1
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Phetruen T, van Dam B, Chanarat S. Andrographolide Induces ROS-Mediated Cytotoxicity, Lipid Peroxidation, and Compromised Cell Integrity in Saccharomyces cerevisiae. Antioxidants (Basel) 2023; 12:1765. [PMID: 37760068 PMCID: PMC10525756 DOI: 10.3390/antiox12091765] [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: 08/28/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Andrographolide, a bioactive compound found in Andrographis paniculata, has gained significant attention for its potential therapeutic properties. Despite its promising benefits, the understanding of its side effects and underlying mechanisms remains limited. Here, we investigated the impact of andrographolide in Saccharomyces cerevisiae and observed that andrographolide induced cytotoxicity, particularly when oxidative phosphorylation was active. Furthermore, andrographolide affected various cellular processes, including vacuole fragmentation, endoplasmic reticulum stress, lipid droplet accumulation, reactive oxygen species levels, and compromised cell integrity. Moreover, we unexpectedly observed that andrographolide induced the precipitation of biomolecules secreted from yeast cells, adding an additional source of stress. Overall, this study provides insights into the cellular effects and potential mechanisms of andrographolide in yeast, shedding light on its side effects and underlying cytotoxicity pathways.
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Affiliation(s)
| | | | - Sittinan Chanarat
- Laboratory of Molecular Cell Biology, Department of Biochemistry, Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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2
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Deprez MA, Caligaris M, Rosseels J, Hatakeyama R, Ghillebert R, Sampaio-Marques B, Mudholkar K, Eskes E, Meert E, Ungermann C, Ludovico P, Rospert S, De Virgilio C, Winderickx J. The nutrient-responsive CDK Pho85 primes the Sch9 kinase for its activation by TORC1. PLoS Genet 2023; 19:e1010641. [PMID: 36791155 PMCID: PMC9974134 DOI: 10.1371/journal.pgen.1010641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 02/28/2023] [Accepted: 01/27/2023] [Indexed: 02/16/2023] Open
Abstract
Yeast cells maintain an intricate network of nutrient signaling pathways enabling them to integrate information on the availability of different nutrients and adjust their metabolism and growth accordingly. Cells that are no longer capable of integrating this information, or that are unable to make the necessary adaptations, will cease growth and eventually die. Here, we studied the molecular basis underlying the synthetic lethality caused by loss of the protein kinase Sch9, a key player in amino acid signaling and proximal effector of the conserved growth-regulatory TORC1 complex, when combined with either loss of the cyclin-dependent kinase (CDK) Pho85 or loss of its inhibitor Pho81, which both have pivotal roles in phosphate sensing and cell cycle regulation. We demonstrate that it is specifically the CDK-cyclin pair Pho85-Pho80 or the partially redundant CDK-cyclin pairs Pho85-Pcl6/Pcl7 that become essential for growth when Sch9 is absent. Interestingly, the respective three CDK-cyclin pairs regulate the activity and distribution of the phosphatidylinositol-3 phosphate 5-kinase Fab1 on endosomes and vacuoles, where it generates phosphatidylinositol-3,5 bisphosphate that serves to recruit both TORC1 and its substrate Sch9. In addition, Pho85-Pho80 directly phosphorylates Sch9 at Ser726, and to a lesser extent at Thr723, thereby priming Sch9 for its subsequent phosphorylation and activation by TORC1. The TORC1-Sch9 signaling branch therefore integrates Pho85-mediated information at different levels. In this context, we also discovered that loss of the transcription factor Pho4 rescued the synthetic lethality caused by loss of Pho85 and Sch9, indicating that both signaling pathways also converge on Pho4, which appears to be wired to a feedback loop involving the high-affinity phosphate transporter Pho84 that fine-tunes Sch9-mediated responses.
