1
|
Carmon T, Hill N, Sripathi VR, Gossett ZB, Fakas S. The PAH1-encoded phosphatidate phosphatase of Yarrowia lipolytica differentially affects gene expression and lipid biosynthesis. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159544. [PMID: 39089641 PMCID: PMC11380575 DOI: 10.1016/j.bbalip.2024.159544] [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: 04/30/2024] [Revised: 07/25/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
Yarrowia lipolytica is a model oleaginous yeast with a strong capacity for lipid accumulation, yet its lipid metabolic pathways and regulatory mechanisms remain largely unexplored. The PAH1-encoded phosphatidate (PA) phosphatase governs lipid biosynthesis by its enzymatic activity and regulating the transcription of genes involved in phospholipid biosynthesis. In this work, we examined the effect of the loss of Pah1 (i.e., pah1Δ) on cell metabolism in cells growing in low- and high-glucose media. Multi-omics analyses revealed the global effect of the pah1Δ mutation on lipid and central carbon metabolism. Lipidomics analyses showed that the pah1Δ mutation caused a massive decrease in the masses of triacylglycerol (TAG) and diacylglycerol (DAG), and these effects were independent of glucose concentration in the media. Conversely, phospholipid levels declined in low-glucose media but increased in high-glucose media. The loss of Pah1 affected the expression of genes involved in key pathways of glucose metabolism, such as glycolysis, citric acid cycle, oxidative phosphorylation, and the pentose phosphate pathway, and these effects were more pronounced in high-glucose media. In lipid biosynthesis, the genes catalyzing phosphatidylcholine (PC) synthesis from phosphatidylethanolamine (PE) were upregulated within the CDP-DAG pathway. In contrast, PC synthesis through the Kennedy pathway was downregulated. The ethanolamine branch of the Kennedy pathway that synthesizes PE was also upregulated in pah1Δ. Interestingly, we noted a massive increase in the levels of lysophospholipids, consistent with the upregulation of genes involved in lipid turnover. Overall, this work identified novel regulatory roles of Pah1 in lipid biosynthesis and gene expression.
Collapse
Affiliation(s)
- Taylor Carmon
- Department of Food and Animal Sciences, Alabama A&M University, Normal, AL 35762, USA
| | - Na'Taja Hill
- Department of Food and Animal Sciences, Alabama A&M University, Normal, AL 35762, USA
| | | | - Zachary B Gossett
- Department of Food and Animal Sciences, Alabama A&M University, Normal, AL 35762, USA
| | - Stylianos Fakas
- Department of Food and Animal Sciences, Alabama A&M University, Normal, AL 35762, USA.
| |
Collapse
|
2
|
Stukey GJ, Han GS, Carman GM. Architecture and function of yeast phosphatidate phosphatase Pah1 domains/regions. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159547. [PMID: 39103045 DOI: 10.1016/j.bbalip.2024.159547] [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: 06/11/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024]
Abstract
Phosphatidate (PA) phosphatase, which catalyzes the Mg2+-dependent dephosphorylation of PA to produce diacylglycerol, provides a direct precursor for the synthesis of the storage lipid triacylglycerol and the membrane phospholipids phosphatidylcholine and phosphatidylethanolamine. The enzyme controlling the key phospholipid PA also plays a crucial role in diverse aspects of lipid metabolism and cell physiology. PA phosphatase is a peripheral membrane enzyme that is composed of multiple domains/regions required for its catalytic function and subcellular localization. In this review, we discuss the domains/regions of PA phosphatase from the yeast Saccharomyces cerevisiae with reference to the homologous enzyme from mammalian cells.
Collapse
Affiliation(s)
- Geordan J Stukey
- Department of Food Science and the Rutgers Center for Lipid Research, Rutgers University, New Brunswick, NJ 08901, USA
| | - Gil-Soo Han
- Department of Food Science and the Rutgers Center for Lipid Research, Rutgers University, New Brunswick, NJ 08901, USA
| | - George M Carman
- Department of Food Science and the Rutgers Center for Lipid Research, Rutgers University, New Brunswick, NJ 08901, USA.
| |
Collapse
|
3
|
Amari C, Carletti M, Yan S, Michaud M, Salvaing J. Lipid droplets degradation mechanisms from microalgae to mammals, a comparative overview. Biochimie 2024:S0300-9084(24)00216-5. [PMID: 39299537 DOI: 10.1016/j.biochi.2024.09.006] [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: 07/01/2024] [Revised: 08/15/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
Abstract
Lipid droplets (LDs) are organelles composed of a hydrophobic core (mostly triacylglycerols and steryl esters) delineated by a lipid monolayer and found throughout the tree of life. LDs were seen for a long time as simple energy storage organelles but recent works highlighted their versatile roles in several fundamental cellular processes, particularly during stress response. LDs biogenesis occurs in the ER and their number and size can be dynamically regulated depending on their function, e.g. during development or stress. Understanding their biogenesis and degradation mechanisms is thus essential to better apprehend their roles. LDs degradation can occur in the cytosol by lipolysis or after their internalization into lytic compartments (e.g. vacuoles or lysosomes) using diverse mechanisms that depend on the considered organism, tissue, developmental stage or environmental condition. In this review, we summarize our current knowledge on the different LDs degradation pathways in several main phyla of model organisms, unicellular or pluricellular, photosynthetic or not (budding yeast, mammals, land plants and microalgae). We highlight the conservation of the main degradation pathways throughout evolution, but also the differences between organisms, or inside an organism between different organs. Finally, we discuss how this comparison can help to shed light on relationships between LDs degradation pathways and LDs functions.
Collapse
Affiliation(s)
- Chems Amari
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et Aux Energies Alternatives, IRIG, CEA-Grenoble, 17 Rue des Martyrs, 38000, Grenoble, France; Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Marta Carletti
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et Aux Energies Alternatives, IRIG, CEA-Grenoble, 17 Rue des Martyrs, 38000, Grenoble, France
| | - Siqi Yan
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et Aux Energies Alternatives, IRIG, CEA-Grenoble, 17 Rue des Martyrs, 38000, Grenoble, France
| | - Morgane Michaud
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et Aux Energies Alternatives, IRIG, CEA-Grenoble, 17 Rue des Martyrs, 38000, Grenoble, France
| | - Juliette Salvaing
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et Aux Energies Alternatives, IRIG, CEA-Grenoble, 17 Rue des Martyrs, 38000, Grenoble, France.
| |
Collapse
|
4
|
Ptak C, Rehman S, Wozniak RW. Mechanisms of nuclear envelope expansion. Curr Opin Cell Biol 2024; 91:102425. [PMID: 39250858 DOI: 10.1016/j.ceb.2024.102425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 09/11/2024]
Abstract
In actively dividing eukaryotic cells, the nuclear envelope membrane (NEM) expands during the cell cycle to accommodate increases in nuclear volume and formation of two nuclei as a cell passes through mitosis to form daughter cells. NEM expansion is driven by glycerophospholipid (GPL) synthesis that is regulated by the lipin family of phosphatidic acid phosphatases (PAPs). How, and when during the cell cycle, PAPs regulate membrane expansion differs between organisms undergoing a closed or open mitosis. Here, we discuss recent studies that shed light on the mechanisms of NE expansion. Moreover, we examine evidence that NEM expansion not only employs GPLs synthesized in the ER but also lipids whose synthesis is regulated by events at the inner nuclear membrane.
Collapse
Affiliation(s)
- Christopher Ptak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Saif Rehman
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Richard W Wozniak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada.
| |
Collapse
|
5
|
Lysyganicz PK, Barbosa AD, Khondker S, Stewart NA, Carman GM, Stansfeld PJ, Dymond MK, Siniossoglou S. The partitioning of fatty acids between membrane and storage lipids controls ER membrane expansion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.05.611378. [PMID: 39282465 PMCID: PMC11398528 DOI: 10.1101/2024.09.05.611378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
The biogenesis of membrane-bound organelles involves the synthesis, remodelling and degradation of their constituent phospholipids. How these pathways regulate organelle size, remains still poorly understood. Here we demonstrate that a lipid degradation pathway inhibits the expansion of the endoplasmic reticulum (ER) membrane. Phospholipid diacylglycerol acyltransferases (PDATs) use endogenous phospholipids as fatty acyl donors to generate triglyceride stored in lipid droplets. The significance of this non-canonical triglyceride biosynthetic pathway has remained elusive. We find that the activity of the yeast PDAT Lro1 is regulated by a membrane- proximal domain facing the luminal side of the ER bilayer. To reveal the biological roles of PDATs, we engineered an Lro1 variant with derepressed activity. We show that active Lro1 mediates the retraction of ER membrane expansion driven by phospholipid synthesis. Furthermore, the subcellular distribution and membrane turnover activity of Lro1 are controlled by diacylglycerol, produced by the activity of Pah1, a conserved member of the lipin family. Collectively, our findings reveal a lipid metabolic network that regulates endoplasmic reticulum biogenesis by converting phospholipids into storage lipids.
Collapse
|
6
|
Khondker S, Han GS, Carman GM. Protein kinase Hsl1 phosphorylates Pah1 to inhibit phosphatidate phosphatase activity and regulate lipid synthesis in Saccharomyces cerevisiae. J Biol Chem 2024; 300:107572. [PMID: 39009344 PMCID: PMC11342776 DOI: 10.1016/j.jbc.2024.107572] [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: 06/22/2024] [Revised: 07/08/2024] [Accepted: 07/10/2024] [Indexed: 07/17/2024] Open
Abstract
In Saccharomyces cerevisiae, Pah1 phosphatidate (PA) phosphatase, which catalyzes the Mg2+-dependent dephosphorylation of PA to produce diacylglycerol, plays a key role in utilizing PA for the synthesis of the neutral lipid triacylglycerol and thereby controlling the PA-derived membrane phospholipids. The enzyme function is controlled by its subcellular location as regulated by phosphorylation and dephosphorylation. Pah1 is initially inactivated in the cytosol through phosphorylation by multiple protein kinases and then activated via its recruitment and dephosphorylation by the protein phosphatase Nem1-Spo7 at the nuclear/endoplasmic reticulum membrane where the PA phosphatase reaction occurs. Many of the protein kinases that phosphorylate Pah1 have yet to be characterized with the identification of the target residues. Here, we established Pah1 as a bona fide substrate of septin-associated Hsl1, a protein kinase involved in mitotic morphogenesis checkpoint signaling. The Hsl1 activity on Pah1 was dependent on reaction time and the amounts of protein kinase, Pah1, and ATP. The Hsl1 phosphorylation of Pah1 occurred on Ser-748 and Ser-773, and the phosphorylated protein exhibited a 5-fold reduction in PA phosphatase catalytic efficiency. Analysis of cells expressing the S748A and S773A mutant forms of Pah1 indicated that Hsl1-mediated phosphorylation of Pah1 promotes membrane phospholipid synthesis at the expense of triacylglycerol, and ensures the dependence of Pah1 function on the Nem1-Spo7 protein phosphatase. This work advances the understanding of how Hsl1 facilitates membrane phospholipid synthesis through the phosphorylation-mediated regulation of Pah1.
