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Cereghetti G, Kissling VM, Koch LM, Arm A, Schmidt CC, Thüringer Y, Zamboni N, Afanasyev P, Linsenmeier M, Eichmann C, Kroschwald S, Zhou J, Cao Y, Pfizenmaier DM, Wiegand T, Cadalbert R, Gupta G, Boehringer D, Knowles TPJ, Mezzenga R, Arosio P, Riek R, Peter M. An evolutionarily conserved mechanism controls reversible amyloids of pyruvate kinase via pH-sensing regions. Dev Cell 2024:S1534-5807(24)00271-5. [PMID: 38788715 DOI: 10.1016/j.devcel.2024.04.018] [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: 06/01/2022] [Revised: 10/15/2023] [Accepted: 04/26/2024] [Indexed: 05/26/2024]
Abstract
Amyloids are known as irreversible aggregates associated with neurodegenerative diseases. However, recent evidence shows that a subset of amyloids can form reversibly and fulfill essential cellular functions. Yet, the molecular mechanisms regulating functional amyloids and distinguishing them from pathological aggregates remain unclear. Here, we investigate the conserved principles of amyloid reversibility by studying the essential metabolic enzyme pyruvate kinase (PK) in yeast and human cells. We demonstrate that yeast PK (Cdc19) and human PK (PKM2) form reversible amyloids through a pH-sensitive amyloid core. Stress-induced cytosolic acidification promotes aggregation via protonation of specific glutamate (yeast) or histidine (human) residues within the amyloid core. Mutations mimicking protonation cause constitutive PK aggregation, while non-protonatable PK mutants remain soluble even upon stress. Physiological PK aggregation is coupled to metabolic rewiring and glycolysis arrest, causing severe growth defects when misregulated. Our work thus identifies an evolutionarily conserved, potentially widespread mechanism regulating functional amyloids during stress.
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Affiliation(s)
- Gea Cereghetti
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland; Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK.
| | - Vera M Kissling
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland; Particles-Biology Interactions Laboratory, Department of Materials Meet Life, Empa, 9014 St. Gallen, Switzerland
| | - Lisa M Koch
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Alexandra Arm
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Claudia C Schmidt
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Yannik Thüringer
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Pavel Afanasyev
- Cryo-EM Knowledge Hub (CEMK), ETH Zurich, 8093 Zürich, Switzerland
| | - Miriam Linsenmeier
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Cédric Eichmann
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Sonja Kroschwald
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Jiangtao Zhou
- Department of Health Sciences & Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Yiping Cao
- Department of Health Sciences & Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Dorota M Pfizenmaier
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Thomas Wiegand
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland; Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany; Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Riccardo Cadalbert
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Govind Gupta
- Particles-Biology Interactions Laboratory, Department of Materials Meet Life, Empa, 9014 St. Gallen, Switzerland
| | | | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK
| | - Raffaele Mezzenga
- Department of Health Sciences & Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Paolo Arosio
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Matthias Peter
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.
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2
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Heinrich S, Hondele M, Marchand D, Derrer CP, Zedan M, Oswald A, Malinovska L, Uliana F, Khawaja S, Mancini R, Grunwald D, Weis K. Glucose stress causes mRNA retention in nuclear Nab2 condensates. Cell Rep 2024; 43:113593. [PMID: 38113140 DOI: 10.1016/j.celrep.2023.113593] [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: 03/10/2022] [Revised: 10/12/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023] Open
Abstract
Nuclear mRNA export via nuclear pore complexes is an essential step in eukaryotic gene expression. Although factors involved in mRNA transport have been characterized, a comprehensive mechanistic understanding of this process and its regulation is lacking. Here, we use single-RNA imaging in yeast to show that cells use mRNA retention to control mRNA export during stress. We demonstrate that, upon glucose withdrawal, the essential RNA-binding factor Nab2 forms RNA-dependent condensate-like structures in the nucleus. This coincides with a reduced abundance of the DEAD-box ATPase Dbp5 at the nuclear pore. Depleting Dbp5, and consequently blocking mRNA export, is necessary and sufficient to trigger Nab2 condensation. The state of Nab2 condensation influences the extent of nuclear mRNA accumulation and can be recapitulated in vitro, where Nab2 forms RNA-dependent liquid droplets. We hypothesize that cells use condensation to regulate mRNA export and control gene expression during stress.
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Affiliation(s)
- Stephanie Heinrich
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland.
| | - Maria Hondele
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland; Biozentrum, Center for Molecular Life Sciences, University of Basel, 4056 Basel, Switzerland
| | - Désirée Marchand
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Carina Patrizia Derrer
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Mostafa Zedan
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Alexandra Oswald
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Liliana Malinovska
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Federico Uliana
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Sarah Khawaja
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Roberta Mancini
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - David Grunwald
- University of Massachusetts Chan Medical School, RNA Therapeutics Institute, Worcester, MA 01605, USA
| | - Karsten Weis
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland.
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3
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Mouton SN, Boersma AJ, Veenhoff LM. A physicochemical perspective on cellular ageing. Trends Biochem Sci 2023; 48:949-962. [PMID: 37716870 DOI: 10.1016/j.tibs.2023.08.007] [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: 04/21/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/18/2023]
Abstract
Cellular ageing described at the molecular level is a multifactorial process that leads to a spectrum of ageing trajectories. There has been recent discussion about whether a decline in physicochemical homeostasis causes aberrant phase transitions, which are a driver of ageing. Indeed, the function of all biological macromolecules, regardless of their participation in biomolecular condensates, depends on parameters such as pH, crowding, and redox state. We expand on the physicochemical homeostasis hypothesis and summarise recent evidence that the intracellular milieu influences molecular processes involved in ageing.
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Affiliation(s)
- Sara N Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Arnold J Boersma
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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4
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Alfatah M, Cui L, Goh CJH, Cheng TYN, Zhang Y, Naaz A, Wong JH, Lewis J, Poh WJ, Arumugam P. Metabolism of glucose activates TORC1 through multiple mechanisms in Saccharomyces cerevisiae. Cell Rep 2023; 42:113205. [PMID: 37792530 DOI: 10.1016/j.celrep.2023.113205] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/30/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
Target of Rapamycin Complex 1 (TORC1) is a conserved eukaryotic protein complex that links the presence of nutrients with cell growth. In Saccharomyces cerevisiae, TORC1 activity is positively regulated by the presence of amino acids and glucose in the medium. However, the mechanisms underlying nutrient-induced TORC1 activation remain poorly understood. By utilizing an in vivo TORC1 activation assay, we demonstrate that differential metabolism of glucose activates TORC1 through three distinct pathways in yeast. The first "canonical Rag guanosine triphosphatase (GTPase)-dependent pathway" requires conversion of glucose to fructose 1,6-bisphosphate, which activates TORC1 via the Rag GTPase heterodimer Gtr1GTP-Gtr2GDP. The second "non-canonical Rag GTPase-dependent pathway" requires conversion of glucose to glucose 6-phosphate, which activates TORC1 via a process that involves Gtr1GTP-Gtr2GTP and mitochondrial function. The third "Rag GTPase-independent pathway" requires complete glycolysis and vacuolar ATPase reassembly for TORC1 activation. We have established a roadmap to deconstruct the link between glucose metabolism and TORC1 activation.
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Affiliation(s)
- Mohammad Alfatah
- Bioinformatics Institute, A(∗)STAR, 30 Biopolis Street, Singapore 138671, Singapore.
| | - Liang Cui
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore 138602, Singapore
| | - Corinna Jie Hui Goh
- Bioinformatics Institute, A(∗)STAR, 30 Biopolis Street, Singapore 138671, Singapore
| | | | - Yizhong Zhang
- Bioinformatics Institute, A(∗)STAR, 30 Biopolis Street, Singapore 138671, Singapore
| | - Arshia Naaz
- Genome Institute of Singapore, A(∗)STAR, 60 Biopolis Street, Genome #02-01, Singapore 138672, Singapore
| | - Jin Huei Wong
- Bioinformatics Institute, A(∗)STAR, 30 Biopolis Street, Singapore 138671, Singapore
| | - Jacqueline Lewis
- Institute of Molecular and Cellular Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Wei Jie Poh
- Bioinformatics Institute, A(∗)STAR, 30 Biopolis Street, Singapore 138671, Singapore
| | - Prakash Arumugam
- Singapore Institute of Food and Biotechnology Innovation, A(∗)STAR, 31 Biopolis Way, Singapore 138669, Singapore; Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore.
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5
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Zhu X, Wang Y, Shen C, Zhang S, Wang W. The participation of vacuoles and the regulation of various metabolic pathways under acid stress promote the differentiation of chlamydospore in Trichoderma harzianum T4. J Appl Microbiol 2023; 134:lxad203. [PMID: 37669895 DOI: 10.1093/jambio/lxad203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/25/2023] [Accepted: 09/04/2023] [Indexed: 09/07/2023]
Abstract
AIMS Chlamydospores are a special, differentiated type with high environmental resistance. Consequently, the chlamydospores of Trichoderma harzianum T4 can used to industrialize the latter. This study aimed to investigate the key factors affecting the sporulation type of T. harzianum T4 and the mechanisms underlying this effect. METHODS AND RESULTS In the liquid fermentation of T. harzianum T4, ammonium sulfate (AS) inhibited conidia formation and chlamydospore production. Fermentation tests revealed that acid stress induced sporulation type alteration. Transcriptomic analysis was used to evaluate the adaptation strategy and mechanism underlying spore type alteration under acid stress. The fermentation experiments involving the addition of amino acids revealed that branched-chain amino acids benefited conidia production, whereas β-alanine benefited chlamydospore production. Confocal microscope fluorescence imaging and chloroquine intervention demonstrated that vacuole function was closely related to chlamydospore production. CONCLUSION The sporulation type of T. harzianum T4 can be controlled by adjusting the fermentation pH. T. harzianum T4 cells employ various self-protection measures against strong acid stress, including regulating their metabolism to produce a large number of chlamydospores for survival.
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Affiliation(s)
- Xiaochong Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yaping Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Chao Shen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Songhan Zhang
- Agriculture Technology Extension Service Center of Shanghai, Shanghai 201103, China
| | - Wei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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6
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Johnson DL, Kumar R, Kakhniashvili D, Pfeffer LM, Laribee RN. Ccr4-Not ubiquitin ligase signaling regulates ribosomal protein homeostasis and inhibits 40S ribosomal autophagy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555095. [PMID: 37693548 PMCID: PMC10491097 DOI: 10.1101/2023.08.28.555095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The Ccr4-Not complex containing the Not4 ubiquitin ligase regulates gene transcription and mRNA decay, yet it also has poorly defined roles in translation, proteostasis, and endolysosomal-dependent nutrient signaling. To define how Ccr4-Not mediated ubiquitin signaling regulates these additional processes, we performed quantitative proteomics in the yeast Saccharomyces cerevisiae lacking the Not4 ubiquitin ligase, and also in cells overexpressing either wild-type or functionally inactive ligase. Herein, we provide evidence that both increased and decreased Ccr4-Not ubiquitin signaling disrupts ribosomal protein (RP) homeostasis independently of reduced RP mRNA changes or reductions in known Not4 ribosomal substrates. Surprisingly, we also find that both Not4-mediated ubiquitin signaling, and the Ccr4 subunit, actively inhibit 40S ribosomal autophagy. This 40S autophagy is independent of canonical Atg7-dependent macroautophagy, thus indicating microautophagy activation is responsible. Furthermore, the Not4 ligase genetically interacts with endolysosomal pathway effectors to control both RP expression and 40S autophagy efficiency. Overall, we demonstrate that balanced Ccr4-Not ligase activity maintains RP homeostasis, and that Ccr4-Not ubiquitin signaling interacts with the endolysosomal pathway to both regulate RP expression and inhibit 40S ribosomal autophagy.