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Affiliation(s)
- Marie-Anne Deprez
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
| | - Marco Caligaris
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Joëlle Rosseels
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
| | - Riko Hatakeyama
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Ruben Ghillebert
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
| | - Belém Sampaio-Marques
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga/Guimarães, Braga, Portugal
| | - Kaivalya Mudholkar
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Elja Eskes
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
| | - Els Meert
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
| | - Christian Ungermann
- Department of Biology/Chemistry & Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga/Guimarães, Braga, Portugal
| | - Sabine Rospert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Claudio De Virgilio
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- * E-mail: (CDV); (JW)
| | - Joris Winderickx
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
- * E-mail: (CDV); (JW)
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3
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2-deoxyglucose transiently inhibits yeast AMPK signaling and triggers glucose transporter endocytosis, potentiating the drug toxicity. PLoS Genet 2022; 18:e1010169. [PMID: 35951639 PMCID: PMC9398028 DOI: 10.1371/journal.pgen.1010169] [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: 03/28/2022] [Revised: 08/23/2022] [Accepted: 07/20/2022] [Indexed: 11/19/2022] Open
Abstract
2-deoxyglucose is a glucose analog that impacts many aspects of cellular physiology. After its uptake and its phosphorylation into 2-deoxyglucose-6-phosphate (2DG6P), it interferes with several metabolic pathways including glycolysis and protein N-glycosylation. Despite this systemic effect, resistance can arise through strategies that are only partially understood. In yeast, 2DG resistance is often associated with mutations causing increased activity of the yeast 5’-AMP activated protein kinase (AMPK), Snf1. Here we focus on the contribution of a Snf1 substrate in 2DG resistance, namely the alpha-arrestin Rod1 involved in nutrient transporter endocytosis. We report that 2DG triggers the endocytosis of many plasma membrane proteins, mostly in a Rod1-dependent manner. Rod1 participates in 2DG-induced endocytosis because 2DG, following its phosphorylation by hexokinase Hxk2, triggers changes in Rod1 post-translational modifications and promotes its function in endocytosis. Mechanistically, this is explained by a transient, 2DG-induced inactivation of Snf1/AMPK by protein phosphatase 1 (PP1). We show that 2DG-induced endocytosis is detrimental to cells, and the lack of Rod1 counteracts this process by stabilizing glucose transporters at the plasma membrane. This facilitates glucose uptake, which may help override the metabolic blockade caused by 2DG, and 2DG export—thus terminating the process of 2DG detoxification. Altogether, these results shed a new light on the regulation of AMPK signaling in yeast and highlight a remarkable strategy to bypass 2DG toxicity involving glucose transporter regulation.
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4
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Gokbayrak ZD, Patel D, Brett CL. Acetate and hypertonic stress stimulate vacuole membrane fission using distinct mechanisms. PLoS One 2022; 17:e0271199. [PMID: 35834522 PMCID: PMC9282455 DOI: 10.1371/journal.pone.0271199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/25/2022] [Indexed: 11/19/2022] Open
Abstract
Vacuoles in plants and fungi play critical roles in cell metabolism and osmoregulation. To support these functions, vacuoles change their morphology, e.g. they fragment when these organisms are challenged with draught, high salinity or metabolic stress (e.g. acetate accumulation). In turn, morphology reflects an equilibrium between membrane fusion and fission that determines size, shape and copy number. By studying Saccharomyces cerevisiae and its vacuole as models, conserved molecular mechanisms responsible for fusion have been revealed. However, a detailed understanding of vacuole fission and how these opposing processes respond to metabolism or osmoregulation remain elusive. Herein we describe a new fluorometric assay to measure yeast vacuole fission in vitro. For proof–of–concept, we use this assay to confirm that acetate, a metabolic stressor, triggers vacuole fission and show it blocks homotypic vacuole fusion in vitro. Similarly, hypertonic stress induced by sorbitol or glucose caused robust vacuole fission in vitro whilst inhibiting fusion. Using wortmannin to inhibit phosphatidylinositol (PI) -kinases or rGyp1-46 to inactivate Rab–GTPases, we show that acetate stress likely targets PI signaling, whereas osmotic stress affects Rab signaling on vacuole membranes to stimulate fission. This study sets the stage for further investigation into the mechanisms that change vacuole morphology to support cell metabolism and osmoregulation.
