1
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Joshi K, Luisi B, Wunderlin G, Saleh S, Lilly A, Okusolubo T, Farabaugh PJ. An evolutionarily conserved phosphoserine-arginine salt bridge in the interface between ribosomal proteins uS4 and uS5 regulates translational accuracy in Saccharomyces cerevisiae. Nucleic Acids Res 2024; 52:3989-4001. [PMID: 38340338 DOI: 10.1093/nar/gkae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/08/2024] [Accepted: 02/08/2024] [Indexed: 02/12/2024] Open
Abstract
Protein-protein and protein-rRNA interactions at the interface between ribosomal proteins uS4 and uS5 are thought to maintain the accuracy of protein synthesis by increasing selection of cognate aminoacyl-tRNAs. Selection involves a major conformational change-domain closure-that stabilizes aminoacyl-tRNA in the ribosomal acceptor (A) site. This has been thought a constitutive function of the ribosome ensuring consistent accuracy. Recently, the Saccharomyces cerevisiae Ctk1 cyclin-dependent kinase was demonstrated to ensure translational accuracy and Ser238 of uS5 proposed as its target. Surprisingly, Ser238 is outside the uS4-uS5 interface and no obvious mechanism has been proposed to explain its role. We show that the true target of Ctk1 regulation is another uS5 residue, Ser176, which lies in the interface opposite to Arg57 of uS4. Based on site specific mutagenesis, we propose that phospho-Ser176 forms a salt bridge with Arg57, which should increase selectivity by strengthening the interface. Genetic data show that Ctk1 regulates accuracy indirectly; the data suggest that the kinase Ypk2 directly phosphorylates Ser176. A second kinase pathway involving TORC1 and Pkc1 can inhibit this effect. The level of accuracy appears to depend on competitive action of these two pathways to regulate the level of Ser176 phosphorylation.
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Affiliation(s)
- Kartikeya Joshi
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore 21250, USA
| | - Brooke Luisi
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore 21250, USA
| | - Grant Wunderlin
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore 21250, USA
| | - Sima Saleh
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore 21250, USA
| | - Anna Lilly
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore 21250, USA
| | - Temiloluwa Okusolubo
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore 21250, USA
| | - Philip J Farabaugh
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore 21250, USA
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2
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Caligaris M, De Virgilio C. Proxies introduce bias in decoding TORC1 activity. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001170. [PMID: 38605723 PMCID: PMC11007552 DOI: 10.17912/micropub.biology.001170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/13/2024]
Abstract
The eukaryotic TORC1 kinase integrates and links nutritional, energy, and hormonal signals to cell growth and homeostasis, and its deregulation is associated with human diseases including neurodegeneration, cancer, and metabolic syndrome. Quantification of TORC1 activities in various genetic settings and defined physiological conditions generally relies on the assessment of the phosphorylation level of residues in TORC1 targets. Here we show that two commonly used TORC1 effectors in yeast, namely Sch9 and Rps6, exhibit distinct phosphorylation patterns in response to rapamycin treatment or changes in nitrogen availability, indicating that the choice of TORC1 proxies introduces a bias in decoding TORC1 activity.
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Affiliation(s)
- Marco Caligaris
- Department of Biology, University of Fribourg, Fribourg, Fribourg, Switzerland
| | - Claudio De Virgilio
- Department of Biology, University of Fribourg, Fribourg, Fribourg, Switzerland
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3
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Williams TD, Rousseau A. Translation regulation in response to stress. FEBS J 2024. [PMID: 38308808 DOI: 10.1111/febs.17076] [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: 11/09/2023] [Revised: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/05/2024]
Abstract
Cell stresses occur in a wide variety of settings: in disease, during industrial processes, and as part of normal day-to-day rhythms. Adaptation to these stresses requires cells to alter their proteome. Cells modify the proteins they synthesize to aid proteome adaptation. Changes in both mRNA transcription and translation contribute to altered protein synthesis. Here, we discuss the changes in translational mechanisms that occur following the onset of stress, and the impact these have on stress adaptation.