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Affiliation(s)
- Daniel L. Johnson
- Molecular Bioinformatics Core and the University of Tennessee Health Science Center Office of Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Ravinder Kumar
- Department of Pathology and Laboratory Medicine, College of Medicine and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - David Kakhniashvili
- Proteomics and Metabolomics Core and the University of Tennessee Health Science Center Office of Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Lawrence M. Pfeffer
- Department of Pathology and Laboratory Medicine, College of Medicine and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - R. Nicholas Laribee
- Department of Pathology and Laboratory Medicine, College of Medicine and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
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Caligaris M, Sampaio-Marques B, Hatakeyama R, Pillet B, Ludovico P, De Virgilio C, Winderickx J, Nicastro R. The Yeast Protein Kinase Sch9 Functions as a Central Nutrient-Responsive Hub That Calibrates Metabolic and Stress-Related Responses. J Fungi (Basel) 2023; 9:787. [PMID: 37623558 PMCID: PMC10455444 DOI: 10.3390/jof9080787] [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: 05/30/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Yeast cells are equipped with different nutrient signaling pathways that enable them to sense the availability of various nutrients and adjust metabolism and growth accordingly. These pathways are part of an intricate network since most of them are cross-regulated and subject to feedback regulation at different levels. In yeast, a central role is played by Sch9, a protein kinase that functions as a proximal effector of the conserved growth-regulatory TORC1 complex to mediate information on the availability of free amino acids. However, recent studies established that Sch9 is more than a TORC1-effector as its activity is tuned by several other kinases. This allows Sch9 to function as an integrator that aligns different input signals to achieve accuracy in metabolic responses and stress-related molecular adaptations. In this review, we highlight the latest findings on the structure and regulation of Sch9, as well as its role as a nutrient-responsive hub that impacts on growth and longevity of yeast cells. Given that most key players impinging on Sch9 are well-conserved, we also discuss how studies on Sch9 can be instrumental to further elucidate mechanisms underpinning healthy aging in mammalians.
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Affiliation(s)
- Marco Caligaris
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; (M.C.); (B.P.); (C.D.V.)
| | - Belém Sampaio-Marques
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (B.S.-M.); (P.L.)
- ICVS/3B’s-PT Government Associate Laboratory, 4806-909 Guimarães, Portugal
| | - Riko Hatakeyama
- Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK;
| | - Benjamin Pillet
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; (M.C.); (B.P.); (C.D.V.)
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (B.S.-M.); (P.L.)
- ICVS/3B’s-PT Government Associate Laboratory, 4806-909 Guimarães, Portugal
| | - Claudio De Virgilio
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; (M.C.); (B.P.); (C.D.V.)
| | - Joris Winderickx
- Department of Biology, Functional Biology, KU Leuven, B-3001 Heverlee, Belgium;
| | - Raffaele Nicastro
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; (M.C.); (B.P.); (C.D.V.)
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Yin J, He W, Zhang M, He W, Zhang G, Ni B. https://elsevier.proofcentral.com/en-us/landing-page.html?token=baf280639f2773e07701834b1c13daInhibition of spermatogenesis by hypoxia is mediated by V-ATPase via the JNK/c-Jun pathway in mice. Reprod Biol 2023; 23:100761. [PMID: 37023662 DOI: 10.1016/j.repbio.2023.100761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 04/07/2023]
Abstract
Spermatocyte apoptosis is the primary cause of a poor outcome after hypoxia-triggered spermatogenesis reduction (HSR). Vacuolar H+-ATPase (V-ATPase) is involved in the regulation of hypoxia-induced spermatocyte apoptosis; however, the underlying mechanism remains to be elucidated. The aim of this study was to investigate the effect of V-ATPase deficiency on spermatocyte apoptosis and the relationship between c-Jun and apoptosis in primary spermatocytes induced by hypoxia. We found that mice under hypoxia exposure for 30 days demonstrated a marked spermatogenesis reduction and downregulation of V-ATPase expression, which were assessed by a TUNEL assay and western blotting, respectively. V-ATPase deficiency resulted in more severe spermatogenesis reduction and spermatocyte apoptosis after hypoxia exposure. We also observed that silencing V-ATPase expression enhanced JNK/c-Jun activation and death receptor-mediated apoptosis in primary spermatocytes. However, inhibition of c-Jun attenuated V-ATPase deficiency-induced spermatocyte apoptosis in primary spermatocytes. In conclusion, the data in this study suggest that V-ATPase deficiency aggravated hypoxia-induced spermatogenesis reduction by promoting spermatocyte apoptosis in mice via the JNK/c-Jun pathway.
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Affiliation(s)
- Jun Yin
- Department of Pathophysiology/Key Laboratory of High Altitude Environment Medicine, Ministry of Education/Key Laboratory of High Altitude Medicine, College of High Altitude Military Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Wenjuan He
- Department of Pathophysiology/Key Laboratory of High Altitude Environment Medicine, Ministry of Education/Key Laboratory of High Altitude Medicine, College of High Altitude Military Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Mengjie Zhang
- Department of Pathophysiology/Key Laboratory of High Altitude Environment Medicine, Ministry of Education/Key Laboratory of High Altitude Medicine, College of High Altitude Military Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Wei He
- Chongqing ILinda Biomedical Research Corporation Limited, PR China
| | - Gang Zhang
- Department of High Altitude Operational Medicine, College of High Altitude Military Medicine, Third Military Medical University, Chongqing 400038, PR China.
| | - Bing Ni
- Department of Pathophysiology/Key Laboratory of High Altitude Environment Medicine, Ministry of Education/Key Laboratory of High Altitude Medicine, College of High Altitude Military Medicine, Third Military Medical University, Chongqing 400038, PR China.
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9
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Wilson HB, Lorenz MC. Candida albicans Hyphal Morphogenesis within Macrophages Does Not Require Carbon Dioxide or pH-Sensing Pathways. Infect Immun 2023; 91:e0008723. [PMID: 37078861 PMCID: PMC10187119 DOI: 10.1128/iai.00087-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/29/2023] [Indexed: 04/21/2023] Open
Abstract
The opportunistic fungal pathogen Candida albicans has evolved a variety of mechanisms for surviving inside and escaping macrophages, including the initiation of filamentous growth. Although several distinct models have been proposed to explain this process at the molecular level, the signals driving hyphal morphogenesis in this context have yet to be clarified. Here, we evaluate the following three molecular signals as potential hyphal inducers within macrophage phagosomes: CO2, intracellular pH, and extracellular pH. Additionally, we revisit previous work suggesting that the intracellular pH of C. albicans fluctuates in tandem with morphological changes in vitro. Using time-lapse microscopy, we observed that C. albicans mutants lacking components of the CO2-sensing pathway were able to undergo hyphal morphogenesis within macrophages. Similarly, a rim101Δ strain was competent in hyphal induction, suggesting that neutral/alkaline pH sensing is not necessary for the initiation of morphogenesis within phagosomes either. Contrary to previous findings, single-cell pH-tracking experiments revealed that the cytosolic pH of C. albicans remains tightly regulated both within macrophage phagosomes and under a variety of in vitro conditions throughout the process of morphogenesis. This finding suggests that intracellular pH is not a signal contributing to morphological changes.
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Affiliation(s)
- Hannah B. Wilson
- Graduate School for Biomedical Sciences, University of Texas Science Center at Houston, Houston, Texas, USA
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Michael C. Lorenz
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
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10
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Laribee RN, Boucher AB, Madireddy S, Pfeffer LM. The STAT3-Regulated Autophagy Pathway in Glioblastoma. Pharmaceuticals (Basel) 2023; 16:671. [PMID: 37242454 PMCID: PMC10223172 DOI: 10.3390/ph16050671] [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: 03/22/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Glioblastoma (GBM) is the most common primary brain malignancy in adults with a dismal prognosis. Despite advances in genomic analysis and surgical technique and the development of targeted therapeutics, most treatment options are ineffective and mainly palliative. Autophagy is a form of cellular self-digestion with the goal of recycling intracellular components to maintain cell metabolism. Here, we describe some recent findings that suggest GBM tumors are more sensitive to the excessive overactivation of autophagy leading to autophagy-dependent cell death. GBM cancer stem cells (GSCs) are a subset of the GBM tumor population that play critical roles in tumor formation and progression, metastasis, and relapse, and they are inherently resistant to most therapeutic strategies. Evidence suggests that GSCs are able to adapt to a tumor microenvironment of hypoxia, acidosis, and lack of nutrients. These findings have suggested that autophagy may promote and maintain the stem-like state of GSCs as well as their resistance to cancer treatment. However, autophagy is a double-edged sword and may have anti-tumor properties under certain conditions. The role of the STAT3 transcription factor in autophagy is also described. These findings provide the basis for future research aimed at targeting the autophagy-dependent pathway to overcome the inherent therapeutic resistance of GBM in general and to specifically target the highly therapy-resistant GSC population through autophagy regulation.
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Affiliation(s)
- Ronald Nicholas Laribee
- Department of Pathology and Laboratory Medicine, The Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Andrew B. Boucher
- Department of Neurosurgery, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Saivikram Madireddy
- College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Lawrence M. Pfeffer
- Department of Pathology and Laboratory Medicine, The Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
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11
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Abstract
Mitogen-activated protein kinases (MAPKs) regulate a variety of cellular processes in eukaryotes. In fungal pathogens, conserved MAPK pathways control key virulence functions such as infection-related development, invasive hyphal growth, or cell wall remodeling. Recent findings suggest that ambient pH acts as a key regulator of MAPK-mediated pathogenicity, but the underlying molecular events are unknown. Here, we found that in the fungal pathogen Fusarium oxysporum, pH controls another infection-related process, hyphal chemotropism. Using the ratiometric pH sensor pHluorin we show that fluctuations in cytosolic pH (pHc) induce rapid reprogramming of the three conserved MAPKs in F. oxysporum, and that this response is conserved in the fungal model organism Saccharomyces cerevisiae. Screening of a subset of S. cerevisiae mutants identified the sphingolipid-regulated AGC kinase Ypk1/2 as a key upstream component of pHc-modulated MAPK responses. We further show that acidification of the cytosol in F. oxysporum leads to an increase of the long-chain base (LCB) sphingolipid dihydrosphingosine (dhSph) and that exogenous addition of dhSph activates Mpk1 phosphorylation and chemotropic growth. Our results reveal a pivotal role of pHc in the regulation of MAPK signaling and suggest new ways to target fungal growth and pathogenicity. IMPORTANCE Fungal phytopathogens cause devastating losses in global agriculture. All plant-infecting fungi use conserved MAPK signaling pathways to successfully locate, enter, and colonize their hosts. In addition, many pathogens also manipulate the pH of the host tissue to increase their virulence. Here, we establish a functional link between cytosolic pH (pHc) and MAPK signaling in the control of pathogenicity in the vascular wilt fungal pathogen Fusarium oxysporum. We demonstrate that fluctuations in pHc cause rapid reprogramming of MAPK phosphorylation, which directly impacts key processes required for infection, such as hyphal chemotropism and invasive growth. Targeting pHc homeostasis and MAPK signaling can thus open new ways to combat fungal infection.
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12
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Prouteau M, Bourgoint C, Felix J, Bonadei L, Sadian Y, Gabus C, Savvides SN, Gutsche I, Desfosses A, Loewith R. EGOC inhibits TOROID polymerization by structurally activating TORC1. Nat Struct Mol Biol 2023; 30:273-285. [PMID: 36702972 PMCID: PMC10023571 DOI: 10.1038/s41594-022-00912-6] [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: 01/07/2022] [Accepted: 11/21/2022] [Indexed: 01/27/2023]
Abstract
Target of rapamycin complex 1 (TORC1) is a protein kinase controlling cell homeostasis and growth in response to nutrients and stresses. In Saccharomyces cerevisiae, glucose depletion triggers a redistribution of TORC1 from a dispersed localization over the vacuole surface into a large, inactive condensate called TOROID (TORC1 organized in inhibited domains). However, the mechanisms governing this transition have been unclear. Here, we show that acute depletion and repletion of EGO complex (EGOC) activity is sufficient to control TOROID distribution, independently of other nutrient-signaling pathways. The 3.9-Å-resolution structure of TORC1 from TOROID cryo-EM data together with interrogation of key interactions in vivo provide structural insights into TORC1-TORC1' and TORC1-EGOC interaction interfaces. These data support a model in which glucose-dependent activation of EGOC triggers binding to TORC1 at an interface required for TOROID assembly, preventing TORC1 polymerization and promoting release of active TORC1.