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Affiliation(s)
| | - Dipti Patel
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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5
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Takuma T, Ushimaru T. Vacuolar fragmentation promotes fluxes of microautophagy and micronucleophagy but not of macroautophagy. Biochem Biophys Res Commun 2022; 614:161-168. [PMID: 35597153 DOI: 10.1016/j.bbrc.2022.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/07/2022] [Indexed: 11/17/2022]
Abstract
Vacuoles and lysosomes are organelles involved in the degradation of cytoplasmic proteins and organelles. Vacuolar morphology is dynamically regulated by fission and fusion in budding yeast. Vacuolar fusion is elicited in nutrient-depleted conditions and mediated by inactivation of target of rapamycin complex 1 (TORC1) protein kinase. However, it is unknown whether and how vacuolar morphology affects macroautophagy and microautophagy, which are induced by nutrient starvation and TORC1 inactivation. Here, we developed a system to control vacuolar fission in budding yeast. Vacuolar fragmentation promoted microautophagy but not macroautophagy. Vacuolar fragmentation caused multiple nucleus-vacuole junctions. Multiple vacuoles caused by vacuolar fragmentation also improved micronucleophagy (microautophagic degradation of a portion of the nucleus). However, vacuolar morphology did not impact nucleolar remodeling, condensation of the rDNA (rRNA gene) region, or separation of ribosomal DNA from nucleolar proteins, which is evoked by TORC1 inactivation. Thus, this study provides insights into the impacts of vacuolar/lysosomal morphology on macroautophagy and microautophagy.
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Affiliation(s)
- Tsuneyuki Takuma
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan
| | - Takashi Ushimaru
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan; Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan.
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6
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Oxidative Stress Causes Vacuolar Fragmentation in the Human Fungal Pathogen Cryptococcus neoformans. J Fungi (Basel) 2021; 7:jof7070523. [PMID: 34210104 PMCID: PMC8305764 DOI: 10.3390/jof7070523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/07/2021] [Accepted: 06/26/2021] [Indexed: 02/04/2023] Open
Abstract
Vacuoles are dynamic cellular organelles, and their morphology is altered by various stimuli or stresses. Vacuoles play an important role in the physiology and virulence of many fungal pathogens. For example, a Cryptococcus neoformans mutant deficient in vacuolar functions showed significantly reduced expression of virulence factors such as capsule and melanin synthesis and was avirulent in a mouse model of cryptococcosis. In the current study, we found significantly increased vacuolar fragmentation in the C. neoformans mutants lacking SOD1 or SOD2, which respectively encode Zn, Cu-superoxide dismutase and Mn-superoxide dismutase. The sod2 mutant showed a greater level of vacuole fragmentation than the sod1 mutant. We also observed that the vacuoles were highly fragmented when wild-type cells were grown in a medium containing high concentrations of iron, copper, or zinc. Moreover, elevated temperature and treatment with the antifungal drug fluconazole caused increased vacuolar fragmentation. These conditions also commonly cause an increase in the levels of intracellular reactive oxygen species in the fungus, suggesting that vacuoles are fragmented in response to oxidative stress. Furthermore, we observed that Sod2 is not only localized in mitochondria but also in the cytoplasm within phagocytosed C. neoformans cells, possibly due to copper or iron limitation.