Collapse
Affiliation(s)
- Shoily Khondker
- Department of Food Science and the Rutgers Center for Lipid Research, Rutgers University, New Brunswick, New Jersey, USA
| | - Gil-Soo Han
- Department of Food Science and the Rutgers Center for Lipid Research, Rutgers University, New Brunswick, New Jersey, USA
| | - George M Carman
- Department of Food Science and the Rutgers Center for Lipid Research, Rutgers University, New Brunswick, New Jersey, USA.
| |
Collapse
|
7
|
Zhu Y, Tong X, Xue J, Qiu H, Zhang D, Zheng DQ, Tu ZC, Ye C. Phospholipid biosynthesis modulates nucleotide metabolism and reductive capacity. Nat Chem Biol 2024:10.1038/s41589-024-01689-z. [PMID: 39060393 DOI: 10.1038/s41589-024-01689-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 07/02/2024] [Indexed: 07/28/2024]
Abstract
Phospholipid and nucleotide syntheses are fundamental metabolic processes in eukaryotic organisms, with their dysregulation implicated in various disease states. Despite their importance, the interplay between these pathways remains poorly understood. Using genetic and metabolic analyses in Saccharomyces cerevisiae, we elucidate how cytidine triphosphate usage in the Kennedy pathway for phospholipid synthesis influences nucleotide metabolism and redox balance. We find that deficiencies in the Kennedy pathway limit nucleotide salvage, prompting compensatory activation of de novo nucleotide synthesis and the pentose phosphate pathway. This metabolic shift enhances the production of antioxidants such as NADPH and glutathione. Moreover, we observe that the Kennedy pathway for phospholipid synthesis is inhibited during replicative aging, indicating its role in antioxidative defense as an adaptive mechanism in aged cells. Our findings highlight the critical role of phospholipid synthesis pathway choice in the integrative regulation of nucleotide metabolism, redox balance and membrane properties for cellular defense.
Collapse
Affiliation(s)
- Yibing Zhu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xiaomeng Tong
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jingyuan Xue
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Hong Qiu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Dan Zhang
- Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dao-Qiong Zheng
- Ocean College, Zhejiang University, Zhoushan, China
- Hainan Institute, Zhejiang University, Sanya, China
| | - Zong-Cai Tu
- National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang, China
| | - Cunqi Ye
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
- Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Hainan Institute, Zhejiang University, Sanya, China.
- National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang, China.
| |
Collapse
|
8
|
Sosa Ponce ML, Cobb JA, Zaremberg V. Lipids and chromatin: a tale of intriguing connections shaping genomic landscapes. Trends Cell Biol 2024:S0962-8924(24)00118-1. [PMID: 39060139 DOI: 10.1016/j.tcb.2024.06.004] [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: 03/01/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 07/28/2024]
Abstract
Recent studies in yeast reveal an intricate interplay between nuclear envelope (NE) architecture and lipid metabolism, and between lipid signaling and both epigenome and genome integrity. In this review, we highlight the reciprocal connection between lipids and histone modifications, which enable metabolic reprogramming in response to nutrients. The endoplasmic reticulum (ER)-NE regulates the compartmentalization and temporal availability of epigenetic metabolites and its lipid composition also impacts nuclear processes, such as transcriptional silencing and the DNA damage response (DDR). We also discuss recent work providing mechanistic insight into lipid droplet (LD) formation and sterols in the nucleus, and the collective data showing Opi1 as a central factor in both membrane sensing and transcriptional regulation of lipid-chromatin interrelated processes.
Collapse
Affiliation(s)
- Maria Laura Sosa Ponce
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Jennifer A Cobb
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Vanina Zaremberg
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
| |
Collapse
|
9
|
Laframboise SJ, Deneault LF, Denoncourt A, Downey M, Baetz K. Uncovering the Role of the Yeast Lysine Acetyltransferase NuA4 in the Regulation of Nuclear Shape and Lipid Metabolism. Mol Cell Biol 2024; 44:273-288. [PMID: 38961766 PMCID: PMC11253884 DOI: 10.1080/10985549.2024.2366206] [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: 10/16/2023] [Accepted: 05/19/2024] [Indexed: 07/05/2024] Open
Abstract
Here, we report a novel role for the yeast lysine acetyltransferase NuA4 in regulating phospholipid availability for organelle morphology. Disruption of the NuA4 complex results in 70% of cells displaying nuclear deformations and nearly 50% of cells exhibiting vacuolar fragmentation. Cells deficient in NuA4 also show severe defects in the formation of nuclear-vacuole junctions (NJV), as well as a decrease in piecemeal microautophagy of the nucleus (PMN). To determine the cause of these defects we focused on Pah1, an enzyme that converts phosphatidic acid into diacylglycerol, favoring accumulation of lipid droplets over phospholipids that are used for membrane expansion. NuA4 subunit Eaf1 was required for Pah1 localization to the inner nuclear membrane and artificially tethering of Pah1 to the nuclear membrane rescued nuclear deformation and vacuole fragmentation defects, but not defects related to the formation of NVJs. Mutation of a NuA4-dependent acetylation site on Pah1 also resulted in aberrant Pah1 localization and defects in nuclear morphology and NVJ. Our work suggests a critical role for NuA4 in organelle morphology that is partially mediated through the regulation of Pah1 subcellular localization.
Collapse
Affiliation(s)
- Sarah Jane Laframboise
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Lauren F. Deneault
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Alix Denoncourt
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Downey
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Kristin Baetz
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
10
|
Carrasquillo Rodríguez JW, Uche O, Gao S, Lee S, Airola MV, Bahmanyar S. Differential reliance of CTD-nuclear envelope phosphatase 1 on its regulatory subunit in ER lipid synthesis and storage. Mol Biol Cell 2024; 35:ar101. [PMID: 38776127 PMCID: PMC11244170 DOI: 10.1091/mbc.e23-09-0382] [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: 10/10/2023] [Revised: 05/06/2024] [Accepted: 05/17/2024] [Indexed: 06/04/2024] Open
Abstract
Lipin 1 is an ER enzyme that produces diacylglycerol, the lipid intermediate that feeds into the synthesis of glycerophospholipids for membrane expansion or triacylglycerol for storage into lipid droplets. CTD-Nuclear Envelope Phosphatase 1 (CTDNEP1) regulates lipin 1 to restrict ER membrane synthesis, but a role for CTDNEP1 in lipid storage in mammalian cells is not known. Furthermore, how NEP1R1, the regulatory subunit of CTDNEP1, contributes to these functions in mammalian cells is not fully understood. Here, we show that CTDNEP1 is reliant on NEP1R1 for its stability and function in limiting ER expansion. CTDNEP1 contains an amphipathic helix at its N-terminus that targets to the ER, nuclear envelope and lipid droplets. We identify key residues at the binding interface of CTDNEP1 and NEP1R1 and show that they facilitate complex formation in vivo and in vitro. We demonstrate that NEP1R1 binding to CTDNEP1 shields CTDNEP1 from proteasomal degradation to regulate lipin 1 and restrict ER size. Unexpectedly, NEP1R1 was not required for CTDNEP1's role in restricting lipid droplet biogenesis. Thus, the reliance of CTDNEP1 function on NEP1R1 depends on cellular demands for membrane production versus lipid storage. Together, our work provides a framework into understanding how the ER regulates lipid synthesis under different metabolic conditions.
Collapse
Affiliation(s)
| | - Onyedikachi Uche
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
| | - Shujuan Gao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook NY 11794
| | - Shoken Lee
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
| | - Michael V. Airola
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook NY 11794
| | - Shirin Bahmanyar
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
| |
Collapse
|
11
|
Hirano Y, Sato T, Miura A, Kubota Y, Shindo T, Fukase K, Fukagawa T, Kabayama K, Haraguchi T, Hiraoka Y. Disordered region of nuclear membrane protein Bqt4 recruits phosphatidic acid to the nuclear envelope to maintain its structural integrity. J Biol Chem 2024; 300:107430. [PMID: 38825008 PMCID: PMC11253665 DOI: 10.1016/j.jbc.2024.107430] [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: 01/16/2024] [Revised: 05/09/2024] [Accepted: 05/18/2024] [Indexed: 06/04/2024] Open
Abstract
The nuclear envelope (NE) is a permeable barrier that maintains nuclear-cytoplasmic compartmentalization and ensures nuclear function; however, it ruptures in various situations such as mechanical stress and mitosis. Although the protein components for sealing a ruptured NE have been identified, the mechanism by which lipid components are involved in this process remains to be elucidated. Here, we found that an inner nuclear membrane (INM) protein Bqt4 directly interacts with phosphatidic acid (PA) and serves as a platform for NE maintenance in the fission yeast Schizosaccharomyces pombe. The intrinsically disordered region (IDR) of Bqt4, proximal to the transmembrane domain, binds to PA and forms a solid aggregate in vitro. Excessive accumulation of Bqt4 IDR in INM results in membrane overproliferation and lipid droplet formation in the nucleus, leading to centromere dissociation from the NE and chromosome missegregation. Our findings suggest that Bqt4 IDR controls nuclear membrane homeostasis by recruiting PA to the INM, thereby maintaining the structural integrity of the NE.
Collapse
Affiliation(s)
- Yasuhiro Hirano
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.
| | - Tsukino Sato
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Ayane Miura
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Yoshino Kubota
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | | | - Koichi Fukase
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Tatsuo Fukagawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Kazuya Kabayama
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.
| |
Collapse
|
12
|
Zemlianski V, Marešová A, Princová J, Holič R, Häsler R, Ramos Del Río MJ, Lhoste L, Zarechyntsava M, Převorovský M. Nitrogen availability is important for preventing catastrophic mitosis in fission yeast. J Cell Sci 2024; 137:jcs262196. [PMID: 38780300 DOI: 10.1242/jcs.262196] [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: 04/10/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
Mitosis is a crucial stage in the cell cycle, controlled by a vast network of regulators responding to multiple internal and external factors. The fission yeast Schizosaccharomyces pombe demonstrates catastrophic mitotic phenotypes due to mutations or drug treatments. One of the factors provoking catastrophic mitosis is a disturbed lipid metabolism, resulting from, for example, mutations in the acetyl-CoA/biotin carboxylase (cut6), fatty acid synthase (fas2, also known as lsd1) or transcriptional regulator of lipid metabolism (cbf11) genes, as well as treatment with inhibitors of fatty acid synthesis. It has been previously shown that mitotic fidelity in lipid metabolism mutants can be partially rescued by ammonium chloride supplementation. In this study, we demonstrate that mitotic fidelity can be improved by multiple nitrogen sources. Moreover, this improvement is not limited to lipid metabolism disturbances but also applies to a number of unrelated mitotic mutants. Interestingly, the partial rescue is not achieved by restoring the lipid metabolism state, but rather indirectly. Our results highlight a novel role for nitrogen availability in mitotic fidelity.
Collapse
Affiliation(s)
- Viacheslav Zemlianski
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Anna Marešová
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Jarmila Princová
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Roman Holič
- Centre of Biosciences SAS, Institute of Animal Biochemistry and Genetics, Dúbravská cesta 9, 840 05 Bratislava, Slovak Republic
| | - Robert Häsler
- Center for Inflammatory Skin Diseases, Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Rosalind-Franklin-Straße 9, 24105 Kiel, Germany
| | - Manuel José Ramos Del Río
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Laurane Lhoste
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Maryia Zarechyntsava
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| |
Collapse
|
13
|
Gao S, Carrasquillo Rodríguez JW, Bahmanyar S, Airola MV. Structure and mechanism of the human CTDNEP1-NEP1R1 membrane protein phosphatase complex necessary to maintain ER membrane morphology. Proc Natl Acad Sci U S A 2024; 121:e2321167121. [PMID: 38776370 PMCID: PMC11145253 DOI: 10.1073/pnas.2321167121] [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: 12/01/2023] [Accepted: 04/12/2024] [Indexed: 05/25/2024] Open
Abstract
C-terminal Domain Nuclear Envelope Phosphatase 1 (CTDNEP1) is a noncanonical protein serine/threonine phosphatase that has a conserved role in regulating ER membrane biogenesis. Inactivating mutations in CTDNEP1 correlate with the development of medulloblastoma, an aggressive childhood cancer. The transmembrane protein Nuclear Envelope Phosphatase 1 Regulatory Subunit 1 (NEP1R1) binds CTDNEP1, but the molecular details by which NEP1R1 regulates CTDNEP1 function are unclear. Here, we find that knockdown of NEP1R1 generates identical phenotypes to reported loss of CTDNEP1 in mammalian cells, establishing CTDNEP1-NEP1R1 as an evolutionarily conserved membrane protein phosphatase complex that restricts ER expansion. Mechanistically, NEP1R1 acts as an activating regulatory subunit that directly binds and increases the phosphatase activity of CTDNEP1. By defining a minimal NEP1R1 domain sufficient to activate CTDNEP1, we determine high-resolution crystal structures of the CTDNEP1-NEP1R1 complex bound to a peptide sequence acting as a pseudosubstrate. Structurally, NEP1R1 engages CTDNEP1 at a site distant from the active site to stabilize and allosterically activate CTDNEP1. Substrate recognition is facilitated by a conserved Arg residue in CTDNEP1 that binds and orients the substrate peptide in the active site. Together, this reveals mechanisms for how NEP1R1 regulates CTDNEP1 and explains how cancer-associated mutations inactivate CTDNEP1.