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Affiliation(s)
- Manoël Prouteau
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.
| | - Clélia Bourgoint
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Jan Felix
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.
| | - Lenny Bonadei
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Yashar Sadian
- CryoGEnic facility (DCI Geneva), University of Geneva, Geneva, Switzerland
| | - Caroline Gabus
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Ambroise Desfosses
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Robbie Loewith
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.
- Swiss National Centre for Competence in Research Chemical Biology, Geneva, Switzerland.
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13
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Shimasawa M, Sakamaki JI, Maeda T, Mizushima N. The pH-sensing Rim101 pathway regulates cell size in budding yeast. J Biol Chem 2023; 299:102973. [PMID: 36738789 PMCID: PMC10011510 DOI: 10.1016/j.jbc.2023.102973] [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: 07/05/2022] [Revised: 01/28/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Although cell size regulation is crucial for cellular functions in a variety of organisms from bacteria to humans, the underlying mechanisms remain elusive. Here, we identify Rim21, a component of the pH-sensing Rim101 pathway, as a positive regulator of cell size through a flow cytometry-based genome-wide screen of Saccharomyces cerevisiae deletion mutants. We found that mutants defective in the Rim101 pathway were consistently smaller than wildtype cells in the log and stationary phases. We show that the expression of the active form of Rim101 increased the size of wildtype cells. Furthermore, the size of wildtype cells increased in response to external alkalization. Microscopic observation revealed that this cell size increase was associated with changes in both vacuolar and cytoplasmic volume. We also found that these volume changes were dependent on Rim21 and Rim101. In addition, a mutant lacking Vph1, a component of V-ATPase that is transcriptionally regulated by Rim101, was also smaller than wildtype cells, with no increase in size in response to alkalization. We demonstrate that the loss of Vph1 suppressed the Rim101-induced increase in cell size under physiological pH conditions. Taken together, our results suggest that the cell size of budding yeast is regulated by the Rim101-V-ATPase axis under physiological conditions as well as in response to alkaline stresses.
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Affiliation(s)
- Masaru Shimasawa
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun-Ichi Sakamaki
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tatsuya Maeda
- Department of Biology, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
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14
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TORC1 Signaling in Fungi: From Yeasts to Filamentous Fungi. Microorganisms 2023; 11:microorganisms11010218. [PMID: 36677510 PMCID: PMC9864104 DOI: 10.3390/microorganisms11010218] [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: 12/30/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Target of rapamycin complex 1 (TORC1) is an important regulator of various signaling pathways. It can control cell growth and development by integrating multiple signals from amino acids, glucose, phosphate, growth factors, pressure, oxidation, and so on. In recent years, it has been reported that TORC1 is of great significance in regulating cytotoxicity, morphology, protein synthesis and degradation, nutrient absorption, and metabolism. In this review, we mainly discuss the upstream and downstream signaling pathways of TORC1 to reveal its role in fungi.
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15
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Liu NN, Zhou J, Jiang T, Tarsio M, Yu F, Zheng X, Qi W, Liu L, Tan JC, Wei L, Ding J, Li J, Zeng L, Ren B, Huang X, Peng Y, Cao YB, Zhao Y, Zhang XY, Kane PM, Chen C, Wang H. A dual action small molecule enhances azoles and overcomes resistance through co-targeting Pdr5 and Vma1. Transl Res 2022; 247:39-57. [PMID: 35452875 DOI: 10.1016/j.trsl.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/26/2022] [Accepted: 04/12/2022] [Indexed: 11/19/2022]
Abstract
Fungal infection threatens human health worldwide due to the limited arsenal of antifungals and the rapid emergence of resistance. Epidermal growth factor receptor (EGFR) is demonstrated to mediate epithelial cell endocytosis of the leading human fungal pathogen, Candida albicans. However, whether EGFR inhibitors act on fungal cells remains unknown. Here, we discovered that the specific EGFR inhibitor osimertinib mesylate (OSI) potentiates azole efficacy against diverse fungal pathogens and overcomes azole resistance. Mechanistic investigation revealed a conserved activity of OSI by promoting intracellular fluconazole accumulation via inhibiting Pdr5 and disrupting V-ATPase function via targeting Vma1 at serine 274, eventually leading to inactivation of the global regulator TOR. Evaluation of the in vivo efficacy and toxicity of OSI demonstrated its potential clinical application in impeding fluconazole resistance. Thus, the identification of OSI as a dual action antifungal with co-targeting activity proposes a potentially effective therapeutic strategy to treat life-threatening fungal infection and overcome antifungal resistance.
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Affiliation(s)
- Ning-Ning Liu
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jia Zhou
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tong Jiang
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Maureen Tarsio
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Feifei Yu
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai, China
| | - Xuehan Zheng
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Wanjun Qi
- Division of Infectious Diseases, Boston Children's Hospital/Harvard Medical School, Boston, MA, USA
| | - Lin Liu
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing-Cong Tan
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Luqi Wei
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Ding
- Computational biology department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Jingquan Li
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lingbing Zeng
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Biao Ren
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, Sichuan, China
| | - Xiaotian Huang
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, Jiangxi, China
| | - Yibing Peng
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Faculty of Medical Laboratory Science, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yong-Bing Cao
- Department of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Shanghai TCM-Integrated Institute of Vascular Disease, Shanghai, China
| | - Yanbin Zhao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | - Xin-Yu Zhang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Changbin Chen
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.
| | - Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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16
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Muccini AJ, Gustafson MA, Fromme JC. Structural basis for activation of Arf1 at the Golgi complex. Cell Rep 2022; 40:111282. [PMID: 36044848 PMCID: PMC9469209 DOI: 10.1016/j.celrep.2022.111282] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/11/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022] Open
Abstract
The Golgi complex is the central sorting station of the eukaryotic secretory pathway. Traffic through the Golgi requires activation of Arf guanosine triphosphatases that orchestrate cargo sorting and vesicle formation by recruiting an array of effector proteins. Arf activation and Golgi membrane association is controlled by large guanine nucleotide exchange factors (GEFs) possessing multiple conserved regulatory domains. Here we present cryoelectron microscopy (cryoEM) structures of full-length Gea2, the yeast paralog of the human Arf-GEF GBF1, that reveal the organization of these regulatory domains and explain how Gea2 binds to the Golgi membrane surface. We find that the GEF domain adopts two different conformations compatible with different stages of the Arf activation reaction. The structure of a Gea2-Arf1 activation intermediate suggests that the movement of the GEF domain primes Arf1 for membrane insertion upon guanosine triphosphate binding. We propose that conformational switching of Gea2 during the nucleotide exchange reaction promotes membrane insertion of Arf1. Arf1 is a GTPase that regulates Golgi trafficking by recruiting many effector proteins. Muccini et al. report cryoEM structures of the Arf1 activator Gea2, capturing Gea2 in multiple conformational states including a Gea2-Arf1 activation intermediate. The structures help explain how Gea2 activates Arf1 on the Golgi membrane surface.
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Affiliation(s)
- Arnold J Muccini
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Margaret A Gustafson
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
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17
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Primo C, Navarre C, Chaumont F, André B. Plasma membrane H +-ATPases promote TORC1 activation in plant suspension cells. iScience 2022; 25:104238. [PMID: 35494253 PMCID: PMC9046228 DOI: 10.1016/j.isci.2022.104238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022] Open
Abstract
The TORC1 (Target of Rapamycin Complex 1) kinase complex plays a pivotal role in controlling cell growth in probably all eukaryotic species. The signals and mechanisms regulating TORC1 have been intensely studied in mammals but those of fungi and plants are much less known. We have previously reported that the yeast plasma membrane H+-ATPase Pma1 promotes TORC1 activation when stimulated by cytosolic acidification or nutrient-uptake-coupled H+ influx. Furthermore, a homologous plant H+-ATPase can substitute for yeast Pma1 to promote this H+-elicited TORC1 activation. We here report that TORC1 activity in Nicotiana tabacum BY-2 cells is also strongly influenced by the activity of plasma membrane H+-ATPases. In particular, stimulation of H+-ATPases by fusicoccin activates TORC1, and this response is also observed in cells transferred to a nutrient-free and auxin-free medium. Our results suggest that plant H+-ATPases, known to be regulated by practically all factors controlling cell growth, contribute to TOR signaling. Isolation of a tobacco BY-2 cell line suitable for analyzing TOR signaling Activation of plasma membrane H+-ATPases in BY-2 suspension cells elicits TOR signaling TOR signaling upon H+-ATPase activation also occurs in the absence of nutrients and auxin
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Affiliation(s)
- Cecilia Primo
- Molecular Physiology of the Cell, Université Libre de Bruxelles (ULB), Biopark, B-6041 Gosselies, Belgium
| | - Catherine Navarre
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, B-1348 Louvain-la-Neuve, Belgium
| | - François Chaumont
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, B-1348 Louvain-la-Neuve, Belgium
| | - Bruno André
- Molecular Physiology of the Cell, Université Libre de Bruxelles (ULB), Biopark, B-6041 Gosselies, Belgium
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18
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Wang X, Li J, Bian Y, Zhao C, Li J, Li X. pH regulates the lumen diameter of tissue-engineered capillaries. Exp Ther Med 2022; 23:284. [PMID: 35317437 PMCID: PMC8908470 DOI: 10.3892/etm.2022.11212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/03/2021] [Indexed: 11/24/2022] Open
Abstract
Angiogenesis is vital in tissue engineering and the size of the capillary lumen diameter directly affects vascular function. Therefore, the involvement of the pH in the regulation of the capillary lumen diameter was investigated in the present study. The cytosolic pH of different pH medium groups was measured using flow cytometry. Bromodeoxyuridine staining and wound-healing assays were performed to detect cell proliferation and migration, respectively. The expression of angiogenesis-related genes was detected using reverse transcription-quantitative PCR. In addition, cell tube formation under different pH conditions was assessed using a tube formation assay and a 3D Matrigel® model. The results indicated that a change in the pH value of the culture medium affected the cytosolic pH of the endothelial cells, which then led to a change in vascular diameter. When the medium's pH ranged from 7.4 to 7.6, the diameter of the lumen formed in the Matrigel was suitable for capillary formation in tissue engineering. The present results revealed an important role for the pH in the process of capillary formation and provided insight for pH regulation during endothelial cell tube formation and angiogenesis in tissue engineering.
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Affiliation(s)
- Xiaolin Wang
- Department of Plastic and Burn Surgery, The Second Affiliated Hospital, Air Force Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Jing Li
- Department of Plastic and Burn Surgery, The Second Affiliated Hospital, Air Force Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Yongqian Bian
- Department of Plastic and Burn Surgery, The Second Affiliated Hospital, Air Force Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Congying Zhao
- Department of Plastic and Burn Surgery, The Second Affiliated Hospital, Air Force Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Jinqing Li
- Department of Plastic and Burn Surgery, The Second Affiliated Hospital, Air Force Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Xueyong Li
- Department of Plastic and Burn Surgery, The Second Affiliated Hospital, Air Force Medical University, Xi'an, Shaanxi 710038, P.R. China
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19
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Gutierrez JI, Brittingham GP, Karadeniz YB, Tran KD, Dutta A, Holehouse AS, Peterson CL, Holt LJ. SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequence. eLife 2022; 11:70344. [PMID: 35129437 PMCID: PMC8890752 DOI: 10.7554/elife.70344] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 02/06/2022] [Indexed: 11/16/2022] Open
Abstract
It is increasingly appreciated that intracellular pH changes are important biological signals. This motivates the elucidation of molecular mechanisms of pH sensing. We determined that a nucleocytoplasmic pH oscillation was required for the transcriptional response to carbon starvation in Saccharomyces cerevisiae. The SWI/SNF chromatin remodeling complex is a key mediator of this transcriptional response. A glutamine-rich low-complexity domain (QLC) in the SNF5 subunit of this complex, and histidines within this sequence, was required for efficient transcriptional reprogramming. Furthermore, the SNF5 QLC mediated pH-dependent recruitment of SWI/SNF to an acidic transcription factor in a reconstituted nucleosome remodeling assay. Simulations showed that protonation of histidines within the SNF5 QLC leads to conformational expansion, providing a potential biophysical mechanism for regulation of these interactions. Together, our results indicate that pH changes are a second messenger for transcriptional reprogramming during carbon starvation and that the SNF5 QLC acts as a pH sensor.