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7
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Characterization of nucleocapsid and matrix proteins of Newcastle disease virus in yeast. 3 Biotech 2021; 11:65. [PMID: 33489683 DOI: 10.1007/s13205-020-02624-4] [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: 11/03/2020] [Accepted: 12/26/2020] [Indexed: 10/22/2022] Open
Abstract
Newcastle disease virus is a member of family Paramyxoviridae that infects chicken. Its genome comprises ~15.2 kb negative-sense RNA that encodes six major proteins. The virus encodes various proteins; among all, nucleocapsid (NP) and matrix (M) help in virus replication and its budding from the host cells, respectively. In this study, we investigated the intracellular distribution of NP and M upon expression in the yeast Saccharomyces cerevisiae. We observed nuclear targeting of M, and vacuolar localization of NP was observed in a fraction of yeast cells. Prolonged expression of GFP fused NP or M resulted in altered cell viability and intracellular production of reactive oxygen species in yeast cells. The expression of viral proteins did not alter the morphology and number of the organelles such as nucleus, mitochondria, endoplasmic reticulum, and peroxisomes. However, a significant effect was observed on vacuolar morphology and number in yeast cells. These observations point towards the importance of host cellular reorganization in viral infection. These findings may enable us to understand the conserved pathways affected in eukaryotic cells as a result of viral protein expression. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-020-02624-4.
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8
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Agrawal P, Manjithaya R, Surolia N. Autophagy‐related protein
Pf
ATG18 participates in food vacuole dynamics and autophagy‐like pathway in
Plasmodium falciparum. Mol Microbiol 2019; 113:766-782. [DOI: 10.1111/mmi.14441] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Palak Agrawal
- Molecular Biology and Genetics Unit Jawaharlal Nehru Centre for Advanced Scientific Research Bangalore India
| | - Ravi Manjithaya
- Molecular Biology and Genetics Unit Jawaharlal Nehru Centre for Advanced Scientific Research Bangalore India
| | - Namita Surolia
- Molecular Biology and Genetics Unit Jawaharlal Nehru Centre for Advanced Scientific Research Bangalore India
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9
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Sphingolipid/Pkh1/2-TORC1/Sch9 Signaling Regulates Ribosome Biogenesis in Tunicamycin-Induced Stress Response in Yeast. Genetics 2019; 212:175-186. [PMID: 30824472 DOI: 10.1534/genetics.118.301874] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/26/2019] [Indexed: 12/26/2022] Open
Abstract
Reduced ribosome biogenesis in response to environmental conditions is a key feature of cell adaptation to stress. For example, ribosomal genes are transcriptionally repressed when cells are exposed to tunicamycin, a protein glycosylation inhibitor that induces endoplasmic reticulum stress and blocks vesicular trafficking in the secretory pathway. Here, we describe a novel regulatory model, in which tunicamycin-mediated stress induces the accumulation of long-chain sphingoid bases and subsequent activation of Pkh1/2 signaling, which leads to decreased expression of ribosomal protein genes via the downstream effectors Pkc1 and Sch9. Target of rapamycin complex 1 (TORC1), an upstream activator of Sch9, is also required. This pathway links ribosome biogenesis to alterations in membrane lipid composition under tunicamycin-induced stress conditions. Our results suggest that sphingolipid/Pkh1/2-TORC1/Sch9 signaling is an important determinant for adaptation to tunicamycin-induced stress.
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10
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Ouahoud S, Fiet MD, Martínez-Montañés F, Ejsing CS, Kuss O, Roden M, Markgraf DF. Lipid droplet consumption is functionally coupled to vacuole homeostasis independent of lipophagy. J Cell Sci 2018; 131:jcs.213876. [PMID: 29678904 DOI: 10.1242/jcs.213876] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/13/2018] [Indexed: 01/19/2023] Open
Abstract
Lipid droplets (LDs) store neutral lipids and are integrated into a cellular metabolic network that relies on functional coupling with various organelles. Factors mediating efficient coupling and mechanisms regulating them remain unknown. Here, we conducted a global screen in S. cerevisiae to identify genes required for the functional coupling of LDs and other organelles during LD consumption. We show that LD utilization during growth resumption is coupled to vacuole homeostasis. ESCRT-, V-ATPase- and vacuole protein sorting-mutants negatively affect LD consumption, independent of lipophagy. Loss of ESCRT function leads to the accumulation of LD-derived diacylglycerol (DAG), preventing its conversion into phosphatidic acid (PA) and membrane lipids. In addition, channeling of DAG from LD-proximal sites to the vacuole is blocked. We demonstrate that utilization of LDs requires intact vacuolar signaling via TORC1 and its downstream effector Sit4p. These data suggest that vacuolar status is coupled to LD catabolism via TORC1-mediated regulation of DAG-PA interconversion and explain how cells coordinate organelle dynamics throughout cell growth.