Collapse
Affiliation(s)
- Shujuan Gao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY11794
| | | | - Shirin Bahmanyar
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT06511
| | - Michael V. Airola
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY11794
| |
Collapse
|
14
|
Gunn AL, Yashchenko AI, Dubrulle J, Johnson J, Hatch EM. A high-content screen reveals new regulators of nuclear membrane stability. Sci Rep 2024; 14:6013. [PMID: 38472343 PMCID: PMC10933478 DOI: 10.1038/s41598-024-56613-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 03/08/2024] [Indexed: 03/14/2024] Open
Abstract
Nuclear membrane rupture is a physiological response to multiple in vivo processes, such as cell migration, that can cause extensive genome instability and upregulate invasive and inflammatory pathways. However, the underlying molecular mechanisms of rupture are unclear and few regulators have been identified. In this study, we developed a reporter that is size excluded from re-compartmentalization following nuclear rupture events. This allows for robust detection of factors influencing nuclear integrity in fixed cells. We combined this with an automated image analysis pipeline in a high-content siRNA screen to identify new proteins that both increase and decrease nuclear rupture frequency in cancer cells. Pathway analysis identified an enrichment of nuclear membrane and ER factors in our hits and we demonstrate that one of these, the protein phosphatase CTDNEP1, is required for nuclear stability. Analysis of known rupture determinants, including an automated quantitative analysis of nuclear lamina gaps, are consistent with CTDNEP1 acting independently of actin and nuclear lamina organization. Our findings provide new insights into the molecular mechanism of nuclear rupture and define a highly adaptable program for rupture analysis that removes a substantial barrier to new discoveries in the field.
Collapse
Affiliation(s)
- Amanda L Gunn
- Divisions of Basic Sciences and Human Biology, The Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Artem I Yashchenko
- Divisions of Basic Sciences and Human Biology, The Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Julien Dubrulle
- Cellular Imaging Shared Resource, The Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jodiene Johnson
- Divisions of Basic Sciences and Human Biology, The Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | - Emily M Hatch
- Divisions of Basic Sciences and Human Biology, The Fred Hutchinson Cancer Center, Seattle, WA, USA.
| |
Collapse
|
15
|
Mannino PJ, Perun A, Surovstev I, Ader NR, Shao L, Melia TJ, King MC, Lusk CP. A quantitative ultrastructural timeline of nuclear autophagy reveals a role for dynamin-like protein 1 at the nuclear envelope. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580336. [PMID: 38405892 PMCID: PMC10888867 DOI: 10.1101/2024.02.14.580336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Autophagic mechanisms that maintain nuclear envelope homeostasis are bulwarks to aging and disease. By leveraging 4D lattice light sheet microscopy and correlative light and electron tomography, we define a quantitative and ultrastructural timeline of a nuclear macroautophagy (nucleophagy) pathway in yeast. Nucleophagy initiates with a rapid local accumulation of the nuclear cargo adaptor Atg39 at the nuclear envelope adjacent to the nucleus-vacuole junction and is delivered to the vacuole in ~300 seconds through an autophagosome intermediate. Mechanistically, nucleophagy incorporates two consecutive and genetically defined membrane fission steps: inner nuclear membrane (INM) fission generates a lumenal vesicle in the perinuclear space followed by outer nuclear membrane (ONM) fission to liberate a double membraned vesicle to the cytosol. ONM fission occurs independently of phagophore engagement and instead relies surprisingly on dynamin-like protein1 (Dnm1), which is recruited to sites of Atg39 accumulation at the nuclear envelope. Loss of Dnm1 compromises nucleophagic flux by stalling nucleophagy after INM fission. Our findings reveal how nuclear and INM cargo are removed from an intact nucleus without compromising its integrity, achieved in part by a non-canonical role for Dnm1 in nuclear envelope remodeling.
Collapse
Affiliation(s)
- Philip J. Mannino
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
| | - Andrew Perun
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
| | - Ivan Surovstev
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
- Department of Physics, Yale University, New Haven, CT, 06511
| | - Nicholas R. Ader
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
| | - Lin Shao
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
| | - Thomas J. Melia
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
| | - Megan C. King
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, 06511
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
| |
Collapse
|
16
|
Han GS, Kwiatek JM, Hu KS, Carman GM. Catalytic core function of yeast Pah1 phosphatidate phosphatase reveals structural insight into its membrane localization and activity control. J Biol Chem 2024; 300:105560. [PMID: 38097185 PMCID: PMC10797186 DOI: 10.1016/j.jbc.2023.105560] [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: 10/13/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023] Open
Abstract
The PAH1-encoded phosphatidate (PA) phosphatase is a major source of diacylglycerol for the production of the storage lipid triacylglycerol and a key regulator for the de novo phospholipid synthesis in Saccharomyces cerevisiae. The catalytic function of Pah1 depends on its membrane localization which is mediated through its phosphorylation by multiple protein kinases and dephosphorylation by the Nem1-Spo7 protein phosphatase complex. The full-length Pah1 is composed of a catalytic core (N-LIP and HAD-like domains, amphipathic helix, and the WRDPLVDID domain) and non-catalytic regulatory sequences (intrinsically disordered regions, RP domain, and acidic tail) for phosphorylation and interaction with Nem1-Spo7. How the catalytic core regulates Pah1 localization and cellular function is not clear. In this work, we analyzed a variant of Pah1 (i.e., Pah1-CC (catalytic core)) that is composed only of the catalytic core. Pah1-CC expressed on a low-copy plasmid complemented the pah1Δ mutant phenotypes (e.g., nuclear/ER membrane expansion, reduced levels of triacylglycerol, and lipid droplet formation) without requiring Nem1-Spo7. The cellular function of Pah1-CC was supported by its PA phosphatase activity mostly associated with the membrane fraction. Although functional, Pah1-CC was distinct from Pah1 in the protein and enzymological properties, which include overexpression toxicity, association with heat shock proteins, and significant reduction of the Vmax value. These findings on the Pah1 catalytic core enhance the understanding of its structural requirements for membrane localization and activity control.
Collapse
Affiliation(s)
- Gil-Soo Han
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA
| | - Joanna M Kwiatek
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA
| | - Kam Shan Hu
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA
| | - George M Carman
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA.
| |
Collapse
|
17
|
Besada-Lombana PB, Chen W, Da Silva NA. An extracellular glucose sensor for substrate-dependent secretion and display of cellulose-degrading enzymes. Biotechnol Bioeng 2024; 121:403-408. [PMID: 37749915 DOI: 10.1002/bit.28549] [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: 06/27/2023] [Revised: 08/17/2023] [Accepted: 08/30/2023] [Indexed: 09/27/2023]
Abstract
The efficient hydrolysis of lignocellulosic biomass into fermentable sugars is key for viable economic production of biofuels and biorenewable chemicals from second-generation feedstocks. Consolidated bioprocessing (CBP) combines lignocellulose saccharification and chemical production in a single step. To avoid wasting valuable resources during CBP, the selective secretion of enzymes (independent or attached to the surface) based on the carbon source available is advantageous. To enable enzyme expression and secretion based on extracellular glucose levels, we implemented a G-protein-coupled receptor (GPCR)-based extracellular glucose sensor; this allows the secretion and display of cellulases in the presence of the cellulosic fraction of lignocellulose by leveraging cellobiose-dependent signal amplification. We focused on the glucose-responsiveness of the HXT1 promoter and engineered PHXT1 by changing its core to that of the strong promoter PTHD3 , increasing extracellular enzyme activity by 81%. We then demonstrated glucose-mediated expression and cell-surface display of the β-glucosidase BglI on the surface of Saccharomyces cerevisiae. The display system was further optimized by re-directing fatty acid pools from lipid droplet synthesis toward formation of membrane precursors via knock-out of PAH1. This resulted in an up to 4.2-fold improvement with respect to the baseline strain. Finally, we observed cellobiose-dependent signal amplification of the system with an increase in enzymatic activity of up to 3.1-fold when cellobiose was added.
Collapse
Affiliation(s)
- Pamela B Besada-Lombana
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
| | - Nancy A Da Silva
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California, USA
| |
Collapse
|
18
|
Yao S, Kim SC, Li J, Tang S, Wang X. Phosphatidic acid signaling and function in nuclei. Prog Lipid Res 2024; 93:101267. [PMID: 38154743 PMCID: PMC10843600 DOI: 10.1016/j.plipres.2023.101267] [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: 10/18/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 12/30/2023]
Abstract
Membrane lipidomes are dynamic and their changes generate lipid mediators affecting various biological processes. Phosphatidic acid (PA) has emerged as an important class of lipid mediators involved in a wide range of cellular and physiological responses in plants, animals, and microbes. The regulatory functions of PA have been studied primarily outside the nuclei, but an increasing number of recent studies indicates that some of the PA effects result from its action in nuclei. PA levels in nuclei are dynamic in response to stimuli. Changes in nuclear PA levels can result from activities of enzymes associated with nuclei and/or from movements of PA generated extranuclearly. PA has also been found to interact with proteins involved in nuclear functions, such as transcription factors and proteins undergoing nuclear translocation in response to stimuli. The nuclear action of PA affects various aspects of plant growth, development, and response to stress and environmental changes.
Collapse
Affiliation(s)
- Shuaibing Yao
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Sang-Chul Kim
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Jianwu Li
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Shan Tang
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Xuemin Wang
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
| |
Collapse
|
19
|
Jog R, Han GS, Carman GM. The Saccharomyces cerevisiae Spo7 basic tail is required for Nem1-Spo7/Pah1 phosphatase cascade function in lipid synthesis. J Biol Chem 2024; 300:105587. [PMID: 38141768 PMCID: PMC10820825 DOI: 10.1016/j.jbc.2023.105587] [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: 10/18/2023] [Revised: 12/04/2023] [Accepted: 12/13/2023] [Indexed: 12/25/2023] Open
Abstract
The Saccharomyces cerevisiae Nem1-Spo7 protein phosphatase complex dephosphorylates and thereby activates Pah1 at the nuclear/endoplasmic reticulum membrane. Pah1, a phosphatidate phosphatase catalyzing the dephosphorylation of phosphatidate to produce diacylglycerol, is one of the most highly regulated enzymes in lipid metabolism. The diacylglycerol produced in the lipid phosphatase reaction is utilized for the synthesis of triacylglycerol that is stored in lipid droplets. Disruptions of the Nem1-Spo7/Pah1 phosphatase cascade cause a plethora of physiological defects. Spo7, the regulatory subunit of the Nem1-Spo7 complex, is required for the Nem1 catalytic function and interacts with the acidic tail of Pah1. Spo7 contains three conserved homology regions (CR1-3) that are important for the interaction with Nem1, but its region for the interaction with Pah1 is unknown. Here, by deletion and site-specific mutational analyses of Spo7, we revealed that the C-terminal basic tail (residues 240-259) containing five arginine and two lysine residues is important for the Nem1-Spo7 complex-mediated dephosphorylation of Pah1 and its cellular function (triacylglycerol synthesis, lipid droplet formation, maintenance of nuclear/endoplasmic reticulum membrane morphology, and cell growth at elevated temperatures). The glutaraldehyde cross-linking analysis of synthetic peptides indicated that the Spo7 basic tail interacts with the Pah1 acidic tail. This work advances our understanding of the Spo7 function and the Nem1-Spo7/Pah1 phosphatase cascade in yeast lipid synthesis.