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Affiliation(s)
| | - Gregory P Brittingham
- Institute for Systems Genetics, New York University Langone Health, New York, United States
| | - Yonca B Karadeniz
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Kathleen D Tran
- Department of Cell and Molecular Biology, University of Rhode Island, South Kingstown, United States
| | - Arnob Dutta
- Department of Cell and Molecular Biology, University of Rhode Island, South Kingstown, United States
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St Louis, United States
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Health, New York, United States
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20
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Loissell-Baltazar YA, Dokudovskaya S. SEA and GATOR 10 Years Later. Cells 2021; 10:cells10102689. [PMID: 34685669 PMCID: PMC8534245 DOI: 10.3390/cells10102689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/30/2021] [Accepted: 10/03/2021] [Indexed: 12/17/2022] Open
Abstract
The SEA complex was described for the first time in yeast Saccharomyces cerevisiae ten years ago, and its human homologue GATOR complex two years later. During the past decade, many advances on the SEA/GATOR biology in different organisms have been made that allowed its role as an essential upstream regulator of the mTORC1 pathway to be defined. In this review, we describe these advances in relation to the identification of multiple functions of the SEA/GATOR complex in nutrient response and beyond and highlight the consequence of GATOR mutations in cancer and neurodegenerative diseases.
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21
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The Role of Sch9 and the V-ATPase in the Adaptation Response to Acetic Acid and the Consequences for Growth and Chronological Lifespan. Microorganisms 2021; 9:microorganisms9091871. [PMID: 34576766 PMCID: PMC8472237 DOI: 10.3390/microorganisms9091871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
Studies with Saccharomyces cerevisiae indicated that non-physiologically high levels of acetic acid promote cellular acidification, chronological aging, and programmed cell death. In the current study, we compared the cellular lipid composition, acetic acid uptake, intracellular pH, growth, and chronological lifespan of wild-type cells and mutants lacking the protein kinase Sch9 and/or a functional V-ATPase when grown in medium supplemented with different acetic acid concentrations. Our data show that strains lacking the V-ATPase are especially more susceptible to growth arrest in the presence of high acetic acid concentrations, which is due to a slower adaptation to the acid stress. These V-ATPase mutants also displayed changes in lipid homeostasis, including alterations in their membrane lipid composition that influences the acetic acid diffusion rate and changes in sphingolipid metabolism and the sphingolipid rheostat, which is known to regulate stress tolerance and longevity of yeast cells. However, we provide evidence that the supplementation of 20 mM acetic acid has a cytoprotective and presumable hormesis effect that extends the longevity of all strains tested, including the V-ATPase compromised mutants. We also demonstrate that the long-lived sch9Δ strain itself secretes significant amounts of acetic acid during stationary phase, which in addition to its enhanced accumulation of storage lipids may underlie its increased lifespan.
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22
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Mei X, Ye D, Zhang F, Di C. Implantable application of polymer‐based biosensors. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210543] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xiangyuan Mei
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids Institute of Chemistry, Chinese Academy of Sciences Beijing China
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing China
| | - Dekai Ye
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids Institute of Chemistry, Chinese Academy of Sciences Beijing China
| | - Fengjiao Zhang
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing China
| | - Chong‐an Di
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids Institute of Chemistry, Chinese Academy of Sciences Beijing China
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23
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Teixeira V, Martins TS, Prinz WA, Costa V. Target of Rapamycin Complex 1 (TORC1), Protein Kinase A (PKA) and Cytosolic pH Regulate a Transcriptional Circuit for Lipid Droplet Formation. Int J Mol Sci 2021; 22:9017. [PMID: 34445723 PMCID: PMC8396576 DOI: 10.3390/ijms22169017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/12/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022] Open
Abstract
Lipid droplets (LDs) are ubiquitous organelles that fulfill essential roles in response to metabolic cues. The identification of several neutral lipid synthesizing and regulatory protein complexes have propelled significant advance on the mechanisms of LD biogenesis in the endoplasmic reticulum (ER). However, our understanding of signaling networks, especially transcriptional mechanisms, regulating membrane biogenesis is very limited. Here, we show that the nutrient-sensing Target of Rapamycin Complex 1 (TORC1) regulates LD formation at a transcriptional level, by targeting DGA1 expression, in a Sit4-, Mks1-, and Sfp1-dependent manner. We show that cytosolic pH (pHc), co-regulated by the plasma membrane H+-ATPase Pma1 and the vacuolar ATPase (V-ATPase), acts as a second messenger, upstream of protein kinase A (PKA), to adjust the localization and activity of the major transcription factor repressor Opi1, which in turn controls the metabolic switch between phospholipid metabolism and lipid storage. Together, this work delineates hitherto unknown molecular mechanisms that couple nutrient availability and pHc to LD formation through a transcriptional circuit regulated by major signaling transduction pathways.
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Affiliation(s)
- Vitor Teixeira
- Yeast Signalling Networks, i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (V.C.)
- Yeast Signalling Networks, IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Telma S. Martins
- Yeast Signalling Networks, i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (V.C.)
- Yeast Signalling Networks, IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - William A. Prinz
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA;
| | - Vítor Costa
- Yeast Signalling Networks, i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (V.C.)
- Yeast Signalling Networks, IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
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Azizoglu A, Brent R, Rudolf F. A precisely adjustable, variation-suppressed eukaryotic transcriptional controller to enable genetic discovery. eLife 2021; 10:69549. [PMID: 34342575 PMCID: PMC8421071 DOI: 10.7554/elife.69549] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/02/2021] [Indexed: 11/13/2022] Open
Abstract
Conditional expression of genes and observation of phenotype remain central to biological discovery. Current methods enable either on/off or imprecisely controlled graded gene expression. We developed a 'well-tempered' controller, WTC846, for precisely adjustable, graded, growth condition independent expression of genes in Saccharomyces cerevisiae. Controlled genes are expressed from a strong semisynthetic promoter repressed by the prokaryotic TetR, which also represses its own synthesis; with basal expression abolished by a second, 'zeroing' repressor. The autorepression loop lowers cell-to-cell variation while enabling precise adjustment of protein expression by a chemical inducer. WTC846 allelic strains in which the controller replaced the native promoters recapitulated known null phenotypes (CDC42, TPI1), exhibited novel overexpression phenotypes (IPL1), showed protein dosage-dependent growth rates and morphological phenotypes (CDC28, TOR2, PMA1 and the hitherto uncharacterized PBR1), and enabled cell cycle synchronization (CDC20). WTC846 defines an 'expression clamp' allowing protein dosage to be adjusted by the experimenter across the range of cellular protein abundances, with limited variation around the setpoint.
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Affiliation(s)
| | - Roger Brent
- Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
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25
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Zhou X, Li J, Tang N, Xie H, Fan X, Chen H, Tang M, Xie X. Genome-Wide Analysis of Nutrient Signaling Pathways Conserved in Arbuscular Mycorrhizal Fungi. Microorganisms 2021; 9:1557. [PMID: 34442636 PMCID: PMC8401276 DOI: 10.3390/microorganisms9081557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 01/03/2023] Open
Abstract
Arbuscular mycorrhizal (AM) fungi form a mutualistic symbiosis with a majority of terrestrial vascular plants. To achieve an efficient nutrient trade with their hosts, AM fungi sense external and internal nutrients, and integrate different hierarchic regulations to optimize nutrient acquisition and homeostasis during mycorrhization. However, the underlying molecular networks in AM fungi orchestrating the nutrient sensing and signaling remain elusive. Based on homology search, we here found that at least 72 gene components involved in four nutrient sensing and signaling pathways, including cAMP-dependent protein kinase A (cAMP-PKA), sucrose non-fermenting 1 (SNF1) protein kinase, target of rapamycin kinase (TOR) and phosphate (PHO) signaling cascades, are well conserved in AM fungi. Based on the knowledge known in model yeast and filamentous fungi, we outlined the possible gene networks functioning in AM fungi. These pathways may regulate the expression of downstream genes involved in nutrient transport, lipid metabolism, trehalase activity, stress resistance and autophagy. The RNA-seq analysis and qRT-PCR results of some core genes further indicate that these pathways may play important roles in spore germination, appressorium formation, arbuscule longevity and sporulation of AM fungi. We hope to inspire further studies on the roles of these candidate genes involved in these nutrient sensing and signaling pathways in AM fungi and AM symbiosis.
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Affiliation(s)
- Xiaoqin Zhou
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Jiangyong Li
- Institute for Environmental and Climate Research, Jinan University, Guangzhou 511443, China;
| | - Nianwu Tang
- UMR Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, 54280 Champenoux, France;
| | - Hongyun Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Xiaoning Fan
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Hui Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
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26
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Alfatah M, Wong JH, Krishnan VG, Lee YC, Sin QF, Goh CJH, Kong KW, Lee WT, Lewis J, Hoon S, Arumugam P. TORC1 regulates the transcriptional response to glucose and developmental cycle via the Tap42-Sit4-Rrd1/2 pathway in Saccharomyces cerevisiae. BMC Biol 2021; 19:95. [PMID: 33957926 PMCID: PMC8103650 DOI: 10.1186/s12915-021-01030-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/18/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Target of Rapamycin Complex 1 (TORC1) is a highly conserved eukaryotic protein complex that couples the presence of growth factors and nutrients in the environment with cellular proliferation. TORC1 is primarily implicated in linking amino acid levels with cellular growth in yeast and mammals. Although glucose deprivation has been shown to cause TORC1 inactivation in yeast, the precise role of TORC1 in glucose signaling and the underlying mechanisms remain unclear. RESULTS We demonstrate that the presence of glucose in the growth medium is both necessary and sufficient for TORC1 activation. TORC1 activity increases upon addition of glucose to yeast cells growing in a non-fermentable carbon source. Conversely, shifting yeast cells from glucose to a non-fermentable carbon source reduces TORC1 activity. Analysis of transcriptomic data revealed that glucose and TORC1 co-regulate about 27% (1668/6004) of yeast genes. We demonstrate that TORC1 orchestrates the expression of glucose-responsive genes mainly via the Tap42-Sit4-Rrd1/2 pathway. To confirm TORC1's function in glucose signaling, we tested its role in spore germination, a glucose-dependent developmental state transition in yeast. TORC1 regulates the glucose-responsive genes during spore germination and inhibition of TORC1 blocks spore germination. CONCLUSIONS Our studies indicate that a regulatory loop that involves activation of TORC1 by glucose and regulation of glucose-responsive genes by TORC1, mediates nutritional control of growth and development in yeast.