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Affiliation(s)
- Sarah Ouahoud
- Institute for Clinical Diabetology, German Diabetes Center, c/o Auf'm Hennekamp 65, D-40225 Düsseldorf, Germany.,German Center for Diabetes Research (DZD e.V.), München, Neuherberg, Germany
| | - Mitchell D Fiet
- Institute for Clinical Diabetology, German Diabetes Center, c/o Auf'm Hennekamp 65, D-40225 Düsseldorf, Germany.,German Center for Diabetes Research (DZD e.V.), München, Neuherberg, Germany
| | - Fernando Martínez-Montañés
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
| | - Oliver Kuss
- German Center for Diabetes Research (DZD e.V.), München, Neuherberg, Germany.,Institute for Biometrics and Epidemiology, German Diabetes Center, Auf'm Hennekamp 65, D-40225 Düsseldorf, Germany
| | - Michael Roden
- Institute for Clinical Diabetology, German Diabetes Center, c/o Auf'm Hennekamp 65, D-40225 Düsseldorf, Germany.,German Center for Diabetes Research (DZD e.V.), München, Neuherberg, Germany.,Division of Endocrinology and Diabetology, Medical Faculty, Heinrich-Heine University, D-40225 Düsseldorf, Germany
| | - Daniel F Markgraf
- Institute for Clinical Diabetology, German Diabetes Center, c/o Auf'm Hennekamp 65, D-40225 Düsseldorf, Germany .,German Center for Diabetes Research (DZD e.V.), München, Neuherberg, Germany
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11
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Conrad M, Kankipati HN, Kimpe M, Van Zeebroeck G, Zhang Z, Thevelein JM. The nutrient transceptor/PKA pathway functions independently of TOR and responds to leucine and Gcn2 in a TOR-independent manner. FEMS Yeast Res 2018; 17:3950251. [PMID: 28810702 PMCID: PMC5812495 DOI: 10.1093/femsyr/fox048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/06/2017] [Indexed: 12/25/2022] Open
Abstract
Two nutrient-controlled signalling pathways, the PKA and TOR pathway, play a major role in nutrient regulation of growth as well as growth-correlated properties in yeast. The relationship between the two pathways is not well understood. We have used Gap1 and Pho84 transceptor-mediated activation of trehalase and phosphorylation of fragmented Sch9 as a read-out for rapid nutrient activation of PKA or TORC1, respectively. We have identified conditions in which L-citrulline-induced activation of Sch9 phosphorylation is compromised, but not activation of trehalase: addition of the TORC1 inhibitor, rapamycin and low levels of L-citrulline. The same disconnection was observed for phosphate activation in phosphate-starved cells. The leu2 auxotrophic mutation reduces amino acid activation of trehalase, which is counteracted by deletion of GCN2. Both effects were also independent of TORC1. Our results show that rapid activation of the TOR pathway by amino acids is not involved in rapid activation of the PKA pathway and that effects of Gcn2 inactivation as well as leu2 auxotrophy all act independently of the TOR pathway. Hence, rapid nutrient signalling to PKA and TOR in cells arrested by nutrient starvation acts through parallel pathways.
