array of aroma compounds that influence beer taste and aroma. The complex interaction between all these aroma compounds results in each beer having its own distinctive palette. This article contains all protocols needed to brew beer in a standard lab environment and focuses on the use of yeast in beer brewing. More specifically, it provides protocols for yeast propagation, brewing calculations and, of course, beer brewing. At the end, we have also included protocols for analyses that can be performed on the resulting brew, with a focus on yeast‐derived aroma compounds. © 2019 The Authors.
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Affiliation(s)
- Florian A Thesseling
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Heverlee, Belgium
| | - Peter W Bircham
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Heverlee, Belgium
| | - Stijn Mertens
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Heverlee, Belgium
| | - Karin Voordeckers
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Heverlee, Belgium
| | - Kevin J Verstrepen
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Heverlee, Belgium
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4
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Szoradi T, Schaeff K, Garcia-Rivera EM, Itzhak DN, Schmidt RM, Bircham PW, Leiss K, Diaz-Miyar J, Chen VK, Muzzey D, Borner GHH, Schuck S. SHRED Is a Regulatory Cascade that Reprograms Ubr1 Substrate Specificity for Enhanced Protein Quality Control during Stress. Mol Cell 2018; 70:1025-1037.e5. [PMID: 29861160 DOI: 10.1016/j.molcel.2018.04.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 03/12/2018] [Accepted: 04/27/2018] [Indexed: 12/31/2022]
Abstract
When faced with proteotoxic stress, cells mount adaptive responses to eliminate aberrant proteins. Adaptive responses increase the expression of protein folding and degradation factors to enhance the cellular quality control machinery. However, it is unclear whether and how this augmented machinery acquires new activities during stress. Here, we uncover a regulatory cascade in budding yeast that consists of the hydrophilin protein Roq1/Yjl144w, the HtrA-type protease Ynm3/Nma111, and the ubiquitin ligase Ubr1. Various stresses stimulate ROQ1 transcription. The Roq1 protein is cleaved by Ynm3. Cleaved Roq1 interacts with Ubr1, transforming its substrate specificity. Altered substrate recognition by Ubr1 accelerates proteasomal degradation of misfolded as well as native proteins at the endoplasmic reticulum membrane and in the cytosol. We term this pathway stress-induced homeostatically regulated protein degradation (SHRED) and propose that it promotes physiological adaptation by reprogramming a key component of the quality control machinery.
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Affiliation(s)
- Tamas Szoradi
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, 69120 Heidelberg, Germany
| | - Katharina Schaeff
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, 69120 Heidelberg, Germany
| | - Enrique M Garcia-Rivera
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel N Itzhak
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Rolf M Schmidt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, 69120 Heidelberg, Germany
| | - Peter W Bircham
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, 69120 Heidelberg, Germany
| | - Kevin Leiss
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, 69120 Heidelberg, Germany
| | - Juan Diaz-Miyar
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, 69120 Heidelberg, Germany
| | - Vivian K Chen
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dale Muzzey
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Georg H H Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Sebastian Schuck
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, 69120 Heidelberg, Germany.
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5
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Venturi V, Little R, Bircham PW, Rodigheri Brito J, Atkinson PH, Maass DR, Teesdale-Spittle PH. Characterisation of the biological response of Saccharomyces cerevisiae to the loss of an allele of the eukaryotic initiation factor 4A. Biochem Biophys Res Commun 2018; 496:1082-1087. [PMID: 29397069 DOI: 10.1016/j.bbrc.2018.01.137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 01/21/2018] [Indexed: 11/29/2022]
Abstract
The translation initiation machinery is emerging as an important target for therapeutic intervention, with potential in the treatment of cancer, viral infections, and muscle wasting. Amongst the targets for pharmacological control of translation initiation is the eukaryotic initiation factor 4A (eIF4A), an RNA helicase that is essential for cap-dependent translation initiation. We set out to explore the system-wide impact of a reduction of functional eIF4A. To this end, we investigated the effect of deletion of TIF1, one of the duplicate genes that produce eIF4A in yeast, through synthetic genetic array interactions and system-wide changes in GFP-tagged protein abundances. We show that there is a biological response to deletion of the TIF1 gene that extends through the proteostasis network. Effects of the deletion are apparent in processes as distributed as chromatin remodelling, ribosome biogenesis, amino acid metabolism, and protein trafficking. The results from this study identify protein complexes and pathways that will make ideal targets for combination therapies with eIF4A inhibitors.