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Affiliation(s)
- Mohammad Alfatah
- Bioinformatics Institute, 30 Biopolis Street, Singapore, 138671, Singapore
| | - Jin Huei Wong
- Bioinformatics Institute, 30 Biopolis Street, Singapore, 138671, Singapore
| | | | - Yong Cheow Lee
- Bioinformatics Institute, 30 Biopolis Street, Singapore, 138671, Singapore
| | - Quan Feng Sin
- Bioinformatics Institute, 30 Biopolis Street, Singapore, 138671, Singapore
| | | | - Kiat Whye Kong
- Molecular Engineering Lab, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Wei Ting Lee
- Bioinformatics Institute, 30 Biopolis Street, Singapore, 138671, Singapore
| | - Jacqueline Lewis
- Bioinformatics Institute, 30 Biopolis Street, Singapore, 138671, Singapore
| | - Shawn Hoon
- Molecular Engineering Lab, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Prakash Arumugam
- Bioinformatics Institute, 30 Biopolis Street, Singapore, 138671, Singapore. .,Singapore Institute for Food and Biotechnology Innovation, 31 Biopolis Way, #01-02 Nanos, Singapore, 138669, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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27
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Liu L, Jiang T, Zhou J, Mei Y, Li J, Tan J, Wei L, Li J, Peng Y, Chen C, Liu NN, Wang H. Repurposing the FDA-approved anticancer agent ponatinib as a fluconazole potentiator by suppression of multidrug efflux and Pma1 expression in a broad spectrum of yeast species. Microb Biotechnol 2021; 15:482-498. [PMID: 33955652 PMCID: PMC8867973 DOI: 10.1111/1751-7915.13814] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 11/29/2022] Open
Abstract
Fungal infections have emerged as a major global threat to human health because of the increasing incidence and mortality rates every year. The emergence of drug resistance and limited arsenal of antifungal agents further aggravates the current situation resulting in a growing challenge in medical mycology. Here, we identified that ponatinib, an FDA‐approved antitumour drug, significantly enhanced the activity of the azole fluconazole, the most widely used antifungal drug. Further detailed investigation of ponatinib revealed that its combination with fluconazole displayed broad‐spectrum synergistic interactions against a variety of human fungal pathogens such as Candida albicans, Saccharomyces cerevisiae and Cryptococcus neoformans. Mechanistic insights into the mode of action unravelled that ponatinib reduced the efflux of fluconazole via Pdr5 and suppressed the expression of the proton pump, Pma1. Taken together, our study identifies ponatinib as a novel antifungal that enhances drug activity of fluconazole against diverse fungal pathogens.
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Affiliation(s)
- Lin Liu
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Tong Jiang
- Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jia Zhou
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yikun Mei
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jinyang Li
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jingcong Tan
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Luqi Wei
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jingquan Li
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yibing Peng
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China.,Faculty of Medical Laboratory Science, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China
| | - Changbin Chen
- Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.,The Nanjing Unicorn Academy of Innovation, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Nanjing, 211135, China
| | - Ning-Ning Liu
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
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28
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Ccr4-Not as a mediator of environmental signaling: a jack of all trades and master of all. Curr Genet 2021; 67:707-713. [PMID: 33791857 DOI: 10.1007/s00294-021-01180-5] [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: 02/19/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 10/21/2022]
Abstract
The cellular response to environmental exposures, such as nutrient shifts and various forms of stress, requires the integration of the signaling apparatus that senses these environmental changes with the downstream gene regulatory machinery. Delineating this molecular circuitry remains essential for understanding how organisms adapt to environmental flux, and it is critical for determining how dysregulation of these mechanisms causes disease. Ccr4-Not is a highly conserved regulatory complex that controls all aspects of the gene expression process. Recent studies in budding yeast have identified novel roles for Ccr4-Not as a key regulator of core nutrient signaling pathways that control cell growth and proliferation, including signaling through the mechanistic target of rapamycin complex 1 (TORC1) pathway. Herein, I will review the current evidence that implicate Ccr4-Not in nutrient signaling regulation, and I will discuss important unanswered questions that should help guide future efforts to delineate Ccr4-Not's role in linking environmental signaling with the gene regulatory machinery. Ccr4-Not is highly conserved throughout eukaryotes, and increasing evidence indicates it is dysregulated in a variety of diseases. Determining how Ccr4-Not regulates these signaling pathways in model organisms such as yeast will provide a guide for defining how it controls these processes in human cells.
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29
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Saliba E, Primo C, Guarini N, André B. A plant plasma-membrane H +-ATPase promotes yeast TORC1 activation via its carboxy-terminal tail. Sci Rep 2021; 11:4788. [PMID: 33637787 PMCID: PMC7910539 DOI: 10.1038/s41598-021-83525-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 01/28/2021] [Indexed: 01/05/2023] Open
Abstract
The Target of Rapamycin Complex 1 (TORC1) involved in coordination of cell growth and metabolism is highly conserved among eukaryotes. Yet the signals and mechanisms controlling its activity differ among taxa, according to their biological specificities. A common feature of fungal and plant cells, distinguishing them from animal cells, is that their plasma membrane contains a highly abundant H+-ATPase which establishes an electrochemical H+ gradient driving active nutrient transport. We have previously reported that in yeast, nutrient-uptake-coupled H+ influx elicits transient TORC1 activation and that the plasma-membrane H+-ATPase Pma1 plays an important role in this activation, involving more than just establishment of the H+ gradient. We show here that the PMA2 H+-ATPase from the plant Nicotiana plumbaginifolia can substitute for Pma1 in yeast, to promote H+-elicited TORC1 activation. This H+-ATPase is highly similar to Pma1 but has a longer carboxy-terminal tail binding 14-3-3 proteins. We report that a C-terminally truncated PMA2, which remains fully active, fails to promote H+-elicited TORC1 activation. Activation is also impaired when binding of PMA2 to 14-3-3 s is hindered. Our results show that at least some plant plasma-membrane H+-ATPases share with yeast Pma1 the ability to promote TORC1 activation in yeast upon H+-coupled nutrient uptake.
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Affiliation(s)
- Elie Saliba
- Molecular Physiology of the Cell, Université Libre de Bruxelles (ULB), 6041, Biopark, Gosselies, Belgium
| | - Cecilia Primo
- Molecular Physiology of the Cell, Université Libre de Bruxelles (ULB), 6041, Biopark, Gosselies, Belgium
| | - Nadia Guarini
- Molecular Physiology of the Cell, Université Libre de Bruxelles (ULB), 6041, Biopark, Gosselies, Belgium
| | - Bruno André
- Molecular Physiology of the Cell, Université Libre de Bruxelles (ULB), 6041, Biopark, Gosselies, Belgium.
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30
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Cogo AJD, Façanha AR, da Silva Teixeira LR, de Souza SB, da Rocha JG, Figueira FF, Eutrópio FJ, Bertolazi AA, de Rezende CE, Krohling CA, Okorokov LA, Cruz C, Ramos AC, Okorokova-Façanha AL. Plasma membrane H + pump at a crossroads of acidic and iron stresses in yeast-to-hypha transition. Metallomics 2020; 12:2174-2185. [PMID: 33320152 DOI: 10.1039/d0mt00179a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Iron is an essential nutrient but is toxic in excess mainly under acidic conditions. Yeasts have emerged as low cost, highly efficient soil inoculants for the decontamination of metal-polluted areas, harnessing an increasing understanding of their metal tolerance mechanisms. Here, we investigated the effects of extracellular iron and acid pH stress on the dimorphism of Yarrowia lipolytica. Its growth was unaffected by 1 or 2 mM FeSO4, while a strong cellular iron accumulation was detected. However, the iron treatments decreased the hyphal length and number, mainly at 2 mM FeSO4 and pH 4.5. Inward cell membrane H+ fluxes were found at pH 4.5 and 6.0 correlated with a pH increase at the cell surface and a conspicuous yeast-to-hypha transition activity. Conversely, a remarkable H+ efflux was detected at pH 3.0, related to the extracellular microenvironment acidification and inhibition of yeast-to-hypha transition. Iron treatments intensified H+ influxes at pH 4.5 and 6.0 and inhibited H+ efflux at pH 3.0. Moreover, iron treatments inhibited the expression and activities of the plasma membrane H+-ATPase, with the H+ transport inhibited to a greater extent than the ATP hydrolysis, suggesting an iron-induced uncoupling of the pump. Our data indicate that Y. lipolytica adaptations to high iron and acidic environments occur at the expense of remodelling the yeast morphogenesis through a cellular pH modulation by H+-ATPases and H+ coupled transporters, highlighting the capacity of this non-conventional yeast to accumulate high amounts of iron and its potential application for bioremediation.
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Affiliation(s)
- Antônio Jesus Dorighetto Cogo
- Laboratório de Bioquímica e Fisiologia de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil.
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31
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Growth Inhibition by Amino Acids in Saccharomyces cerevisiae. Microorganisms 2020; 9:microorganisms9010007. [PMID: 33375077 PMCID: PMC7822121 DOI: 10.3390/microorganisms9010007] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/17/2022] Open
Abstract
Amino acids are essential metabolites but can also be toxic when present at high levels intracellularly. Substrate-induced downregulation of amino acid transporters in Saccharomyces cerevisiae is thought to be a mechanism to avoid this toxicity. It has been shown that unregulated uptake by the general amino acid permease Gap1 causes cells to become sensitive to amino acids. Here, we show that overexpression of eight other amino acid transporters (Agp1, Bap2, Can1, Dip5, Gnp1, Lyp1, Put4, or Tat2) also induces a growth defect when specific single amino acids are present at concentrations of 0.5-5 mM. We can now state that all proteinogenic amino acids, as well as the important metabolite ornithine, are growth inhibitory to S. cerevisiae when transported into the cell at high enough levels. Measurements of initial transport rates and cytosolic pH show that toxicity is due to amino acid accumulation and not to the influx of co-transported protons. The amino acid sensitivity phenotype is a useful tool that reports on the in vivo activity of transporters and has allowed us to identify new transporter-specific substrates.
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32
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Montrose K, López Cabezas RM, Paukštytė J, Saarikangas J. Winter is coming: Regulation of cellular metabolism by enzyme polymerization in dormancy and disease. Exp Cell Res 2020; 397:112383. [PMID: 33212148 DOI: 10.1016/j.yexcr.2020.112383] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/20/2022]
Abstract
Metabolism feeds growth. Accordingly, metabolism is regulated by nutrient-sensing pathways that converge growth promoting signals into biosynthesis by regulating the activity of metabolic enzymes. When the environment does not support growth, organisms invest in survival. For cells, this entails transitioning into a dormant, quiescent state (G0). In dormancy, the activity of biosynthetic pathways is dampened, and catabolic metabolism and stress tolerance pathways are activated. Recent work in yeast has demonstrated that dormancy is associated with alterations in the physicochemical properties of the cytoplasm, including changes in pH, viscosity and macromolecular crowding. Accompanying these changes, numerous metabolic enzymes transition from soluble to polymerized assemblies. These large-scale self-assemblies are dynamic and depolymerize when cells resume growth. Here we review how enzyme polymerization enables metabolic plasticity by tuning carbohydrate, nucleic acid, amino acid and lipid metabolic pathways, with particular focus on its potential adaptive value in cellular dormancy.
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Affiliation(s)
- Kristopher Montrose
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, Finland; Research Programme in Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Rosa María López Cabezas
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, Finland; Research Programme in Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Jurgita Paukštytė
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, Finland; Research Programme in Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Juha Saarikangas
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, Finland; Research Programme in Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland; Neuroscience Center, University of Helsinki, Finland.
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33
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Koch LM, Birkeland ES, Battaglioni S, Helle X, Meerang M, Hiltbrunner S, Ibáñez AJ, Peter M, Curioni-Fontecedro A, Opitz I, Dechant R. Cytosolic pH regulates proliferation and tumour growth by promoting expression of cyclin D1. Nat Metab 2020; 2:1212-1222. [PMID: 33077976 DOI: 10.1038/s42255-020-00297-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 09/10/2020] [Indexed: 01/03/2023]
Abstract
Enhanced growth and proliferation of cancer cells are accompanied by profound changes in cellular metabolism. These metabolic changes are also common under physiological conditions, and include increased glucose fermentation accompanied by elevated cytosolic pH (pHc)1,2. However, how these changes contribute to enhanced cell growth and proliferation is unclear. Here, we show that elevated pHc specifically orchestrates an E2F-dependent transcriptional programme to drive cell proliferation by promoting cyclin D1 expression. pHc-dependent transcription of cyclin D1 requires the transcription factors CREB1, ATF1 and ETS1, and the histone acetyltransferases p300 and CBP. Biochemical characterization revealed that the CREB1-p300/CBP interaction acts as a pH sensor and coincidence detector, integrating different mitotic signals to regulate cyclin D1 transcription. We also show that elevated pHc contributes to increased cyclin D1 expression in malignant pleural mesotheliomas (MPMs), and renders these cells hypersensitive to pharmacological reduction of pHc. Taken together, these data demonstrate that elevated pHc is a critical cellular signal regulating G1 progression, and provide a mechanism linking elevated pHc to oncogenic activation of cyclin D1 in MPMs, and possibly other cyclin D1~dependent tumours. Thus, an increase of pHc may represent a functionally important, early event in the aetiology of cancer that is amenable to therapeutic intervention.