Collapse
Affiliation(s)
- Ruta Jog
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA
| | - Gil-Soo Han
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA
| | - George M Carman
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA.
| |
Collapse
|
20
|
Gao S, Carrasquillo Rodríguez JW, Bahmanyar S, Airola MV. Structure and mechanism of the human CTDNEP1-NEP1R1 membrane protein phosphatase complex necessary to maintain ER membrane morphology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567952. [PMID: 38045299 PMCID: PMC10690229 DOI: 10.1101/2023.11.20.567952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
C-terminal Domain Nuclear Envelope Phosphatase 1 (CTDNEP1) is a non-canonical protein serine/threonine phosphatase that regulates ER membrane biogenesis. Inactivating mutations in CTDNEP1 correlate with development of medulloblastoma, an aggressive childhood cancer. The transmembrane protein Nuclear Envelope Phosphatase 1 Regulatory Subunit 1 (NEP1R1) binds CTDNEP1, but the molecular details by which NEP1R1 regulates CTDNEP1 function are unclear. Here, we find that knockdown of CTDNEP1 or NEP1R1 in human cells generate identical phenotypes, establishing CTDNEP1-NEP1R1 as an evolutionarily conserved membrane protein phosphatase complex that restricts ER expansion. Mechanistically, NEP1R1 acts as an activating regulatory subunit that directly binds and increases the phosphatase activity of CTDNEP1. By defining a minimal NEP1R1 domain sufficient to activate CTDNEP1, we determine high resolution crystal structures of the CTDNEP1-NEP1R1 complex bound to a pseudo-substrate. Structurally, NEP1R1 engages CTDNEP1 at a site distant from the active site to stabilize and allosterically activate CTDNEP1. Substrate recognition is facilitated by a conserved Arg residue that binds and orients the substrate peptide in the active site. Together, this reveals mechanisms for how NEP1R1 regulates CTDNEP1 and explains how cancer-associated mutations inactivate CTDNEP1.
Collapse
Affiliation(s)
- Shujuan Gao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook NY 11794, USA
| | | | - Shirin Bahmanyar
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Michael V. Airola
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook NY 11794, USA
| |
Collapse
|
21
|
Carrasquillo Rodríguez JW, Uche O, Gao S, Lee S, Airola MV, Bahmanyar S. Differential reliance of CTD-nuclear envelope phosphatase 1 on its regulatory subunit in ER lipid synthesis and storage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.12.562096. [PMID: 37873275 PMCID: PMC10592836 DOI: 10.1101/2023.10.12.562096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The endoplasmic reticulum (ER) is the site for the synthesis of the major membrane and storage lipids. Lipin 1 produces diacylglycerol, the lipid intermediate critical for the synthesis of both membrane and storage lipids in the ER. CTD-Nuclear Envelope Phosphatase 1 (CTDNEP1) regulates lipin 1 to restrict ER membrane synthesis, but its role in lipid storage in mammalian cells is unknown. Here, we show that the ubiquitin-proteasome degradation pathway controls the levels of ER/nuclear envelope-associated CTDNEP1 to regulate ER membrane synthesis through lipin 1. The N-terminus of CTDNEP1 is an amphipathic helix that targets to the ER, nuclear envelope and lipid droplets. We identify key residues at the binding interface of CTDNEP1 with its regulatory subunit NEP1R1 and show that they facilitate complex formation in vivo and in vitro . We demonstrate a role for NEP1R1 in temporarily shielding CTDNEP1 from proteasomal degradation to regulate lipin 1 and restrict ER size. Unexpectedly, we found that NEP1R1 is not required for CTDNEP1's role in restricting lipid droplet biogenesis. Thus, the reliance of CTDNEP1 function on its regulatory subunit differs during ER membrane synthesis and lipid storage. Together, our work provides a framework into understanding how the ER regulates lipid synthesis and storage under fluctuating conditions.
Collapse
|
22
|
Zhang Y, Barberis M. Exploring cell cycle-mediated regulations of glycolysis in budding yeast. Front Microbiol 2023; 14:1270487. [PMID: 37886071 PMCID: PMC10598772 DOI: 10.3389/fmicb.2023.1270487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
Coordination of cell cycle with metabolism exists in all cell types that grow by division. It serves to build a new cell, (i) fueling building blocks for the synthesis of proteins, nucleic acids, and membranes, and (ii) producing energy through glycolysis. Cyclin-dependent kinases (Cdks) play an essential role in this coordination, thereby in the regulation of cell division. Cdks are functional homologs across eukaryotes and are the engines that drive cell cycle events and the clocks that time them. Their function is counteracted by stoichiometric inhibitors; specifically, inhibitors of cyclin-cyclin dependent kinase (cyclin/Cdk) complexes allow for their activity at specific times. Here, we provide a new perspective about the yet unknown cell cycle mechanisms impacting on metabolism. We first investigated the effect of the mitotic cyclin/Cdk1 complex Cyclin B/Cdk1-functional homolog in mammalian cells of the budding yeast Clb2/Cdk1-on yeast metabolic enzymes of, or related to, the glycolysis pathway. Six glycolytic enzymes (Glk1, Hxk2, Pgi1, Fba1, Tdh1, and Pgk1) were subjected to in vitro Cdk-mediated phosphorylation assays. Glucose-6-phosphate dehydrogenase (Zwf1), the first enzyme in the pentose phosphate pathway that is important for NADPH production, and 6-phospho-fructo-2-kinase (Pfk27), which catalyzes fructose-2,6-bisphosphate synthesis, a key regulator of glycolysis, were also included in the study. We found that, among these metabolic enzymes, Fba1 and Pgk1 may be phosphorylated by Cdk1, in addition to the known Cdk1-mediated phosphorylation of Gph1. We then investigated the possible effect of Sic1, stoichiometric inhibitor of mitotic cyclin/Cdk1 complexes in budding yeast, on the activities of three most relevant glycolytic enzymes: Hxk2, Glk1, and Tdh1. We found that Sic1 may have a negative effect on Hxk2. Altogether, we reveal possible new routes, to be further explored, through which cell cycle may regulate cellular metabolism. Because of the functional homology of cyclin/Cdk complexes and their stoichiometric inhibitors across evolution, our findings may be relevant for the regulation of cell division in eukaryotes.
Collapse
Affiliation(s)
- Yanfei Zhang
- Molecular Systems Biology, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Matteo Barberis
- Molecular Systems Biology, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
- Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, United Kingdom
| |
Collapse
|
23
|
Le TK, Hirano Y, Asakawa H, Okamoto K, Fukagawa T, Haraguchi T, Hiraoka Y. A ubiquitin-proteasome pathway degrades the inner nuclear membrane protein Bqt4 to maintain nuclear membrane homeostasis. J Cell Sci 2023; 136:jcs260930. [PMID: 37694715 DOI: 10.1242/jcs.260930] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 08/25/2023] [Indexed: 09/12/2023] Open
Abstract
Aberrant accumulation of inner nuclear membrane (INM) proteins is associated with deformed nuclear morphology and mammalian diseases. However, the mechanisms underlying the maintenance of INM homeostasis remain poorly understood. In this study, we explored the degradation mechanisms of the INM protein Bqt4 in the fission yeast Schizosaccharomyces pombe. We have previously shown that Bqt4 interacts with the transmembrane protein Bqt3 at the INM and is degraded in the absence of Bqt3. Here, we reveal that excess Bqt4, unassociated with Bqt3, is targeted for degradation by the ubiquitin-proteasome system localized in the nucleus and Bqt3 antagonizes this process. The degradation process involves the Doa10 E3 ligase complex at the INM. Bqt4 is a tail-anchored protein and the Cdc48 complex is required for its degradation. The C-terminal transmembrane domain of Bqt4 was necessary and sufficient for proteasome-dependent protein degradation. Accumulation of Bqt4 at the INM impaired cell viability with nuclear envelope deformation, suggesting that quantity control of Bqt4 plays an important role in nuclear membrane homeostasis.
Collapse
Affiliation(s)
- Toan Khanh Le
- Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Yasuhiro Hirano
- Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
- Laboratory of Chromosome Biology, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Haruhiko Asakawa
- Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
- Laboratory of Chromosome Biology, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Koji Okamoto
- Laboratory of Mitochondrial Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Tatsuo Fukagawa
- Laboratory of Chromosome Biology, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Tokuko Haraguchi
- Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Yasushi Hiraoka
- Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| |
Collapse
|
24
|
Gunn AL, Yashchenko AI, Dubrulle J, Johnson J, Hatch EM. A high-content screen reveals new regulators of nuclear membrane stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542944. [PMID: 37398267 PMCID: PMC10312541 DOI: 10.1101/2023.05.30.542944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Nuclear membrane rupture is a physiological response to multiple in vivo processes, such as cell migration, that can cause extensive genome instability and upregulate invasive and inflammatory pathways. However, the underlying molecular mechanisms of rupture are unclear and few regulators have been identified. In this study, we developed a reporter that is size excluded from re-compartmentalization following nuclear rupture events. This allows for robust detection of factors influencing nuclear integrity in fixed cells. We combined this with an automated image analysis pipeline in a high-content siRNA screen to identify new proteins that both increase and decrease nuclear rupture frequency in cancer cells. Pathway analysis identified an enrichment of nuclear membrane and ER factors in our hits and we demonstrate that one of these, the protein phosphatase CTDNEP1, is required for nuclear stability. Further analysis of known rupture contributors, including a newly developed automated quantitative analysis of nuclear lamina gaps, strongly suggests that CTDNEP1 acts in a new pathway. Our findings provide new insights into the molecular mechanism of nuclear rupture and define a highly adaptable program for rupture analysis that removes a substantial barrier to new discoveries in the field.
Collapse
Affiliation(s)
- Amanda L. Gunn
- Divisions of Basic Sciences and Human Biology, The Fred Hutchinson Cancer Center, 1100 Fairview Ave, Seattle, Washington 98109, USA
| | - Artem I. Yashchenko
- Divisions of Basic Sciences and Human Biology, The Fred Hutchinson Cancer Center, 1100 Fairview Ave, Seattle, Washington 98109, USA
| | - Julien Dubrulle
- Cellular Imaging Shared Resource, The Fred Hutchinson Cancer Center, 1100 Fairview Ave, Seattle, Washington 98109, USA
| | - Jodiene Johnson
- Divisions of Basic Sciences and Human Biology, The Fred Hutchinson Cancer Center, 1100 Fairview Ave, Seattle, Washington 98109, USA
| | - Emily M. Hatch
- Divisions of Basic Sciences and Human Biology, The Fred Hutchinson Cancer Center, 1100 Fairview Ave, Seattle, Washington 98109, USA
| |
Collapse
|
25
|
Saik NO, Ptak C, Rehman S, Aitchison JD, Montpetit B, Wozniak RW. SUMOylation at the inner nuclear membrane facilitates nuclear envelope biogenesis during mitosis. J Cell Biol 2023; 222:e202208137. [PMID: 37398994 PMCID: PMC10318406 DOI: 10.1083/jcb.202208137] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 03/24/2023] [Accepted: 05/15/2023] [Indexed: 07/04/2023] Open
Abstract
As eukaryotic cells progress through cell division, the nuclear envelope (NE) membrane must expand to accommodate the formation of progeny nuclei. In Saccharomyces cerevisiae, closed mitosis allows visualization of NE biogenesis during mitosis. During this period, the SUMO E3 ligase Siz2 binds the inner nuclear membrane (INM) and initiates a wave of INM protein SUMOylation. Here, we show these events increase INM levels of phosphatidic acid (PA), an intermediate of phospholipid biogenesis, and are necessary for normal mitotic NE membrane expansion. The increase in INM PA is driven by the Siz2-mediated inhibition of the PA phosphatase Pah1. During mitosis, this results from the binding of Siz2 to the INM and dissociation of Spo7 and Nem1, a complex required for the activation of Pah1. As cells enter interphase, the process is then reversed by the deSUMOylase Ulp1. This work further establishes a central role for temporally controlled INM SUMOylation in coordinating processes, including membrane expansion, that regulate NE biogenesis during mitosis.