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Affiliation(s)
- Michaela Conrad
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Harish Nag Kankipati
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Marlies Kimpe
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Zhiqiang Zhang
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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12
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Rahman MA, Mostofa MG, Ushimaru T. The Nem1/Spo7-Pah1/lipin axis is required for autophagy induction after TORC1 inactivation. FEBS J 2018; 285:1840-1860. [PMID: 29604183 DOI: 10.1111/febs.14448] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 02/01/2018] [Accepted: 03/26/2018] [Indexed: 02/06/2023]
Abstract
Autophagy is a process that requires intense membrane remodeling and consumption. The nutrient-responsive TORC1 (target of rapamycin complex 1) kinase regulates autophagy. However, how TORC1 controls autophagy via lipid/membrane biogenesis is unknown. TORC1 regulates the function of yeast phosphatidate phosphatase lipin Pah1 via the Nem1/Spo7 phosphatase complex. Here, we show that the Nem1/Spo7-Pah1 axis is required for autophagy induction after TORC1 inactivation and survival during starvation. Furthermore, this axis was critical for nucleophagy (both micronucleophagy and macronucleophagy) and was required for proper localization of micronucleophagy factor Nvj1 and macronucleophagy receptor Atg39. This study indicated that the Nem1/Spo7-Pah1 axis controlled by TORC1 is a critical branch for autophagy induction in nutrient starvation conditions.
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Affiliation(s)
| | - Md Golam Mostofa
- Graduate School of Science and Technology, Shizuoka University, Japan
| | - Takashi Ushimaru
- Graduate School of Science and Technology, Shizuoka University, Japan.,Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Japan
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13
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Lu AX, Chong YT, Hsu IS, Strome B, Handfield LF, Kraus O, Andrews BJ, Moses AM. Integrating images from multiple microscopy screens reveals diverse patterns of change in the subcellular localization of proteins. eLife 2018; 7:e31872. [PMID: 29620521 PMCID: PMC5935485 DOI: 10.7554/elife.31872] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 03/30/2018] [Indexed: 01/29/2023] Open
Abstract
The evaluation of protein localization changes on a systematic level is a powerful tool for understanding how cells respond to environmental, chemical, or genetic perturbations. To date, work in understanding these proteomic responses through high-throughput imaging has catalogued localization changes independently for each perturbation. To distinguish changes that are targeted responses to the specific perturbation or more generalized programs, we developed a scalable approach to visualize the localization behavior of proteins across multiple experiments as a quantitative pattern. By applying this approach to 24 experimental screens consisting of nearly 400,000 images, we differentiated specific responses from more generalized ones, discovered nuance in the localization behavior of stress-responsive proteins, and formed hypotheses by clustering proteins that have similar patterns. Previous approaches aim to capture all localization changes for a single screen as accurately as possible, whereas our work aims to integrate large amounts of imaging data to find unexpected new cell biology.
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Affiliation(s)
- Alex X Lu
- Department of Computer ScienceUniversity of TorontoTorontoCanada
| | - Yolanda T Chong
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoCanada
| | - Ian Shen Hsu
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
| | - Bob Strome
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
| | | | - Oren Kraus
- Department of Electrical and Computer EngineeringUniversity of TorontoTorontoCanada
| | - Brenda J Andrews
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoCanada
| | - Alan M Moses
- Department of Computer ScienceUniversity of TorontoTorontoCanada
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
- Center for Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoCanada
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14
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Deprez MA, Eskes E, Wilms T, Ludovico P, Winderickx J. pH homeostasis links the nutrient sensing PKA/TORC1/Sch9 ménage-à-trois to stress tolerance and longevity. MICROBIAL CELL 2018; 5:119-136. [PMID: 29487859 PMCID: PMC5826700 DOI: 10.15698/mic2018.03.618] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The plasma membrane H+-ATPase Pma1 and the vacuolar V-ATPase act in close harmony to tightly control pH homeostasis, which is essential for a vast number of physiological processes. As these main two regulators of pH are responsive to the nutritional status of the cell, it seems evident that pH homeostasis acts in conjunction with nutrient-induced signalling pathways. Indeed, both PKA and the TORC1-Sch9 axis influence the proton pumping activity of the V-ATPase and possibly also of Pma1. In addition, it recently became clear that the proton acts as a second messenger to signal glucose availability via the V-ATPase to PKA and TORC1-Sch9. Given the prominent role of nutrient signalling in longevity, it is not surprising that pH homeostasis has been linked to ageing and longevity as well. A first indication is provided by acetic acid, whose uptake by the cell induces toxicity and affects longevity. Secondly, vacuolar acidity has been linked to autophagic processes, including mitophagy. In agreement with this, a decline in vacuolar acidity was shown to induce mitochondrial dysfunction and shorten lifespan. In addition, the asymmetric inheritance of Pma1 has been associated with replicative ageing and this again links to repercussions on vacuolar pH. Taken together, accumulating evidence indicates that pH homeostasis plays a prominent role in the determination of ageing and longevity, thereby providing new perspectives and avenues to explore the underlying molecular mechanisms.