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Affiliation(s)
- Lisa Maria Koch
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
- Life science Zürich, PhD program for Molecular Life Sciences, Zurich, Switzerland
| | - Eivind Salmorin Birkeland
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
- Life science Zürich, PhD program for Molecular Life Sciences, Zurich, Switzerland
| | - Stefania Battaglioni
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
- Biozentrum, University of Basel, Basel, Switzerland
| | - Xiao Helle
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Mayura Meerang
- Department of Thoracic Surgery, University Hospital Zurich, Zurich, Switzerland
| | - Stefanie Hiltbrunner
- Department of Medical Oncology and Hematology, University Hospital Zurich, Comprehensive Cancer Center Zurich, University of Zurich, Zurich, Switzerland
| | - Alfredo J Ibáñez
- Core facility for Omics Research and Applied Biotechnology (ICOBA), Pontificia Universidad Católica del Perú, Lima, Peru
| | - Matthias Peter
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Alessandra Curioni-Fontecedro
- Department of Medical Oncology and Hematology, University Hospital Zurich, Comprehensive Cancer Center Zurich, University of Zurich, Zurich, Switzerland
| | - Isabelle Opitz
- Department of Thoracic Surgery, University Hospital Zurich, Zurich, Switzerland
| | - Reinhard Dechant
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland.
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34
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Bresson S, Shchepachev V, Spanos C, Turowski TW, Rappsilber J, Tollervey D. Stress-Induced Translation Inhibition through Rapid Displacement of Scanning Initiation Factors. Mol Cell 2020; 80:470-484.e8. [PMID: 33053322 PMCID: PMC7657445 DOI: 10.1016/j.molcel.2020.09.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/14/2020] [Accepted: 09/21/2020] [Indexed: 12/03/2022]
Abstract
Cellular responses to environmental stress are frequently mediated by RNA-binding proteins (RBPs). Here, we examined global RBP dynamics in Saccharomyces cerevisiae in response to glucose starvation and heat shock. Each stress induced rapid remodeling of the RNA-protein interactome without corresponding changes in RBP abundance. Consistent with general translation shutdown, ribosomal proteins contacting the mRNA showed decreased RNA association. Among translation components, RNA association was most reduced for initiation factors involved in 40S scanning (eukaryotic initiation factor 4A [eIF4A], eIF4B, and Ded1), indicating a common mechanism of translational repression. In unstressed cells, eIF4A, eIF4B, and Ded1 primarily targeted the 5′ ends of mRNAs. Following glucose withdrawal, 5′ binding was abolished within 30 s, explaining the rapid translation shutdown, but mRNAs remained stable. Heat shock induced progressive loss of 5′ RNA binding by initiation factors over ∼16 min and provoked mRNA degradation, particularly for translation-related factors, mediated by Xrn1. Taken together, these results reveal mechanisms underlying translational control of gene expression during stress. A quantitative proteomic approach reveals global stress-induced changes in RNA binding Translation shutdown is driven by rapid loss of mRNA binding by key initiation factors Heat shock induces general mRNA degradation facilitated by Xrn1
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Affiliation(s)
- Stefan Bresson
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
| | - Vadim Shchepachev
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Tomasz W Turowski
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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Chen H, Miller PW, Johnson DL, Laribee RN. The Ccr4-Not complex regulates TORC1 signaling and mitochondrial metabolism by promoting vacuole V-ATPase activity. PLoS Genet 2020; 16:e1009046. [PMID: 33064727 PMCID: PMC7592917 DOI: 10.1371/journal.pgen.1009046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 10/28/2020] [Accepted: 08/12/2020] [Indexed: 01/30/2023] Open
Abstract
The Ccr4-Not complex functions as an effector of multiple signaling pathways that control gene transcription and mRNA turnover. Consequently, Ccr4-Not contributes to a diverse array of processes, which includes a significant role in cell metabolism. Yet a mechanistic understanding of how it contributes to metabolism is lacking. Herein, we provide evidence that Ccr4-Not activates nutrient signaling through the essential target of rapamycin complex 1 (TORC1) pathway. Ccr4-Not disruption reduces global TORC1 signaling, and it also upregulates expression of the cell wall integrity (CWI) pathway terminal kinase Mpk1. Although CWI signaling represses TORC1 signaling, we find that Ccr4-Not loss inhibits TORC1 independently of CWI activation. Instead, we demonstrate that Ccr4-Not promotes the function of the vacuole V-ATPase, which interacts with the Gtr1 GTPase-containing EGO complex to stimulate TORC1 in response to nutrient sufficiency. Bypassing the V-ATPase requirement in TORC1 activation using a constitutively active Gtr1 mutant fully restores TORC1 signaling in Ccr4-Not deficient cells. Transcriptome analysis and functional studies revealed that loss of the Ccr4 subunit activates the TORC1 repressed retrograde signaling pathway to upregulate mitochondrial activity. Blocking this mitochondrial upregulation in Ccr4-Not deficient cells further represses TORC1 signaling, and it causes synergistic deficiencies in mitochondrial-dependent metabolism. These data support a model whereby Ccr4-Not loss impairs V-ATPase dependent TORC1 activation that forces cells to enhance mitochondrial metabolism to sustain a minimal level of TORC1 signaling necessary for cell growth and proliferation. Therefore, Ccr4-Not plays an integral role in nutrient signaling and cell metabolism by promoting V-ATPase dependent TORC1 activation.
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Affiliation(s)
- Hongfeng Chen
- Department of Pathology and Laboratory Medicine, College of Medicine and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - P. Winston Miller
- Molecular Bioinformatics Core and the University of Tennessee Health Science Center Office of Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Daniel L. Johnson
- Molecular Bioinformatics Core and the University of Tennessee Health Science Center Office of Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - R. Nicholas Laribee
- Department of Pathology and Laboratory Medicine, College of Medicine and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, United States of America
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O' Neill JS, Hoyle NP, Robertson JB, Edgar RS, Beale AD, Peak-Chew SY, Day J, Costa ASH, Frezza C, Causton HC. Eukaryotic cell biology is temporally coordinated to support the energetic demands of protein homeostasis. Nat Commun 2020; 11:4706. [PMID: 32943618 PMCID: PMC7499178 DOI: 10.1038/s41467-020-18330-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/13/2020] [Indexed: 12/17/2022] Open
Abstract
Yeast physiology is temporally regulated, this becomes apparent under nutrient-limited conditions and results in respiratory oscillations (YROs). YROs share features with circadian rhythms and interact with, but are independent of, the cell division cycle. Here, we show that YROs minimise energy expenditure by restricting protein synthesis until sufficient resources are stored, while maintaining osmotic homeostasis and protein quality control. Although nutrient supply is constant, cells sequester and store metabolic resources via increased transport, autophagy and biomolecular condensation. Replete stores trigger increased H+ export which stimulates TORC1 and liberates proteasomes, ribosomes, chaperones and metabolic enzymes from non-membrane bound compartments. This facilitates translational bursting, liquidation of storage carbohydrates, increased ATP turnover, and the export of osmolytes. We propose that dynamic regulation of ion transport and metabolic plasticity are required to maintain osmotic and protein homeostasis during remodelling of eukaryotic proteomes, and that bioenergetic constraints selected for temporal organisation that promotes oscillatory behaviour.
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Affiliation(s)
- John S O' Neill
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| | | | | | - Rachel S Edgar
- Molecular Virology, Department of Medicine, Imperial College, London, W2 1NY, UK
| | - Andrew D Beale
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | | | - Jason Day
- Department of Earth Sciences, University of Cambridge, Cambridge, CB2 3EQ, UK
| | - Ana S H Costa
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Helen C Causton
- Columbia University Medical Center, New York, NY, 10032, USA.
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Birkeland ES, Koch LM, Dechant R. Another Consequence of the Warburg Effect? Metabolic Regulation of Na +/H + Exchangers May Link Aerobic Glycolysis to Cell Growth. Front Oncol 2020; 10:1561. [PMID: 32974190 PMCID: PMC7462004 DOI: 10.3389/fonc.2020.01561] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/20/2020] [Indexed: 12/13/2022] Open
Abstract
To adjust cell growth and proliferation to changing environmental conditions or developmental requirements, cells have evolved a remarkable network of signaling cascades that integrates cues from cellular metabolism, growth factor availability and a large variety of stresses. In these networks, cellular information flow is mostly mediated by posttranslational modifications, most notably phosphorylation, or signaling molecules such as GTPases. Yet, a large body of evidence also implicates cytosolic pH (pHc) as a highly conserved cellular signal driving cell growth and proliferation, suggesting that pH-dependent protonation of specific proteins also regulates cellular signaling. In mammalian cells, pHc is regulated by growth factor derived signals and responds to metabolic cues in response to glucose stimulation. Importantly, high pHc has also been identified as a hall mark of cancer, but mechanisms of pH regulation in cancer are only poorly understood. Here, we discuss potential mechanisms of pH regulation with emphasis on metabolic signals regulating pHc by Na+/H+-exchangers. We hypothesize that elevated NHE activity and pHc in cancer are a direct consequence of the metabolic adaptations in tumor cells including enhanced aerobic glycolysis, generally referred to as the Warburg effect. This hypothesis not only provides an explanation for the growth advantage conferred by a switch to aerobic glycolysis beyond providing precursors for accumulation of biomass, but also suggests that treatments targeting pH regulation as a potential anti-cancer therapy may effectively target the result of altered tumor cell metabolism.
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Affiliation(s)
- Eivind Salmorin Birkeland
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zurich, Switzerland.,Life Science Zurich, Ph.D. Program for Molecular Life Sciences, Zurich, Switzerland
| | - Lisa Maria Koch
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zurich, Switzerland.,Life Science Zurich, Ph.D. Program for Molecular Life Sciences, Zurich, Switzerland
| | - Reinhard Dechant
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zurich, Switzerland
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38
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Andersen JP, Zhang J, Sun H, Liu X, Liu J, Nie J, Shi Y. Aster-B coordinates with Arf1 to regulate mitochondrial cholesterol transport. Mol Metab 2020; 42:101055. [PMID: 32738348 PMCID: PMC7476871 DOI: 10.1016/j.molmet.2020.101055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE Cholesterol plays a pivotal role in mitochondrial steroidogenesis, membrane structure, and respiration. Mitochondrial membranes are intrinsically low in cholesterol content and therefore must be replenished with cholesterol from other subcellular membranes. However, the molecular mechanisms underlying mitochondrial cholesterol transport remains poorly understood. The Aster-B gene encodes a cholesterol binding protein recently implicated in cholesterol trafficking from the plasma membrane to the endoplasmic reticulum (ER). In this study, we investigated the function and underlying mechanism of Aster-B in mediating mitochondrial cholesterol transport. METHODS CRISPR/Cas9 gene editing was carried out to generate cell lines deficient in Aster-B expression. The effect of Aster-B deficiency on mitochondrial cholesterol transport was examined by both confocal imaging analysis and biochemical assays. Deletion mutational analysis was also carried out to identify the function of a putative mitochondrial targeting sequence (MTS) at the N-terminus of Aster-B for its role in targeting Aster-B to mitochondria and in mediating mitochondrial cholesterol trafficking. RESULTS Ablation of Aster-B impaired cholesterol transport from the ER to mitochondria, leading to a significant decrease in mitochondrial cholesterol content. Aster-B is also required for mitochondrial transport of fatty acids derived from hydrolysis of cholesterol esters. A putative MTS at the N-terminus of Aster-B mediates the mitochondrial cholesterol uptake. Deletion of the MTS or ablation of Arf1 GTPase which is required for mitochondrial translocation of ER proteins prevented mitochondrial cholesterol transport, leading to mitochondrial dysfunction. CONCLUSIONS We identified Aster-B as a key regulator of cholesterol transport from the ER to mitochondria. Aster-B also coordinates mitochondrial cholesterol trafficking with uptake of fatty acids derived from cholesterol esters, implicating the Aster-B protein as a novel regulator of steroidogenesis.