Collapse
Affiliation(s)
- Natasha O. Saik
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Christopher Ptak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Saif Rehman
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - John D. Aitchison
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
- Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics and Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Richard W. Wozniak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
26
|
Siniossoglou S. Oiling the wheels of nuclear division: SUMOylation regulates the expansion of the mitotic nuclear membrane. J Cell Biol 2023; 222:e202306126. [PMID: 37440179 PMCID: PMC10345213 DOI: 10.1083/jcb.202306126] [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: 07/14/2023] Open
Abstract
Eukaryotic cell division involves the segregation of chromosomes between two daughter cells and must be coordinated with extensive rearrangement of their nuclear envelopes. In this issue, Saik et al. (2023 J. Cell Biol. https://doi.org/10.1083/jcb.202208137) show that a SUMOylation cascade at the inner nuclear membrane elevates the levels of phosphatidic acid, a key phospholipid precursor, to support the need for nuclear membrane expansion during mitosis.
Collapse
Affiliation(s)
- Symeon Siniossoglou
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| |
Collapse
|
27
|
Stukey GJ, Han GS, Carman GM. Phosphatidate phosphatase Pah1 contains a novel RP domain that regulates its phosphorylation and function in yeast lipid synthesis. J Biol Chem 2023; 299:105025. [PMID: 37423305 PMCID: PMC10406625 DOI: 10.1016/j.jbc.2023.105025] [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: 06/02/2023] [Revised: 06/30/2023] [Accepted: 07/02/2023] [Indexed: 07/11/2023] Open
Abstract
The Saccharomyces cerevisiae PAH1-encoded phosphatidate (PA) phosphatase, which catalyzes the Mg2+-dependent dephosphorylation of PA to produce diacylglycerol, is one of the most highly regulated enzymes in lipid metabolism. The enzyme controls whether cells utilize PA to produce membrane phospholipids or the major storage lipid triacylglycerol. PA levels, which are regulated by the enzyme reaction, also control the expression of UASINO-containing phospholipid synthesis genes via the Henry (Opi1/Ino2-Ino4) regulatory circuit. Pah1 function is largely controlled by its cellular location, which is mediated by phosphorylation and dephosphorylation. Multiple phosphorylations sequester Pah1 in the cytosol and protect it from 20S proteasome-mediated degradation. The endoplasmic reticulum-associated Nem1-Spo7 phosphatase complex recruits and dephosphorylates Pah1 allowing the enzyme to associate with and dephosphorylate its membrane-bound substrate PA. Pah1 contains domains/regions that include the N-LIP and haloacid dehalogenase-like catalytic domains, N-terminal amphipathic helix for membrane binding, C-terminal acidic tail for Nem1-Spo7 interaction, and a conserved tryptophan within the WRDPLVDID domain required for enzyme function. Through bioinformatics, molecular genetics, and biochemical approaches, we identified a novel RP (regulation of phosphorylation) domain that regulates the phosphorylation state of Pah1. We showed that the ΔRP mutation results in a 57% reduction in the endogenous phosphorylation of the enzyme (primarily at Ser-511, Ser-602, and Ser-773/Ser-774), an increase in membrane association and PA phosphatase activity, but reduced cellular abundance. This work not only identifies a novel regulatory domain within Pah1 but emphasizes the importance of the phosphorylation-based regulation of Pah1 abundance, location, and function in yeast lipid synthesis.
Collapse
Affiliation(s)
- Geordan J Stukey
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA
| | - Gil-Soo Han
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA
| | - George M Carman
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA.
| |
Collapse
|
28
|
Khaddaj R, Stribny J, Cottier S, Schneiter R. Perilipin 3 promotes the formation of membrane domains enriched in diacylglycerol and lipid droplet biogenesis proteins. Front Cell Dev Biol 2023; 11:1116491. [PMID: 37465010 PMCID: PMC10350540 DOI: 10.3389/fcell.2023.1116491] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 06/14/2023] [Indexed: 07/20/2023] Open
Abstract
Lipid droplets (LDs) serve as intracellular stores of energy-rich neutral lipids. LDs form at discrete sites in the endoplasmic reticulum (ER) and they remain closely associated with the ER during lipogenic growth and lipolytic consumption. Their hydrophobic neutral lipid core is covered by a monolayer of phospholipids, which harbors a specific set of proteins. This LD surface is coated and stabilized by perilipins, a family of soluble proteins that specifically target LDs from the cytosol. We have previously used chimeric fusion proteins between perilipins and integral ER membrane proteins to test whether proteins that are anchored to the ER bilayer could be dragged onto the LD monolayer. Expression of these chimeric proteins induces repositioning of the ER membrane around LDs. Here, we test the properties of membrane-anchored perilipins in cells that lack LDs. Unexpectedly, membrane-anchored perilipins induce expansion and vesiculation of the perinuclear membrane resulting in the formation of crescent-shaped membrane domains that harbor LD-like properties. These domains are stained by LD-specific lipophilic dyes, harbor LD marker proteins, and they transform into nascent LDs upon induction of neutral lipid synthesis. These ER domains are enriched in diacylglycerol (DAG) and in ER proteins that are important for early steps of LD biogenesis, including seipin and Pex30. Formation of the domains in vivo depends on DAG levels, and we show that perilipin 3 (PLIN3) binds to liposomes containing DAG in vitro. Taken together, these observations indicate that perilipin not only serve to stabilize the surface of mature LDs but that they are likely to exert a more active role in early steps of LD biogenesis at ER subdomains enriched in DAG, seipin, and neutral lipid biosynthetic enzymes.
Collapse
Affiliation(s)
- Rasha Khaddaj
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Jiri Stribny
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Stéphanie Cottier
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Roger Schneiter
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| |
Collapse
|
29
|
Sosa Ponce ML, Remedios MH, Moradi-Fard S, Cobb JA, Zaremberg V. SIR telomere silencing depends on nuclear envelope lipids and modulates sensitivity to a lysolipid. J Cell Biol 2023; 222:e202206061. [PMID: 37042812 PMCID: PMC10103788 DOI: 10.1083/jcb.202206061] [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: 06/13/2022] [Revised: 11/29/2022] [Accepted: 03/24/2023] [Indexed: 04/13/2023] Open
Abstract
The nuclear envelope (NE) is important in maintaining genome organization. The role of lipids in communication between the NE and telomere regulation was investigated, including how changes in lipid composition impact gene expression and overall nuclear architecture. Yeast was treated with the non-metabolizable lysophosphatidylcholine analog edelfosine, known to accumulate at the perinuclear ER. Edelfosine induced NE deformation and disrupted telomere clustering but not anchoring. Additionally, the association of Sir4 at telomeres decreased. RNA-seq analysis showed altered expression of Sir-dependent genes located at sub-telomeric (0-10 kb) regions, consistent with Sir4 dispersion. Transcriptomic analysis revealed that two lipid metabolic circuits were activated in response to edelfosine, one mediated by the membrane sensing transcription factors, Spt23/Mga2, and the other by a transcriptional repressor, Opi1. Activation of these transcriptional programs resulted in higher levels of unsaturated fatty acids and the formation of nuclear lipid droplets. Interestingly, cells lacking Sir proteins displayed resistance to unsaturated-fatty acids and edelfosine, and this phenotype was connected to Rap1.
Collapse
Affiliation(s)
| | | | - Sarah Moradi-Fard
- Departments of Biochemistry and Molecular Biology and Oncology, Cumming School of Medicine, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Calgary, Canada
| | - Jennifer A. Cobb
- Departments of Biochemistry and Molecular Biology and Oncology, Cumming School of Medicine, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Calgary, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| | - Vanina Zaremberg
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| |
Collapse
|
30
|
Zhang Y, van der Zee L, Barberis M. Two-way communication between cell cycle and metabolism in budding yeast: what do we know? Front Microbiol 2023; 14:1187304. [PMID: 37396387 PMCID: PMC10309209 DOI: 10.3389/fmicb.2023.1187304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Coordination of cell cycle and metabolism exists in all cells. The building of a new cell is a process that requires metabolic commitment to the provision of both Gibbs energy and building blocks for proteins, nucleic acids, and membranes. On the other hand, the cell cycle machinery will assess and regulate its metabolic environment before it makes decisions on when to enter the next cell cycle phase. Furthermore, more and more evidence demonstrate that the metabolism can be regulated by cell cycle progression, as different biosynthesis pathways are preferentially active in different cell cycle phases. Here, we review the available literature providing a critical overview on how cell cycle and metabolism may be coupled with one other, bidirectionally, in the budding yeast Saccharomyces cerevisiae.
Collapse
Affiliation(s)
- Yanfei Zhang
- Molecular Systems Biology, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Lucas van der Zee
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Matteo Barberis
- Molecular Systems Biology, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
- Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, Surrey, United Kingdom
| |
Collapse
|
31
|
Ren W, Zhang Y, Zhu M, Liu Z, Lian S, Wang C, Li B, Liu N. The Phosphatase Cascade Nem1/Spo7-Pah1 Regulates Fungal Development, Lipid Homeostasis, and Virulence in Botryosphaeria dothidea. Microbiol Spectr 2023; 11:e0388122. [PMID: 37191532 PMCID: PMC10269782 DOI: 10.1128/spectrum.03881-22] [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: 09/21/2022] [Accepted: 02/28/2023] [Indexed: 05/17/2023] Open
Abstract
Protein phosphatase complex Nem1/Spo7 plays crucial roles in the regulation of various biological processes in eukaryotes. However, its biological functions in phytopathogenic fungi are not well understood. In this study, genome-wide transcriptional profiling analysis revealed that Nem1 was significantly upregulated during the infection process of Botryosphaeria dothidea, and we identified and characterized the phosphatase complex Nem1/Spo7 and its substrate Pah1 (a phosphatidic acid phosphatase) in B. dothidea. Nem1/Spo7 physically interacted with and dephosphorylated Pah1 to promote triacylglycerol (TAG) and subsequent lipid droplet (LD) synthesis. Moreover, the Nem1/Spo7-dependently dephosphorylated Pah1 functioned as a transcriptional repressor of the key nuclear membrane biosynthesis genes to regulate nuclear membrane morphology. In addition, phenotypic analyses showed that the phosphatase cascade Nem1/Spo7-Pah1 was involved in regulating mycelial growth, asexual development, stress responses, and virulence of B. dothidea. IMPORTANCE Botryosphaeria canker and fruit rot caused by the fungus Botryosphaeria dothidea is one of the most destructive diseases of apple worldwide. Our data indicated that the phosphatase cascade Nem1/Spo7-Pah1 plays important roles in the regulation of fungal growth, development, lipid homeostasis, environmental stress responses, and virulence in B. dothidea. The findings will contribute to the in-depth and comprehensive understanding of Nem1/Spo7-Pah1 in fungi and the development of target-based fungicides for disease management.