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Affiliation(s)
- Veronica Venturi
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Richard Little
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Peter W Bircham
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | | | - Paul H Atkinson
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - David R Maass
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
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6
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Low YS, Bircham PW, Maass DR, Atkinson PH. Kinetochore genes are required to fully activate secretory pathway expansion in S. cerevisiae under induced ER stress. Mol Biosyst 2014; 10:1790-802. [PMID: 24722431 DOI: 10.1039/c3mb70414a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Basal ER stress occurs when proteins misfold in normal physiological conditions and are corrected by the unfolded protein response (UPR). Elevated ER stress occurs when misfolding is refractory as found in numerous diseases such as atherosclerosis, Type II diabetes and some cancers. In elevated ER stress it is unclear whether cells utilise the same or different networks of genes as in basal levels of ER stress. To probe this question, we used secretory pathway reporters Yip3p-GFP, Erv29p-GFP, Orm2p-GFP and UPREpr-GFP placed on the yeast deletion mutant array (DMA) genetic background. The reporter's expression levels, measured by automated microscopy, at basal versus elevated ER stress induced by the over-expression of CPY* were compared. A novel group of kinetochore genes (CTF19 complex) were found to be uniquely required for full induction of all four ER stress reporters in elevated stress. A follow-up reporter screen was developed by mating the ctf19Δ kinetochore gene deletion strain into the genome-wide XXXp-GFP tagged library then testing with over-expressed CPY*. This screen identified Bcy1p and Bfr1p as possible signalling points that down-regulate the UPR and secretory pathway when kinetochore proteins are absent under elevated stress conditions. Bfr1p appears to be a checkpoint that monitors the integrity of kinetochores at increased levels of ER stress. This study concludes that functional kinetochores are required for full activation of the secretory pathway in elevated ER stress and that the responses to basal and elevated levels of ER stress require different networks of genes.
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Affiliation(s)
- Yee S Low
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington, New Zealand.
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7
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Yibmantasiri P, Bircham PW, Maass DR, Bellows DS, Atkinson PH. Networks of genes modulating the pleiotropic drug response in Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2014; 10:128-37. [DOI: 10.1039/c3mb70351g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Quek NCH, Matthews JH, Bloor SJ, Jones DA, Bircham PW, Heathcott RW, Atkinson PH. The novel equisetin-like compound, TA-289, causes aberrant mitochondrial morphology which is independent of the production of reactive oxygen species in Saccharomyces cerevisiae. Mol BioSyst 2013; 9:2125-33. [DOI: 10.1039/c3mb70056a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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9
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Bircham PW, Maass DR, Roberts CA, Kiew PY, Low YS, Yegambaram M, Matthews J, Jack CA, Atkinson PH. Secretory pathway genes assessed by high-throughput microscopy and synthetic genetic array analysis. Mol Biosyst 2011; 7:2589-98. [PMID: 21731954 DOI: 10.1039/c1mb05175j] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We developed a procedure for automated confocal microscopy to image the effect of the non-essential yeast gene deletion set on the localisation of the plasma membrane GFP-labelled protein Mrh1p-GFP. To achieve this it was necessary to devise an expression system expressing Redstar2 RFP-fluorescence specifically in the nucleus, mCherry RFP at a lower intensity in the cytoplasm and Mrh1p-GFP in the plasma membrane. This fluorescence labelling scheme utilising specifically designed image analysis scripts allowed automated segmentation of the cells into sub-regions comprising nuclei, cytoplasm and cell-surface. From this high-throughput high content screening approach we were able to determine that gene deletions including emc1Δ, emc2Δ, emc3Δ, emc4Δ, emc5Δ and emc6Δ, caused intracellular mislocalisation at the ER of a plasma membrane protein Mrh1p-GFP. CPY processing patterns were unaffected in these mutants and collectively our data suggest a transport role for the EMC genes within the early secretory pathway. HAC1 is central to the unfolded protein response (UPR) and in its absence, i.e. the absence of UPR, emc1Δ-, emc3Δ-, emc4Δ-, emc5Δ-hac1Δ double mutants were specifically hypersensitive to ER-stress (tunicamycin) lending credence to the usefulness of the high content microscope screening for discovery of functional effects of single mutants.
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Affiliation(s)
- Peter W Bircham
- Department of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington, New Zealand
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Herst PM, Perrone GG, Dawes IW, Bircham PW, Berridge MV. Plasma membrane electron transport in Saccharomyces cerevisiae depends on the presence of mitochondrial respiratory subunits. FEMS Yeast Res 2008; 8:897-905. [PMID: 18657191 DOI: 10.1111/j.1567-1364.2008.00418.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Most investigations into plasma membrane electron transport (PMET) in Saccharomyces cerevisiae have focused on the inducible ferric reductase responsible for iron uptake under iron/copper-limiting conditions. In this paper, we describe a PMET system, distinct from ferric reductase, which reduces the cell-impermeable water-soluble tetrazolium dye, 2-(4-iodophenyl)-3-(4-nitrophenyl)-5-(2,4-disulphophenyl)-2H-tetrazolium monosodium salt (WST-1), under normal iron/copper conditions. WST-1/1-methoxy-phenazine methosulphate reduction was unaffected by anoxia and relatively insensitive to diphenyleneiodonium. Dye reduction was increased when intracellular NADH levels were high, which, in S. cerevisiae, required deletion of numerous genes associated with NADH recycling. Genome-wide screening of all viable nuclear gene-deletion mutants of S. cerevisiae revealed that, although mitochondrial electron transport per se was not required, the presence of several nuclear and mitochondrially encoded subunits of respiratory complexes III and IV was mandatory for PMET. This suggests some form of interaction between components of mitochondrial and plasma membrane electron transport. In support of this, mitochondrial tubular networks in S. cerevisiae were shown to be located in close proximity to the plasma membrane using confocal microscopy.
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Affiliation(s)
- Patries M Herst
- Malaghan Institute of Medical Research, Wellington, New Zealand.
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