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Affiliation(s)
- John-Paul Andersen
- Sam and Ann Barshop Institute for Longevity and Aging Studies, Department of Pharmacology, University of Texas Health Science Center at San Antonio, Texas Research Park Campus - MC 7755, 15355 Lambda Drive, San Antonio, TX, 78245, USA
| | - Jun Zhang
- Sam and Ann Barshop Institute for Longevity and Aging Studies, Department of Pharmacology, University of Texas Health Science Center at San Antonio, Texas Research Park Campus - MC 7755, 15355 Lambda Drive, San Antonio, TX, 78245, USA
| | - Haoran Sun
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, PR China
| | - Xuyun Liu
- Sam and Ann Barshop Institute for Longevity and Aging Studies, Department of Pharmacology, University of Texas Health Science Center at San Antonio, Texas Research Park Campus - MC 7755, 15355 Lambda Drive, San Antonio, TX, 78245, USA; Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical, Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Jiankang Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical, Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Jia Nie
- Sam and Ann Barshop Institute for Longevity and Aging Studies, Department of Pharmacology, University of Texas Health Science Center at San Antonio, Texas Research Park Campus - MC 7755, 15355 Lambda Drive, San Antonio, TX, 78245, USA
| | - Yuguang Shi
- Sam and Ann Barshop Institute for Longevity and Aging Studies, Department of Pharmacology, University of Texas Health Science Center at San Antonio, Texas Research Park Campus - MC 7755, 15355 Lambda Drive, San Antonio, TX, 78245, USA; Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, PR China.
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39
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Zhang J, Andersen JP, Sun H, Liu X, Sonenberg N, Nie J, Shi Y. Aster-C coordinates with COP I vesicles to regulate lysosomal trafficking and activation of mTORC1. EMBO Rep 2020; 21:e49898. [PMID: 32648345 DOI: 10.15252/embr.201949898] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/29/2020] [Accepted: 06/12/2020] [Indexed: 01/27/2023] Open
Abstract
Nutrient sensing by the mTOR complex 1 (mTORC1) requires its translocation to the lysosomal membrane. Upon amino acids removal, mTORC1 becomes cytosolic and inactive, yet its precise subcellular localization and the mechanism of inhibition remain elusive. Here, we identified Aster-C as a negative regulator of mTORC1 signaling. Aster-C earmarked a special rough ER subdomain where it sequestered mTOR together with the GATOR2 complex to prevent mTORC1 activation during nutrient starvation. Amino acids stimulated rapid disassociation of mTORC1 from Aster-C concurrently with assembly of COP I vesicles which escorted mTORC1 to the lysosomal membrane. Consequently, ablation of Aster-C led to spontaneous activation of mTORC1 and dissociation of TSC2 from lysosomes, whereas inhibition of COP I vesicle biogenesis or actin dynamics prevented mTORC1 activation. Together, these findings identified Aster-C as a missing link between lysosomal trafficking and mTORC1 activation by revealing an unexpected role of COP I vesicles in mTORC1 signaling.
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Affiliation(s)
- Jun Zhang
- Department of Pharmacology, Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - John-Paul Andersen
- Department of Pharmacology, Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Haoran Sun
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, China
| | - Xuyun Liu
- Department of Pharmacology, Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Jia Nie
- Department of Pharmacology, Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Yuguang Shi
- Department of Pharmacology, Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, China
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40
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Devare MN, Kim YH, Jung J, Kang WK, Kwon K, Kim J. TORC1 signaling regulates cytoplasmic pH through Sir2 in yeast. Aging Cell 2020; 19:e13151. [PMID: 32449834 PMCID: PMC7294778 DOI: 10.1111/acel.13151] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/20/2020] [Accepted: 03/27/2020] [Indexed: 12/15/2022] Open
Abstract
Glucose controls the phosphorylation of silent information regulator 2 (Sir2), a NAD+‐dependent protein deacetylase, which regulates the expression of the ATP‐dependent proton pump Pma1 and replicative lifespan (RLS) in yeast. TORC1 signaling, which is a central regulator of cell growth and lifespan, is regulated by glucose as well as nitrogen sources. In this study, we demonstrate that TORC1 signaling controls Sir2 phosphorylation through casein kinase 2 (CK2) to regulate PMA1 expression and cytoplasmic pH (pHc) in yeast. Inhibition of TORC1 signaling by either TOR1 deletion or rapamycin treatment decreased PMA1 expression, pHc, and vacuolar pH, whereas activation of TORC1 signaling by expressing constitutively active GTR1 (GTR1Q65L) resulted in the opposite phenotypes. Deletion of SIR2 or expression of a phospho‐mutant form of SIR2 increased PMA1 expression, pHc, and vacuolar pH in the tor1Δ mutant, suggesting a functional interaction between Sir2 and TORC1 signaling. Furthermore, deletion of TOR1 or KNS1 encoding a LAMMER kinase decreased the phosphorylation level of Sir2, suggesting that TORC1 signaling controls Sir2 phosphorylation. It was also found that Sit4, a protein phosphatase 2A (PP2A)‐like phosphatase, and Kns1 are required for TORC1 signaling to regulate PMA1 expression and that TORC1 signaling and the cyclic AMP (cAMP)/protein kinase A (PKA) pathway converge on CK2 to regulate PMA1 expression through Sir2. Taken together, these findings suggest that TORC1 signaling regulates PMA1 expression and pHc through the CK2–Sir2 axis, which is also controlled by cAMP/PKA signaling in yeast.
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Affiliation(s)
- Mayur Nimbadas Devare
- Department of Microbiology and Molecular Biology College of Bioscience and Biotechnology Chungnam National University Daejeon Korea
| | - Yeong Hyeock Kim
- Department of Microbiology and Molecular Biology College of Bioscience and Biotechnology Chungnam National University Daejeon Korea
| | - Joohye Jung
- Department of Microbiology and Molecular Biology College of Bioscience and Biotechnology Chungnam National University Daejeon Korea
| | - Woo Kyu Kang
- Department of Microbiology and Molecular Biology College of Bioscience and Biotechnology Chungnam National University Daejeon Korea
| | - Ki‐Sun Kwon
- Aging Intervention Research Center Korea Research Institute of Bioscience and Biotechnology Daejeon Korea
| | - Jeong‐Yoon Kim
- Department of Microbiology and Molecular Biology College of Bioscience and Biotechnology Chungnam National University Daejeon Korea
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41
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An Arabidopsis Mutant Over-Expressing Subtilase SBT4.13 Uncovers the Role of Oxidative Stress in the Inhibition of Growth by Intracellular Acidification. Int J Mol Sci 2020; 21:ijms21031173. [PMID: 32050714 PMCID: PMC7037345 DOI: 10.3390/ijms21031173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/04/2020] [Accepted: 02/08/2020] [Indexed: 12/29/2022] Open
Abstract
Intracellular acid stress inhibits plant growth by unknown mechanisms and it occurs in acidic soils and as consequence of other stresses. In order to identify mechanisms of acid toxicity, we screened activation-tagging lines of Arabidopsis thaliana for tolerance to intracellular acidification induced by organic acids. A dominant mutant, sbt4.13-1D, was isolated twice and shown to over-express subtilase SBT4.13, a protease secreted into endoplasmic reticulum. Activity measurements and immuno-detection indicate that the mutant contains less plasma membrane H+-ATPase (PMA) than wild type, explaining the small size, electrical depolarization and decreased cytosolic pH of the mutant but not organic acid tolerance. Addition of acetic acid to wild-type plantlets induces production of ROS (Reactive Oxygen Species) measured by dichlorodihydrofluorescein diacetate. Acid-induced ROS production is greatly decreased in sbt4.13-1D and atrboh-D,F mutants. The latter is deficient in two major NADPH oxidases (NOXs) and is tolerant to organic acids. These results suggest that intracellular acidification activates NOXs and the resulting oxidative stress is important for inhibition of growth. The inhibition of acid-activated NOXs in the sbt4.13-1D mutant compensates inhibition of PMA to increase acid tolerance.
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42
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A new pH sensor localized in the Golgi apparatus of Saccharomyces cerevisiae reveals unexpected roles of Vph1p and Stv1p isoforms. Sci Rep 2020; 10:1881. [PMID: 32024908 PMCID: PMC7002768 DOI: 10.1038/s41598-020-58795-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/21/2020] [Indexed: 12/22/2022] Open
Abstract
The gradual acidification of the secretory pathway is conserved and extremely important for eukaryotic cells, but until now there was no pH sensor available to monitor the pH of the early Golgi apparatus in Saccharomyces cerevisiae. Therefore, we developed a pHluorin-based sensor for in vivo measurements in the lumen of the Golgi. By using this new tool we show that the cis- and medial-Golgi pH is equal to 6.6–6.7 in wild type cells during exponential phase. As expected, V-ATPase inactivation results in a near neutral Golgi pH. We also uncover that surprisingly Vph1p isoform of the V-ATPase is prevalent to Stv1p for Golgi acidification. Additionally, we observe that during changes of the cytosolic pH, the Golgi pH is kept relatively stable, mainly thanks to the V-ATPase. Eventually, this new probe will allow to better understand the mechanisms involved in the acidification and the pH control within the secretory pathway.
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43
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Shin JJH, Liu P, Chan LJ, Ullah A, Pan J, Borchers CH, Burke JE, Stefan C, Smits GJ, Loewen CJR. pH Biosensing by PI4P Regulates Cargo Sorting at the TGN. Dev Cell 2020; 52:461-476.e4. [PMID: 31928972 DOI: 10.1016/j.devcel.2019.12.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/04/2019] [Accepted: 12/13/2019] [Indexed: 01/09/2023]
Abstract
Phosphoinositides, diacylglycerolpyrophosphate, ceramide-1-phosphate, and phosphatidic acid belong to a unique class of membrane signaling lipids that contain phosphomonoesters in their headgroups having pKa values in the physiological range. The phosphomonoester headgroup of phosphatidic acid enables this lipid to act as a pH biosensor as changes in its protonation state with intracellular pH regulate binding to effector proteins. Here, we demonstrate that binding of pleckstrin homology (PH) domains to phosphatidylinositol 4-phosphate (PI4P) in the yeast trans-Golgi network (TGN) is dependent on intracellular pH, indicating PI4P is a pH biosensor. pH biosensing by TGN PI4P in response to nutrient availability governs protein sorting at the TGN, likely by regulating sterol transfer to the TGN by Osh1, a member of the conserved oxysterol-binding protein (OSBP) family of lipid transfer proteins. Thus, pH biosensing by TGN PI4P allows for direct metabolic regulation of protein trafficking and cell growth.
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Affiliation(s)
- John J H Shin
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; MRC Laboratory for Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Peter Liu
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Leslie J Chan
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Azmat Ullah
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1018 XH Amsterdam, The Netherlands
| | - Jingxi Pan
- University of Victoria, Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada; Department of Biochemistry & Microbiology, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada
| | - Christoph H Borchers
- University of Victoria, Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada; Department of Biochemistry & Microbiology, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada
| | - John E Burke
- Department of Biochemistry & Microbiology, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada
| | - Christopher Stefan
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Gertien J Smits
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1018 XH Amsterdam, The Netherlands
| | - Christopher J R Loewen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.