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Affiliation(s)
| | - Elja Eskes
- Functional Biology, KU Leuven, Leuven, Belgium
| | | | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
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15
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Eskes E, Deprez MA, Wilms T, Winderickx J. pH homeostasis in yeast; the phosphate perspective. Curr Genet 2017; 64:155-161. [PMID: 28856407 PMCID: PMC5778149 DOI: 10.1007/s00294-017-0743-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 12/22/2022]
Abstract
Recent research further clarified the molecular mechanisms that link nutrient signaling and pH homeostasis with the regulation of growth and survival of the budding yeast Saccharomyces cerevisiae. The central nutrient signaling kinases PKA, TORC1, and Sch9 are intimately associated to pH homeostasis, presumably allowing them to concert far-reaching phenotypical repercussions of nutritional cues. To exemplify such repercussions, we briefly describe consequences for phosphate uptake and signaling and outline interactions between phosphate homeostasis and the players involved in intra- and extracellular pH control. Inorganic phosphate uptake, its subcellular distribution, and its conversion into polyphosphates are dependent on the proton gradients created over different membranes. Conversely, polyphosphate metabolism appears to contribute in determining the intracellular pH. Additionally, inositol pyrophosphates are emerging as potent determinants of growth potential, in this way providing feedback from phosphate metabolism onto the central nutrient signaling kinases. All these data point towards the importance of phosphate metabolism in the reciprocal regulation of nutrient signaling and pH homeostasis.
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Affiliation(s)
- Elja Eskes
- Functional Biology, KU Leuven, Kasteelpark Arenberg 31 box 2433, 3001, Heverlee, Belgium
| | - Marie-Anne Deprez
- Functional Biology, KU Leuven, Kasteelpark Arenberg 31 box 2433, 3001, Heverlee, Belgium
| | - Tobias Wilms
- Functional Biology, KU Leuven, Kasteelpark Arenberg 31 box 2433, 3001, Heverlee, Belgium
| | - Joris Winderickx
- Functional Biology, KU Leuven, Kasteelpark Arenberg 31 box 2433, 3001, Heverlee, Belgium.
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16
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Jin N, Jin Y, Weisman LS. Early protection to stress mediated by CDK-dependent PI3,5P 2 signaling from the vacuole/lysosome. J Cell Biol 2017. [PMID: 28637746 PMCID: PMC5496620 DOI: 10.1083/jcb.201611144] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Adaptation to stress is a critical strategy for all life. Known strategies involve signaling pathways that induce changes in gene expression. These changes take time and cannot protect against acute assaults. Jin et al. reveal an early stress protection pathway regulated by the vacuole/lysosome. Adaptation to environmental stress is critical for cell survival. Adaptation generally occurs via changes in transcription and translation. However, there is a time lag before changes in gene expression, which suggests that more rapid mechanisms likely exist. In this study, we show that in yeast, the cyclin-dependent kinase Pho85/CDK5 provides protection against hyperosmotic stress and acts before long-term adaptation provided by Hog1. This protection requires the vacuolar/endolysosomal signaling lipid PI3,5P2. We show that Pho85/CDK5 directly phosphorylates and positively regulates the PI3P-5 kinase Fab1/PIKfyve complex and provide evidence that this regulation is conserved in mammalian cells. Moreover, this regulation is particularly crucial in yeast for the stress-induced transient elevation of PI3,5P2. Our study reveals a rapid protection mechanism regulated by Pho85/CDK5 via signaling from the vacuole/lysosome, which is distinct temporally and spatially from the previously discovered long-term adaptation Hog1 pathway, which signals from the nucleus.