Collapse
Affiliation(s)
- Weichao Ren
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Yihan Zhang
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Meiqi Zhu
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Zequn Liu
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Sen Lian
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Caixia Wang
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Baohua Li
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Na Liu
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| |
Collapse
|
32
|
Santana-Sosa S, Matos-Perdomo E, Ayra-Plasencia J, Machín F. A Yeast Mitotic Tale for the Nucleus and the Vacuoles to Embrace. Int J Mol Sci 2023; 24:9829. [PMID: 37372977 DOI: 10.3390/ijms24129829] [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: 05/03/2023] [Revised: 06/02/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The morphology of the nucleus is roughly spherical in most eukaryotic cells. However, this organelle shape needs to change as the cell travels through narrow intercellular spaces during cell migration and during cell division in organisms that undergo closed mitosis, i.e., without dismantling the nuclear envelope, such as yeast. In addition, the nuclear morphology is often modified under stress and in pathological conditions, being a hallmark of cancer and senescent cells. Thus, understanding nuclear morphological dynamics is of uttermost importance, as pathways and proteins involved in nuclear shaping can be targeted in anticancer, antiaging, and antifungal therapies. Here, we review how and why the nuclear shape changes during mitotic blocks in yeast, introducing novel data that associate these changes with both the nucleolus and the vacuole. Altogether, these findings suggest a close relationship between the nucleolar domain of the nucleus and the autophagic organelle, which we also discuss here. Encouragingly, recent evidence in tumor cell lines has linked aberrant nuclear morphology to defects in lysosomal function.
Collapse
Affiliation(s)
- Silvia Santana-Sosa
- Research Unit, University Hospital Ntra Sra de Candelaria, Ctra del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
- Institute of Biomedical Technologies, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Emiliano Matos-Perdomo
- Research Unit, University Hospital Ntra Sra de Candelaria, Ctra del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
- Institute of Biomedical Technologies, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Jessel Ayra-Plasencia
- Research Unit, University Hospital Ntra Sra de Candelaria, Ctra del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
- Institute of Biomedical Technologies, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Félix Machín
- Research Unit, University Hospital Ntra Sra de Candelaria, Ctra del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
- Institute of Biomedical Technologies, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
- Faculty of Health Sciences, Fernando Pessoa Canarias University, 35450 Santa María de Guía, Spain
| |
Collapse
|
33
|
Amm I, Weberruss M, Hellwig A, Schwarz J, Tatarek-Nossol M, Lüchtenborg C, Kallas M, Brügger B, Hurt E, Antonin W. Distinct domains in Ndc1 mediate its interaction with the Nup84 complex and the nuclear membrane. J Cell Biol 2023; 222:e202210059. [PMID: 37154843 PMCID: PMC10165475 DOI: 10.1083/jcb.202210059] [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: 10/13/2022] [Revised: 01/31/2023] [Accepted: 03/17/2023] [Indexed: 05/10/2023] Open
Abstract
Nuclear pore complexes (NPCs) are embedded in the nuclear envelope and built from ∼30 different nucleoporins (Nups) in multiple copies, few are integral membrane proteins. One of these transmembrane nucleoporins, Ndc1, is thought to function in NPC assembly at the fused inner and outer nuclear membranes. Here, we show a direct interaction of Ndc1's transmembrane domain with Nup120 and Nup133, members of the pore membrane coating Y-complex. We identify an amphipathic helix in Ndc1's C-terminal domain binding highly curved liposomes. Upon overexpression, this amphipathic motif is toxic and dramatically alters the intracellular membrane organization in yeast. Ndc1's amphipathic motif functionally interacts with related motifs in the C-terminus of the nucleoporins Nup53 and Nup59, important for pore membrane binding and interconnecting NPC modules. The essential function of Ndc1 can be suppressed by deleting the amphipathic helix from Nup53. Our data indicate that nuclear membrane and presumably NPC biogenesis depends on a balanced ratio between amphipathic motifs in diverse nucleoporins.
Collapse
Affiliation(s)
- Ingo Amm
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Marion Weberruss
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Andrea Hellwig
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), University of Heidelberg, Heidelberg, Germany
| | - Johannes Schwarz
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Marianna Tatarek-Nossol
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Christian Lüchtenborg
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Martina Kallas
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Ed Hurt
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| |
Collapse
|
34
|
Chen D, Cai X, Xing J, Chen S, Zhao J, Qu Z, Li G, Liu H, Zheng L, Huang J, Chen XL. A lipid droplet-associated protein Nem1 regulates appressorium function for infection of Magnaporthe oryzae. ABIOTECH 2023; 4:108-123. [PMID: 37581021 PMCID: PMC10423190 DOI: 10.1007/s42994-023-00098-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/01/2023] [Indexed: 08/16/2023]
Abstract
Lipid droplets are important storages in fungal conidia and can be used by plant pathogenic fungi for infection. However, the regulatory mechanism of lipid droplets formation and the utilization during fungal development and infection are largely unknown. Here, in Magnaporthe oryzae, we identified a lipid droplet-associated protein Nem1 that played a key role in lipid droplets biogenesis and utilization. Nem1 was highly expressed in conidia, but lowly expressed in appressoria, and its encoded protein was localized to lipid droplets. Deletion of NEM1 resulted in reduced numbers of lipid droplets and decreased content of diacylglycerol (DAG) or triacylglycerol (TAG). NEM1 was required for asexual development especially conidia production. The Δnem1 mutant was nearly loss of virulence to host plants due to defects in appressorial penetration and invasive growth. Remarkably, Nem1 was regulated by the TOR signaling pathway and involved in the autophagy process. The Ser303 residue of Nem1 could be phosphorylated by the cAMP-PKA signaling pathway and was important for biological function of Nem1. Together, our study revealed a regulatory mechanism of lipid biogenesis and metabolism during the conidium and appressorium formation of the rice blast fungus. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-023-00098-5.
Collapse
Affiliation(s)
- Deng Chen
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xuan Cai
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Junjie Xing
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125 China
| | - Shen Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Juan Zhao
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zhiguang Qu
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Guotian Li
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Hao Liu
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Lu Zheng
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Junbin Huang
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiao-Lin Chen
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| |
Collapse
|
35
|
Jog R, Han GS, Carman GM. Conserved regions of the regulatory subunit Spo7 are required for Nem1-Spo7/Pah1 phosphatase cascade function in yeast lipid synthesis. J Biol Chem 2023; 299:104683. [PMID: 37030502 DOI: 10.1016/j.jbc.2023.104683] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/30/2023] [Accepted: 04/02/2023] [Indexed: 04/08/2023] Open
Abstract
In the yeast Saccharomyces cerevisiae, the Nem1-Spo7 complex is a protein phosphatase that activates Pah1 phosphatidate (PA) phosphatase at the nuclear/endoplasmic reticulum membrane for the synthesis of triacylglycerol. The Nem1-Spo7/Pah1 phosphatase cascade largely controls whether PA is partitioned into the storage lipid triacylglycerol or into membrane phospholipids. The regulated synthesis of the lipids is crucial for diverse physiological processes during cell growth. Spo7 in the protein phosphatase complex is required as a regulatory subunit for the Nem1 catalytic subunit to dephosphorylate Pah1. The regulatory subunit contains three conserved homology regions (CR1, CR2, and CR3). Previous work showed that the hydrophobicity of LLI (residues 54-56) within CR1 is important for Spo7 function in the Nem1-Spo7/Pah1 phosphatase cascade. In this work, by deletion and site-specific mutational analyses, we revealed that CR2 and CR3 are also required for Spo7 function. Mutations in any one of the conserved regions were sufficient to disrupt the function of the Nem1-Spo7 complex. We determined that the uncharged hydrophilicity of STN (residues 141-143) within CR2 was required for Nem1-Spo7 complex formation. Additionally, the hydrophobicity of LL (residues 217 and 219) within CR3 was important for Spo7 stability, which indirectly affected complex formation. Finally, we showed the loss of Spo7 CR2 or CR3 function by the phenotypes (e.g., reduced amounts of triacylglycerol and lipid droplets, temperature sensitivity) that are attributed to defects in membrane translocation and dephosphorylation of Pah1 by the Nem1-Spo7 complex. These findings advance knowledge of the Nem1-Spo7 complex and its role in lipid synthesis regulation.
Collapse
Affiliation(s)
- Ruta Jog
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA
| | - Gil-Soo Han
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA
| | - George M Carman
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA.
| |
Collapse
|
36
|
Hammer SE, Polymenis M. One-carbon metabolic enzymes are regulated during cell division and make distinct contributions to the metabolome and cell cycle progression in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2023; 13:6983127. [PMID: 36627750 PMCID: PMC9997564 DOI: 10.1093/g3journal/jkad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023]
Abstract
Enzymes of one-carbon (1C) metabolism play pivotal roles in proliferating cells. They are involved in the metabolism of amino acids, nucleotides, and lipids and the supply of all cellular methylations. However, there is limited information about how these enzymes are regulated during cell division and how cell cycle kinetics are affected in several loss-of-function mutants of 1C metabolism. Here, we report that the levels of the S. cerevisiae enzymes Ade17p and Cho2p, involved in the de novo synthesis of purines and phosphatidylcholine (PC), respectively, are cell cycle-regulated. Cells lacking Ade17p, Cho2p, or Shm2p (an enzyme that supplies 1C units from serine) have distinct alterations in size homeostasis and cell cycle kinetics. Loss of Ade17p leads to a specific delay at START, when cells commit to a new round of cell division, while loss of Shm2p has broader effects, reducing growth rate. Furthermore, the inability to synthesize PC de novo in cho2Δ cells delays START and reduces the coherence of nuclear elongation late in the cell cycle. Loss of Cho2p also leads to profound metabolite changes. Besides the expected changes in the lipidome, cho2Δ cells have reduced levels of amino acids, resembling cells shifted to poorer media. These results reveal the different ways that 1C metabolism allocates resources to affect cell proliferation at multiple cell cycle transitions.
Collapse
Affiliation(s)
- Staci E Hammer
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| |
Collapse
|
37
|
Foo S, Cazenave-Gassiot A, Wenk MR, Oliferenko S. Diacylglycerol at the inner nuclear membrane fuels nuclear envelope expansion in closed mitosis. J Cell Sci 2023; 136:286881. [PMID: 36695178 DOI: 10.1242/jcs.260568] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 12/22/2022] [Indexed: 01/26/2023] Open
Abstract
Nuclear envelope (NE) expansion must be controlled to maintain nuclear shape and function. The nuclear membrane expands massively during closed mitosis, enabling chromosome segregation within an intact NE. Phosphatidic acid (PA) and diacylglycerol (DG) can both serve as biosynthetic precursors for membrane lipid synthesis. How they are regulated in time and space and what the implications are of changes in their flux for mitotic fidelity are largely unknown. Using genetically encoded PA and DG probes, we show that DG is depleted from the inner nuclear membrane during mitosis in the fission yeast Schizosaccharomyces pombe, but PA does not accumulate, indicating that it is rerouted to membrane synthesis. We demonstrate that DG-to-PA conversion catalyzed by the diacylglycerol kinase Dgk1 (also known as Ptp4) and direct glycerophospholipid synthesis from DG by diacylglycerol cholinephosphotransferase/ethanolaminephosphotransferase Ept1 reinforce NE expansion. We conclude that DG consumption through both the de novo pathway and the Kennedy pathway fuels a spike in glycerophospholipid biosynthesis, controlling NE expansion and, ultimately, mitotic fidelity.