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Pedersen SF, Counillon L. The SLC9A-C Mammalian Na +/H + Exchanger Family: Molecules, Mechanisms, and Physiology. Physiol Rev 2019; 99:2015-2113. [PMID: 31507243 DOI: 10.1152/physrev.00028.2018] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Na+/H+ exchangers play pivotal roles in the control of cell and tissue pH by mediating the electroneutral exchange of Na+ and H+ across cellular membranes. They belong to an ancient family of highly evolutionarily conserved proteins, and they play essential physiological roles in all phyla. In this review, we focus on the mammalian Na+/H+ exchangers (NHEs), the solute carrier (SLC) 9 family. This family of electroneutral transporters constitutes three branches: SLC9A, -B, and -C. Within these, each isoform exhibits distinct tissue expression profiles, regulation, and physiological roles. Some of these transporters are highly studied, with hundreds of original articles, and some are still only rudimentarily understood. In this review, we present and discuss the pioneering original work as well as the current state-of-the-art research on mammalian NHEs. We aim to provide the reader with a comprehensive view of core knowledge and recent insights into each family member, from gene organization over protein structure and regulation to physiological and pathophysiological roles. Particular attention is given to the integrated physiology of NHEs in the main organ systems. We provide several novel analyses and useful overviews, and we pinpoint main remaining enigmas, which we hope will inspire novel research on these highly versatile proteins.
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Affiliation(s)
- S F Pedersen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; and Université Côte d'Azur, CNRS, Laboratoire de Physiomédecine Moléculaire, LP2M, France, and Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
| | - L Counillon
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; and Université Côte d'Azur, CNRS, Laboratoire de Physiomédecine Moléculaire, LP2M, France, and Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
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45
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Brito AS, Soto Diaz S, Van Vooren P, Godard P, Marini AM, Boeckstaens M. Pib2-Dependent Feedback Control of the TORC1 Signaling Network by the Npr1 Kinase. iScience 2019; 20:415-433. [PMID: 31622882 PMCID: PMC6817644 DOI: 10.1016/j.isci.2019.09.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 05/10/2019] [Accepted: 09/13/2019] [Indexed: 01/21/2023] Open
Abstract
To adjust cell growth and metabolism according to environmental conditions, the conserved TORC1 signaling network controls autophagy, protein synthesis, and turnover. Here, we dissected the signals controlling phosphorylation and activity of the TORC1-effector kinase Npr1, involved in tuning the plasma membrane permeability to nitrogen sources. By evaluating a role of pH as a signal, we show that, although a transient cytosolic acidification accompanies nitrogen source entry and is correlated to a rapid TORC1-dependent phosphorylation of Npr1, a pH drop is not a prerequisite for TORC1 activation. We show that the Gtr1/Gtr2 and Pib2 regulators of TORC1 both independently and differently contribute to regulate Npr1 phosphorylation and activity. Finally, our data reveal that Npr1 mediates nitrogen-dependent phosphorylation of Pib2, as well as a Pib2-dependent inhibition of TORC1. This work highlights a feedback control loop likely enabling efficient downregulation and faster re-activation of TORC1 in response to a novel stimulating signal.
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Affiliation(s)
- Ana Sofia Brito
- Laboratory of Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium
| | - Silvia Soto Diaz
- Laboratory of Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium
| | - Pascale Van Vooren
- Laboratory of Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium
| | - Patrice Godard
- UCB Pharma, Chemin du Foriest, 1420 Braine-l'Alleud, Belgium
| | - Anna Maria Marini
- Laboratory of Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium
| | - Mélanie Boeckstaens
- Laboratory of Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium.
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46
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Cell organelles and yeast longevity: an intertwined regulation. Curr Genet 2019; 66:15-41. [PMID: 31535186 DOI: 10.1007/s00294-019-01035-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 12/16/2022]
Abstract
Organelles are dynamic structures of a eukaryotic cell that compartmentalize various essential functions and regulate optimum functioning. On the other hand, ageing is an inevitable phenomenon that leads to irreversible cellular damage and affects optimum functioning of cells. Recent research shows compelling evidence that connects organelle dysfunction to ageing-related diseases/disorders. Studies in several model systems including yeast have led to seminal contributions to the field of ageing in uncovering novel pathways, proteins and their functions, identification of pro- and anti-ageing factors and so on. In this review, we present a comprehensive overview of findings that highlight the role of organelles in ageing and ageing-associated functions/pathways in yeast.
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van Leeuwen W, Rabouille C. Cellular stress leads to the formation of membraneless stress assemblies in eukaryotic cells. Traffic 2019; 20:623-638. [PMID: 31152627 PMCID: PMC6771618 DOI: 10.1111/tra.12669] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/10/2019] [Accepted: 05/30/2019] [Indexed: 12/28/2022]
Abstract
In cells at steady state, two forms of cell compartmentalization coexist: membrane-bound organelles and phase-separated membraneless organelles that are present in both the nucleus and the cytoplasm. Strikingly, cellular stress is a strong inducer of the reversible membraneless compartments referred to as stress assemblies. Stress assemblies play key roles in survival during cell stress and in thriving of cells upon stress relief. The two best studied stress assemblies are the RNA-based processing-bodies (P-bodies) and stress granules that form in response to oxidative, endoplasmic reticulum (ER), osmotic and nutrient stress as well as many others. Interestingly, P-bodies and stress granules are heterogeneous with respect to both the pathways that lead to their formation and their protein and RNA content. Furthermore, in yeast and Drosophila, nutrient stress also leads to the formation of many other types of prosurvival cytoplasmic stress assemblies, such as metabolic enzymes foci, proteasome storage granules, EIF2B bodies, U-bodies and Sec bodies, some of which are not RNA-based. Nutrient stress leads to a drop in cytoplasmic pH, which combined with posttranslational modifications of granule contents, induces phase separation.
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Affiliation(s)
- Wessel van Leeuwen
- Hubrecht Institute of the Royal Netherlands Academy of Arts and Sciencesand University Medical Center UtrechtUtrechtthe Netherlands
| | - Catherine Rabouille
- Hubrecht Institute of the Royal Netherlands Academy of Arts and Sciencesand University Medical Center UtrechtUtrechtthe Netherlands
- Department of Biomedical Science of Cells and SystemsUniversity Medical Center GroningenGroningenthe Netherlands
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Chung CYS, Shin HR, Berdan CA, Ford B, Ward CC, Olzmann JA, Zoncu R, Nomura DK. Covalent targeting of the vacuolar H +-ATPase activates autophagy via mTORC1 inhibition. Nat Chem Biol 2019; 15:776-785. [PMID: 31285595 PMCID: PMC6641988 DOI: 10.1038/s41589-019-0308-4] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/15/2019] [Indexed: 02/06/2023]
Abstract
Autophagy is a lysosomal degradation pathway that eliminates aggregated proteins and damaged organelles to maintain cellular homeostasis. A major route for activating autophagy involves inhibition of the mTORC1 kinase, but current mTORC1-targeting compounds do not allow complete and selective mTORC1 blockade. Here, we have coupled screening of a covalent ligand library with activity-based protein profiling to discover EN6, a small-molecule in vivo activator of autophagy that covalently targets cysteine 277 in the ATP6V1A subunit of the lysosomal v-ATPase, which activates mTORC1 via the Rag guanosine triphosphatases. EN6-mediated ATP6V1A modification decouples the v-ATPase from the Rags, leading to inhibition of mTORC1 signaling, increased lysosomal acidification and activation of autophagy. Consistently, EN6 clears TDP-43 aggregates, a causative agent in frontotemporal dementia, in a lysosome-dependent manner. Our results provide insight into how the v-ATPase regulates mTORC1, and reveal a unique approach for enhancing cellular clearance based on covalent inhibition of lysosomal mTORC1 signaling.
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Affiliation(s)
- Clive Yik-Sham Chung
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
| | - Hijai R Shin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA, USA
| | - Charles A Berdan
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA
| | - Breanna Ford
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA
| | - Carl C Ward
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA, USA.
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA.
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49
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Dolz‐Edo L, van der Deen M, Brul S, Smits GJ. Caloric restriction controls stationary phase survival through Protein Kinase A (PKA) and cytosolic pH. Aging Cell 2019; 18:e12921. [PMID: 30790427 PMCID: PMC6516148 DOI: 10.1111/acel.12921] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 12/30/2018] [Accepted: 01/23/2019] [Indexed: 11/28/2022] Open
Abstract
Calorie restriction is the only physiological intervention that extends lifespan throughout all kingdoms of life. In the budding yeast Saccharomyces cerevisiae, cytosolic pH (pHc) controls growth and responds to nutrient availability, decreasing upon glucose depletion. We investigated the interactions between glucose availability, pHc and the central nutrient signalling cAMP‐Protein Kinase A (PKA) pathway. Glucose abundance during the growth phase enhanced acidification upon glucose depletion, via modulation of PKA activity. This actively controlled reduction in starvation pHc correlated with reduced stationary phase survival. Whereas changes in PKA activity affected both acidification and survival, targeted manipulation of starvation pHc showed that cytosolic acidification was downstream of PKA and the causal agent of the reduced chronological lifespan. Thus, caloric restriction controls stationary phase survival through PKA and cytosolic pH.
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Affiliation(s)
- Laura Dolz‐Edo
- Department of Molecular Biology and Microbial Food Safety Swammerdam Institute for Life Sciences, University of Amsterdam Amsterdam The Netherlands
| | - Margaretha van der Deen
- Department of Molecular Biology and Microbial Food Safety Swammerdam Institute for Life Sciences, University of Amsterdam Amsterdam The Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety Swammerdam Institute for Life Sciences, University of Amsterdam Amsterdam The Netherlands
| | - Gertien Jacoba Smits
- Department of Molecular Biology and Microbial Food Safety Swammerdam Institute for Life Sciences, University of Amsterdam Amsterdam The Netherlands
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50
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Rane HS, Hayek SR, Frye JE, Abeyta EL, Bernardo SM, Parra KJ, Lee SA. Candida albicans Pma1p Contributes to Growth, pH Homeostasis, and Hyphal Formation. Front Microbiol 2019; 10:1012. [PMID: 31143168 PMCID: PMC6521590 DOI: 10.3389/fmicb.2019.01012] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/24/2019] [Indexed: 12/30/2022] Open
Abstract
Candida albicans occupies diverse ecological niches within the host and must tolerate a wide range of environmental pH. The plasma membrane H+-ATPase Pma1p is the major regulator of cytosolic pH in fungi. Pma1p extrudes protons from the cytosol to maintain neutral-to-alkaline pH and is a potential drug target due to its essentiality and fungal specificity. We characterized mutants in which one allele of PMA1 has been deleted and the other truncated by 18–38 amino acids. Increasing C-terminal truncation caused corresponding decreases in plasma membrane ATPase-specific activity and cytosolic pH. Pma1p is regulated by glucose: glucose rapidly activates the ATPase, causing a sharp increase in cytosolic pH. Increasing Pma1p truncation severely impaired this glucose response. Pma1p truncation also altered cation responses, disrupted vacuolar morphology and pH, and reduced filamentation competence. Early studies of cytosolic pH and filamentation have described a rapid, transient alkalinization of the cytosol preceding germ tube formation; Pma1p has been proposed as a regulator of this process. We find Pma1p plays a role in the establishment of cell polarity, and distribution of Pma1p is non-homogenous in emerging hyphae. These findings suggest a role of PMA1 in cytosolic alkalinization and in the specialized form of polarized growth that is filamentation.
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Affiliation(s)
- Hallie S Rane
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Science Center, Albuquerque, NM, United States
| | - Summer R Hayek
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Science Center, Albuquerque, NM, United States
| | - Jillian E Frye
- Section of Infectious Diseases, New Mexico VA Healthcare System, Albuquerque, NM, United States
| | - Esteban L Abeyta
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Science Center, Albuquerque, NM, United States
| | - Stella M Bernardo
- Division of Infectious Diseases, University of New Mexico Health Science Center, Albuquerque, NM, United States
| | - Karlett J Parra
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Science Center, Albuquerque, NM, United States
| | - Samuel A Lee
- Medicine Service, White River Junction VA Medical Center, White River Junction, VT, United States.,Infectious Disease Section, Department of Medicine, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, United States
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