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Affiliation(s)
- Natsuko Jin
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - Yui Jin
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - Lois S Weisman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI .,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI
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17
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Yang X, Cui H, Cheng J, Xie J, Jiang D, Hsiang T, Fu Y. A HOPS protein, CmVps39, is required for vacuolar morphology, autophagy, growth, conidiogenesis and mycoparasitic functions of Coniothyrium minitans. Environ Microbiol 2016; 18:3785-3797. [PMID: 27105005 DOI: 10.1111/1462-2920.13334] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coniothyrium minitans is an important sclerotial and hyphal parasite of the plant pathogen Sclerotinia sclerotiorum. Previously, a conidiation-deficient mutant, ZS-1N22225, was screened from a T-DNA insertional library of C. minitans. CmVps39, a homologue of Vam6p/Vps39p that plays a critical role in vacuolar morphogenesis in yeast, was disrupted by a T-DNA insertion in this mutant. CmVps39 is composed of 1071 amino acids with an amino-terminal citron homology domain and a central clathrin homology domain, as observed for other Vam6p/Vps39p family proteins. Abnormal fragmented vacuoles were observed in ΔCmVps39 under light microscopy and transmission electron microscopy, and ΔCmVps39 showed impairment in autophagy. ΔCmVps39 also exhibited significantly reduced hyphal development, poor conidiation and decreased sclerotial mycoparasitism. In addition, deletion of CmVps39 affected osmotic adaptation, pH homeostasis and cell wall integrity. Taken together, our results suggest that CmVps39 has an essential function in vacuolar morphology, autophagy, fungal development and mycoparasitism in C. minitans.
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Affiliation(s)
- Xiaoxiang Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Hui Cui
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Jiasen Cheng
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Jiatao Xie
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Tom Hsiang
- Department of Environmental Biology, University of Guelph, Guelph, ON, Canada
| | - Yanping Fu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
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18
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Stauffer B, Powers T. Target of rapamycin signaling mediates vacuolar fragmentation. Curr Genet 2016; 63:35-42. [PMID: 27233284 DOI: 10.1007/s00294-016-0616-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 05/13/2016] [Accepted: 05/17/2016] [Indexed: 11/26/2022]
Abstract
In eukaryotic cells, cellular homeostasis requires that different organelles respond to intracellular as well as environmental signals and modulate their behavior as conditions demand. Understanding the molecular mechanisms required for these changes remains an outstanding goal. One such organelle is the lysosome/vacuole, which undergoes alterations in size and number in response to environmental and physiological stimuli. Changes in the morphology of this organelle are mediated in part by the equilibrium between fusion and fission processes. While the fusion of the yeast vacuole has been studied intensively, the regulation of vacuolar fission remains poorly characterized by comparison. In recent years, a number of studies have incorporated genome-wide visual screens and high-throughput microscopy to identify factors required for vacuolar fission in response to diverse cellular insults, including hyperosmotic and endoplasmic reticulum stress. Available evidence now demonstrates that the rapamycin-sensitive TOR network, a master regulator of cell growth, is required for vacuolar fragmentation in response to stress. Importantly, many of the genes identified in these studies provide new insights into potential links between the vacuolar fission machinery and TOR signaling. Together these advances both extend our understanding of the regulation of vacuolar fragmentation in yeast as well as underscore the role of analogous events in mammalian cells.
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Affiliation(s)
- Bobbiejane Stauffer
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
| | - Ted Powers
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA.
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