Collapse
Affiliation(s)
- Sherman Foo
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Amaury Cazenave-Gassiot
- Singapore Lipidomics Incubator, Life Sciences Institute and Precision Medicine Translational Research Program, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, 117596 Singapore
| | - Markus R Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute and Precision Medicine Translational Research Program, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, 117596 Singapore
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| |
Collapse
|
38
|
Matos-Perdomo E, Santana-Sosa S, Ayra-Plasencia J, Medina-Suárez S, Machín F. The vacuole shapes the nucleus and the ribosomal DNA loop during mitotic delays. Life Sci Alliance 2022; 5:5/10/e202101161. [PMID: 35961781 PMCID: PMC9375157 DOI: 10.26508/lsa.202101161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 11/24/2022] Open
Abstract
Chromosome structuring and condensation is one of the main features of mitosis. Here, Matos-Perdomo et al show how the nuclear envelope reshapes around the vacuole to give rise to the outstanding ribosomal DNA loop in budding yeast. The ribosomal DNA (rDNA) array of Saccharomyces cerevisiae has served as a model to address chromosome organization. In cells arrested before anaphase (mid-M), the rDNA acquires a highly structured chromosomal organization referred to as the rDNA loop, whose length can double the cell diameter. Previous works established that complexes such as condensin and cohesin are essential to attain this structure. Here, we report that the rDNA loop adopts distinct presentations that arise as spatial adaptations to changes in the nuclear morphology triggered during mid-M arrests. Interestingly, the formation of the rDNA loop results in the appearance of a space under the loop (SUL) which is devoid of nuclear components yet colocalizes with the vacuole. We show that the rDNA-associated nuclear envelope (NE) often reshapes into a ladle to accommodate the vacuole in the SUL, with the nucleus becoming bilobed and doughnut-shaped. Finally, we demonstrate that the formation of the rDNA loop and the SUL require TORC1, membrane synthesis and functional vacuoles, yet is independent of nucleus–vacuole junctions and rDNA-NE tethering.
Collapse
Affiliation(s)
- Emiliano Matos-Perdomo
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Silvia Santana-Sosa
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Jessel Ayra-Plasencia
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Sara Medina-Suárez
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Félix Machín
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain .,Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Santa María de Guía, Spain
| |
Collapse
|
39
|
Kwiatek JM, Gutierrez B, Izgu EC, Han GS, Carman GM. Phosphatidic acid mediates the Nem1-Spo7/Pah1 phosphatase cascade in yeast lipid synthesis. J Lipid Res 2022; 63:100282. [DOI: 10.1016/j.jlr.2022.100282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 10/31/2022] Open
|
40
|
Khondker S, Kwiatek JM, Han GS, Carman GM. Glycogen synthase kinase homolog Rim11 regulates lipid synthesis through the phosphorylation of Pah1 phosphatidate phosphatase in yeast. J Biol Chem 2022; 298:102221. [PMID: 35780834 PMCID: PMC9352556 DOI: 10.1016/j.jbc.2022.102221] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/24/2022] Open
Abstract
Pah1 phosphatidate (PA) phosphatase plays a major role in triacylglycerol synthesis in Saccharomyces cerevisiae by producing its precursor diacylglycerol and concurrently regulates de novo phospholipid synthesis by consuming its precursor PA. The function of Pah1 requires its membrane localization, which is controlled by its phosphorylation state. Pah1 is dephosphorylated by the Nem1-Spo7 protein phosphatase, whereas its phosphorylation occurs by multiple known and unknown protein kinases. In this work, we show that Rim11, a yeast homolog of mammalian glycogen synthase kinase-3β, is a protein kinase that phosphorylates Pah1 on serine (Ser12, Ser602, and Ser818) and threonine (Thr163, Thr164, Thr522) residues. Enzymological characterization of Rim11 showed that its Km for Pah1 (0.4 μM) is similar to those of other Pah1-phosphorylating protein kinases, but its Km for ATP (30 μM) is significantly higher than those of these same kinases. Furthermore, we demonstrate Rim11 phosphorylation of Pah1 does not require substrate prephosphorylation but was increased ∼2-fold upon its prephosphorylation by the Pho85-Pho80 protein kinase. In addition, we show Rim11-phosphorylated Pah1 was a substrate for dephosphorylation by Nem1-Spo7. Finally, we demonstrate the Rim11 phosphorylation of Pah1 exerted an inhibitory effect on its PA phosphatase activity by reduction of its catalytic efficiency. Mutational analysis of the major phosphorylation sites (Thr163, Thr164, and Ser602) indicated that Rim11-mediated phosphorylation at these sites was required to ensure Nem1-Spo7-dependent localization of the enzyme to the membrane. Overall, these findings advance our understanding of the phosphorylation-mediated regulation of Pah1 function in lipid synthesis.
Collapse
Affiliation(s)
- Shoily Khondker
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA
| | - Joanna M Kwiatek
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA
| | - Gil-Soo Han
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA
| | - George M Carman
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA.
| |
Collapse
|
41
|
Ranganathan PR, Narayanan AK, Nawada N, Rao MJ, Reju KS, Priya SC, Gujarathi T, Manjithaya R, Venkata Rao DK. Diacylglycerol kinase alleviates autophagic degradation of the endoplasmic reticulum in SPT10-deficient yeast to enhance triterpene biosynthesis. FEBS Lett 2022; 596:1778-1794. [PMID: 35661158 DOI: 10.1002/1873-3468.14418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/12/2022] [Accepted: 05/18/2022] [Indexed: 11/08/2022]
Abstract
A recent study showed that deletion of the gene encoding the transcription regulator SuPpressor of Ty10 (SPT10) increases total phospholipids, and our previous study established a critical link between phospholipids and the mevalonate/ergosterol (MEV/ERG) pathway, which synthesizes triterpenes. This study aims to use spt10Δ yeast to improve triterpene production. Though MEV/ERG pathway was highly expressed in spt10Δ yeast, results showed insufficient accumulation of key metabolites and also revealed massive endoplasmic reticulum (ER) degradation. We found a stable, massive ER structure when we overexpressed diacylglycerol kinase1 (DGK1OE ) in spt10Δ yeast. Analyses of ER-stress and autophagy suggest that DGK1OE in the spt10Δ strain decreased autophagy, resulting in increased MEV/ERG pathway activity. Heterologous expression of β-amyrin synthase showed significant production of the triterpene β-amyrin in DGK1OE spt10Δ yeast. Overall, our study provides a strategic approach to improve triterpene production by increasing ER biogenesis while limiting ER degradation.
Collapse
Affiliation(s)
- Poornima Ramani Ranganathan
- Biochemistry laboratory, CSIR-Central Institute of Medicinal & Aromatic Plants, Research Center, GKVK (post), Allalasandra, India.,Academy of Scientific and Innovative Research (AcSIR), Kamla Nehru Nagar, Sector 19, Ghaziabad, Uttar Pradesh-201 002, India
| | - Ananth Krishna Narayanan
- Biochemistry laboratory, CSIR-Central Institute of Medicinal & Aromatic Plants, Research Center, GKVK (post), Allalasandra, India.,Academy of Scientific and Innovative Research (AcSIR), Kamla Nehru Nagar, Sector 19, Ghaziabad, Uttar Pradesh-201 002, India
| | - Niveditha Nawada
- Biochemistry laboratory, CSIR-Central Institute of Medicinal & Aromatic Plants, Research Center, GKVK (post), Allalasandra, India.,Academy of Scientific and Innovative Research (AcSIR), Kamla Nehru Nagar, Sector 19, Ghaziabad, Uttar Pradesh-201 002, India
| | - Monala Jayaprakash Rao
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore-560064, India
| | - Kalyani Sai Reju
- Biochemistry laboratory, CSIR-Central Institute of Medicinal & Aromatic Plants, Research Center, GKVK (post), Allalasandra, India
| | - S Chaithra Priya
- Biochemistry laboratory, CSIR-Central Institute of Medicinal & Aromatic Plants, Research Center, GKVK (post), Allalasandra, India
| | - Tejal Gujarathi
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore-560064, India
| | - Ravi Manjithaya
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore-560064, India
| | - D K Venkata Rao
- Biochemistry laboratory, CSIR-Central Institute of Medicinal & Aromatic Plants, Research Center, GKVK (post), Allalasandra, India.,Academy of Scientific and Innovative Research (AcSIR), Kamla Nehru Nagar, Sector 19, Ghaziabad, Uttar Pradesh-201 002, India
| |
Collapse
|
42
|
PPAR-γ Agonist Pioglitazone Restored Mouse Liver mRNA Expression of Clock Genes and Inflammation-Related Genes Disrupted by Reversed Feeding. PPAR Res 2022; 2022:7537210. [PMID: 35663475 PMCID: PMC9162826 DOI: 10.1155/2022/7537210] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/27/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022] Open
Abstract
Introduction The master clock, which is located in the suprachiasmatic nucleus (SCN), harmonizes clock genes present in the liver to synchronize life rhythms and bioactivity with the surrounding environment. The reversed feeding disrupts the expression of clock genes in the liver. Recently, a novel role of PPAR-γ as a regulator in correlating circadian rhythm and metabolism was demonstrated. This study examined the influence of PPAR-γ agonist pioglitazone (PG) on the mRNA expression profile of principle clock genes and inflammation-related genes in the mouse liver disrupted by reverse feeding. Methods Mice were randomly assigned to daytime-feeding and nighttime-feeding groups. Mice in daytime-feeding groups received food from 7 AM to 7 PM, and mice in nighttime-feeding groups received food from 7 PM to 7 AM. PG was administered in the dose of 20 mg/kg per os as aqueous suspension 40 μl at 7 AM or 7 PM. Each group consisted of 12 animals. On day 8 of the feeding intervention, mice were sacrificed by cervical dislocation at noon (05 hours after light onset (HALO)) and midnight (HALO 17). Liver expressions of Bmal1, Clock, Rev-erb alpha, Cry1, Cry2, Per1, Per2, Cxcl5, Nrf2, and Ppar-γ were determined by quantitative reverse transcription PCR. Liver expression of PPAR-γ, pNF-κB, and IL-6 was determined by Western blotting. Glucose, ceruloplasmin, total cholesterol, triglyceride concentrations, and ALT and AST activities were measured in sera by photometric methods. The null hypothesis tested was that PG and the time of its administration have no influence on the clock gene expression impaired by reverse feeding. Results Administration of PG at 7 AM to nighttime-feeding mice did not reveal any influence on the expression of the clock or inflammation-related genes either at midnight or at noon. In the daytime-feeding group, PG intake at 7 PM led to an increase in Per2 and Rev-erb alpha mRNA at noon, an increase in Ppar-γ mRNA at midnight, and a decrease in Nfκb (p65) mRNA at noon. In general, PG administration at 7 PM slightly normalized the impaired expression of clock genes and increased anti-inflammatory potency impaired by reversed feeding. This pattern was supported by biochemical substrate levels—glucose, total cholesterol, ALT, and AST activities. The decrease in NF-κB led to the inhibition of serum ceruloplasmin levels as well as IL-6 in liver tissue. According to our data, PG intake at 7 PM exerts strong normalization of clock gene expression with a further increase in Nrf2 and, especially, Ppar-γ and PPAR-γ expression with inhibition of Nfκb and pNF-κB expression in daytime-feeding mice. These expression changes resulted in decreased hyperglycemia, hypercholesterolemia, ALT, and AST activities. Thus, PG had a potent chronopharmacological effect when administered at 7 PM to daytime-feeding mice. Conclusions Our study indicates that reversed feeding induced the disruption of mouse liver circadian expression pattern of clock genes accompanied by increasing Nfκb and pNF-κB and IL-6 expression and decreasing Nrf2 and PPAR-γ. Administration of PG restored the clock gene expression profile and decreased Nfκb, pNF-κB, and IL-6, as well as increased Nrf2, Ppar-γ, and PPAR-γ expression. PG intake at 7 PM was more effective than at 7 AM in reversed feeding mice.
Collapse
|
43
|
Khondker S, Han GS, Carman GM. Phosphorylation-mediated regulation of the Nem1-Spo7/Pah1 phosphatase cascade in yeast lipid synthesis. Adv Biol Regul 2022; 84:100889. [PMID: 35231723 PMCID: PMC9149063 DOI: 10.1016/j.jbior.2022.100889] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/08/2022] [Accepted: 02/15/2022] [Indexed: 05/03/2023]
Abstract
The PAH1-encoded phosphatidate phosphatase, which catalyzes the dephosphorylation of phosphatidate to produce diacylglycerol, controls the divergence of phosphatidate into triacylglycerol synthesis and phospholipid synthesis. Pah1 is inactive in the cytosol as a phosphorylated form and becomes active on the nuclear/endoplasmic reticulum membrane as a dephosphorylated form by the Nem1-Spo7 protein phosphatase complex. The phosphorylation of Pah1 by protein kinases, which include casein kinases I and II, Pho85-Pho80, Cdc28-cyclin B, and protein kinases A and C, controls its cellular location, catalytic activity, and susceptibility to proteasomal degradation. Nem1 (catalytic subunit) and Spo7 (regulatory subunit), which form a protein phosphatase complex catalyzing the dephosphorylation of Pah1 for its activation, are phosphorylated by protein kinases A and C. In this review, we discuss the functions and interrelationships of the protein kinases in the control of the Nem1-Spo7/Pah1 phosphatase cascade and lipid synthesis.
Collapse
Affiliation(s)
- Shoily Khondker
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Gil-Soo Han
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ, 08901, USA
| | - George M Carman
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ, 08901, USA.
| |
Collapse
|
44
|
Park Y, Stukey GJ, Jog R, Kwiatek JM, Han GS, Carman GM. Mutant phosphatidate phosphatase Pah1-W637A exhibits altered phosphorylation, membrane association, and enzyme function in yeast. J Biol Chem 2022; 298:101578. [PMID: 35026226 PMCID: PMC8819029 DOI: 10.1016/j.jbc.2022.101578] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/30/2021] [Accepted: 01/04/2022] [Indexed: 02/05/2023] Open
Abstract
The Saccharomyces cerevisiae PAH1-encoded phosphatidate (PA) phosphatase, which catalyzes the dephosphorylation of PA to produce diacylglycerol, controls the bifurcation of PA into triacylglycerol synthesis and phospholipid synthesis. Pah1 is inactive in the cytosol as a phosphorylated form and becomes active on the membrane as a dephosphorylated form by the Nem1-Spo7 protein phosphatase. We show that the conserved Trp-637 residue of Pah1, located in the intrinsically disordered region, is required for normal synthesis of membrane phospholipids, sterols, triacylglycerol, and the formation of lipid droplets. Analysis of mutant Pah1-W637A showed that the tryptophan residue is involved in the phosphorylation-mediated/dephosphorylation-mediated membrane association of the enzyme and its catalytic activity. The endogenous phosphorylation of Pah1-W637A was increased at the sites of the N-terminal region but was decreased at the sites of the C-terminal region. The altered phosphorylation correlated with an increase in its membrane association. In addition, membrane-associated PA phosphatase activity in vitro was elevated in cells expressing Pah1-W637A as a result of the increased membrane association of the mutant enzyme. However, the inherent catalytic function of Pah1 was not affected by the W637A mutation. Prediction of Pah1 structure by AlphaFold shows that Trp-637 and the catalytic residues Asp-398 and Asp-400 in the haloacid dehalogenase-like domain almost lie in the same plane, suggesting that these residues are important to properly position the enzyme for substrate recognition at the membrane surface. These findings underscore the importance of Trp-637 in Pah1 regulation by phosphorylation, membrane association of the enzyme, and its function in lipid synthesis.
Collapse
Affiliation(s)
- Yeonhee Park
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA
| | - Geordan J Stukey
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA
| | - Ruta Jog
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA
| | - Joanna M Kwiatek
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA
| | - Gil-Soo Han
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA
| | - George M Carman
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey, USA.
| |
Collapse
|
45
|
Maitra N, Hammer S, Kjerfve C, Bankaitis VA, Polymenis M. Translational control of lipogenesis links protein synthesis and phosphoinositide signaling with nuclear division in Saccharomyces cerevisiae. Genetics 2022; 220:iyab171. [PMID: 34849864 PMCID: PMC8733439 DOI: 10.1093/genetics/iyab171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/23/2021] [Indexed: 12/21/2022] Open
Abstract
Continuously dividing cells coordinate their growth and division. How fast cells grow in mass determines how fast they will multiply. Yet, there are few, if any, examples of a metabolic pathway that actively drives a cell cycle event instead of just being required for it. Here, we show that translational upregulation of lipogenic enzymes in Saccharomyces cerevisiae increased the abundance of lipids and promoted nuclear elongation and division. Derepressing translation of acetyl-CoA carboxylase and fatty acid synthase also suppressed cell cycle-related phenotypes, including delayed nuclear division, associated with Sec14p phosphatidylinositol transfer protein deficiencies, and the irregular nuclear morphologies of mutants defective in phosphatidylinositol 4-OH kinase activities. Our results show that increased lipogenesis drives a critical cell cycle landmark and report a phosphoinositide signaling axis in control of nuclear division. The broad conservation of these lipid metabolic and signaling pathways raises the possibility these activities similarly govern nuclear division in other eukaryotes.
Collapse
Affiliation(s)
- Nairita Maitra
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Staci Hammer
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Clara Kjerfve
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Vytas A Bankaitis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Molecular & Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX 77843, USA
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| |
Collapse
|
46
|
Mauro MS, Celma G, Zimyanin V, Magaj MM, Gibson KH, Redemann S, Bahmanyar S. Ndc1 drives nuclear pore complex assembly independent of membrane biogenesis to promote nuclear formation and growth. eLife 2022; 11:75513. [PMID: 35852146 PMCID: PMC9296133 DOI: 10.7554/elife.75513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 06/15/2022] [Indexed: 01/19/2023] Open
Abstract
The nuclear envelope (NE) assembles and grows from bilayer lipids produced at the endoplasmic reticulum (ER). How ER membrane incorporation coordinates with assembly of nuclear pore complexes (NPCs) to generate a functional NE is not well understood. Here, we use the stereotypical first division of the early C. elegans embryo to test the role of the membrane-associated nucleoporin Ndc1 in coupling NPC assembly to NE formation and growth. 3D-EM tomography of reforming and expanded NEs establishes that Ndc1 determines NPC density. Loss of ndc1 results in faster turnover of the outer scaffold nucleoporin Nup160 at the NE, providing an explanation for how Ndc1 controls NPC number. NE formation fails in the absence of both Ndc1 and the inner ring component Nup53, suggesting partially redundant roles in NPC assembly. Importantly, upregulation of membrane synthesis restored the slow rate of nuclear growth resulting from loss of ndc1 but not from loss of nup53. Thus, membrane biogenesis can be decoupled from Ndc1-mediated NPC assembly to promote nuclear growth. Together, our data suggest that Ndc1 functions in parallel with Nup53 and membrane biogenesis to control NPC density and nuclear size.
Collapse
Affiliation(s)
- Michael Sean Mauro
- Department of Molecular, Cellular and Developmental Biology, Yale UniversityNew HavenUnited States
| | - Gunta Celma
- Department of Molecular, Cellular and Developmental Biology, Yale UniversityNew HavenUnited States
| | - Vitaly Zimyanin
- Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States,Department of Molecular Physiology and Biological Physics, University of Virginia, School of MedicineCharlottesvilleUnited States
| | - Magdalena M Magaj
- Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States,Department of Molecular Physiology and Biological Physics, University of Virginia, School of MedicineCharlottesvilleUnited States
| | - Kimberley H Gibson
- Center for Cellular and Molecular Imaging: Electron Microscopy, Department of Cell Biology, Yale School of MedicineNew HavenUnited States
| | - Stefanie Redemann
- Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States,Department of Molecular Physiology and Biological Physics, University of Virginia, School of MedicineCharlottesvilleUnited States,Department of Cell Biology, University of VirginiaCharlottesvilleUnited States
| | - Shirin Bahmanyar
- Department of Molecular, Cellular and Developmental Biology, Yale UniversityNew HavenUnited States
| |
Collapse
|
47
|
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] [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.
Collapse
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
| |
Collapse
|
48
|
Maheshwari R, Rahman MM, Joseph-Strauss D, Cohen-Fix O. An RNAi screen for genes that affect nuclear morphology in Caenorhabditis elegans reveals the involvement of unexpected processes. G3 (BETHESDA, MD.) 2021; 11:jkab264. [PMID: 34849797 PMCID: PMC8527477 DOI: 10.1093/g3journal/jkab264] [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: 06/30/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Aberration in nuclear morphology is one of the hallmarks of cellular transformation. However, the processes that, when mis-regulated, result aberrant nuclear morphology are poorly understood. In this study, we carried out a systematic, high-throughput RNAi screen for genes that affect nuclear morphology in Caenorhabditis elegans embryos. The screen employed over 1700 RNAi constructs against genes required for embryonic viability. Nuclei of early embryos are typically spherical, and their NPCs are evenly distributed. The screen was performed on early embryos expressing a fluorescently tagged component of the nuclear pore complex (NPC), allowing visualization of nuclear shape as well as the distribution of NPCs around the nuclear envelope. Our screen uncovered 182 genes whose downregulation resulted in one or more abnormal nuclear phenotypes, including multiple nuclei, micronuclei, abnormal nuclear shape, anaphase bridges, and abnormal NPC distribution. Many of these genes fall into common functional groups, including some that were not previously known to affect nuclear morphology, such as genes involved in mitochondrial function, the vacuolar ATPase, and the CCT chaperonin complex. The results of this screen add to our growing knowledge of processes that affect nuclear morphology and that may be altered in cancer cells that exhibit abnormal nuclear shape.
Collapse
Affiliation(s)
- Richa Maheshwari
- The Laboratory of Biochemistry and Genetics, The National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, MD 20892, USA
| | - Mohammad M Rahman
- The Laboratory of Biochemistry and Genetics, The National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, MD 20892, USA
| | - Daphna Joseph-Strauss
- The Laboratory of Biochemistry and Genetics, The National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, MD 20892, USA
| | - Orna Cohen-Fix
- The Laboratory of Biochemistry and Genetics, The National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
49
|
Abstract
Nuclear shape and size depend on nuclear membrane availability through an unknown process. A new study of asymmetric cell division reveals that nuclear membrane is derived from the endoplasmic reticulum and that limiting nuclear membrane expansion can affect cell fate.
Collapse
Affiliation(s)
- Orna Cohen-Fix
- The Laboratory of Biochemistry and Genetics, NIDDK, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
50
|
Torán-Vilarrubias A, Moriel-Carretero M. Oxidative agents elicit endoplasmic reticulum morphological changes suggestive of alterations in lipid metabolism. MICROPUBLICATION BIOLOGY 2021; 2021. [PMID: 34557658 PMCID: PMC8453305 DOI: 10.17912/micropub.biology.000462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/03/2021] [Accepted: 09/10/2021] [Indexed: 11/06/2022]
Abstract
The endoplasmic reticulum (ER) is a central organelle in charge of correct protein folding; lipids synthesis, modification, and sorting; as well as of maintenance of calcium homeostasis. To accomplish these functions, the ER lumen possesses an oxidative potential. Challenging cells with reductive agents therefore provokes an ER stress that immediately affects protein folding, and which morphologically manifests by an expansion of the cytoplasmic ER network. Yet less is known about the impact on the ER of exposing cells to oxidative agents, which risk to exacerbate the basal, physiologically oxidative environment. We have monitored the morphology of the ER of Saccharomyces cerevisiae in response to this type of treatment. We bring the notion that oxidative agents give rise to diverse alterations in the perinuclear ER subdomain that are suggestive of lipid metabolism perturbations.
Collapse
Affiliation(s)
- Alba Torán-Vilarrubias
- Institut de Génétique Humaine (IGH), Université de Montpellier, Centre National de la Recherche Scientifique, 34396 Montpellier CEDEX 05, France
| | - 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
| |
Collapse
|