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Affiliation(s)
- Thomas D Williams
- MRC-PPU, School of Life Sciences, University of Dundee, UK
- Sir William Dunn School of Pathology, University of Oxford, UK
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4
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Fierling N, Billard P, Bauda P, Blaudez D. Global deletome profile of Saccharomyces cerevisiae exposed to lithium. Metallomics 2024; 16:mfad073. [PMID: 38142127 DOI: 10.1093/mtomcs/mfad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/22/2023] [Indexed: 12/25/2023]
Abstract
The increasing use of lithium (Li) in new technologies raises the question of its impact on living microorganisms. In the present study, we aimed to identify putative Li targets and resistance mechanisms in the yeast model Saccharomyces cerevisiae using a deletomic approach based on the screening of a collection of 4733 knockout mutants under Li exposure. This screening highlighted 60 mutants resistant to Li and 124 mutants sensitive to Li. Through functional enrichment analyses, transport systems were identified as playing a central role in cell resistance to toxic concentrations of Li. In contrast, the AKT/protein kinase B family, signal transduction or cell communication were identified as potential toxic targets of Li. The majority of the mutants with a Li-sensitive phenotype were also sensitive to other alkali and alkaline earth metals, whereas the Li-resistance phenotype was mostly resistant to Na but poorly resistant to other metals. A comparison with the results of deletomics studies carried out in the presence of other metals highlighted Li-specific phenotypes. Three genes (NAM7, NMD2, UPF3) of the nonsense-mediated decay pathway were specifically involved in resistance to Li. In contrast, mutants with the NCA2, SPT20, GCN5, YOR376W, YPK3, and DCW1 genes deleted were specifically resistant to Li. These genes encode various functions from putative mannosidase to constitution of the Spt-Ada-Gcn5 acetyltransferase complex. This work provides a better understanding of potential specific resistance mechanisms and cellular targets of Li in yeast.
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5
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Liang J, Tang H, Snyder LF, Youngstrom CE, He BZ. Divergence of TORC1-mediated stress response leads to novel acquired stress resistance in a pathogenic yeast. PLoS Pathog 2023; 19:e1011748. [PMID: 37871123 PMCID: PMC10621968 DOI: 10.1371/journal.ppat.1011748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/02/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
Acquired stress resistance (ASR) enables organisms to prepare for environmental changes that occur after an initial stressor. However, the genetic basis for ASR and how the underlying network evolved remain poorly understood. In this study, we discovered that a short phosphate starvation induces oxidative stress response (OSR) genes in the pathogenic yeast C. glabrata and protects it against a severe H2O2 stress; the same treatment, however, provides little benefit in the low pathogenic-potential relative, S. cerevisiae. This ASR involves the same transcription factors (TFs) as the OSR, but with different combinatorial logics. We show that Target-of-Rapamycin Complex 1 (TORC1) is differentially inhibited by phosphate starvation in the two species and contributes to the ASR via its proximal effector, Sch9. Therefore, evolution of the phosphate starvation-induced ASR involves the rewiring of TORC1's response to phosphate limitation and the repurposing of TF-target gene networks for the OSR using new regulatory logics.
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Affiliation(s)
- Jinye Liang
- Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Hanxi Tang
- Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Lindsey F. Snyder
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, Iowa, United States of America
| | | | - Bin Z. He
- Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, Iowa, United States of America
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6
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Liang J, Tang H, Snyder LF, Youngstrom CE, He BZ. Divergence of TORC1-mediated Stress Response Leads to Novel Acquired Stress Resistance in a Pathogenic Yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.20.545716. [PMID: 37781605 PMCID: PMC10541095 DOI: 10.1101/2023.06.20.545716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Acquired stress resistance (ASR) enables organisms to prepare for environmental changes that occur after an initial stressor. However, the genetic basis for ASR and how the underlying network evolved remain poorly understood. In this study, we discovered that a short phosphate starvation induces oxidative stress response (OSR) genes in the pathogenic yeast C. glabrata and protects it against a severe H2O2 stress; the same treatment, however, provides little benefit in the low pathogenic-potential relative, S. cerevisiae. This ASR involves the same transcription factors (TFs) as the OSR, but with different combinatorial logics. We show that Target-of-Rapamycin Complex 1 (TORC1) is differentially inhibited by phosphate starvation in the two species and contributes to the ASR via its proximal effector, Sch9. Therefore, evolution of the phosphate starvation-induced ASR involves the rewiring of TORC1's response to phosphate limitation and the repurposing of TF-target gene networks for the OSR using new regulatory logics.
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Affiliation(s)
- Jinye Liang
- Biology Department, The University of Iowa, Iowa City, IA 52242
| | - Hanxi Tang
- Biology Department, The University of Iowa, Iowa City, IA 52242
| | - Lindsey F. Snyder
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242
| | | | - Bin Z. He
- Biology Department, The University of Iowa, Iowa City, IA 52242
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7
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Blank HM, Reuse C, Schmidt‐Hohagen K, Hammer SE, Hiller K, Polymenis M. Branched-chain amino acid synthesis is coupled to TOR activation early in the cell cycle in yeast. EMBO Rep 2023; 24:e57372. [PMID: 37497662 PMCID: PMC10481666 DOI: 10.15252/embr.202357372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023] Open
Abstract
How cells coordinate their metabolism with division determines the rate of cell proliferation. Dynamic patterns of metabolite synthesis during the cell cycle are unexplored. We report the first isotope tracing analysis in synchronous, growing budding yeast cells. Synthesis of leucine, a branched-chain amino acid (BCAA), increases through the G1 phase of the cell cycle, peaking later during DNA replication. Cells lacking Bat1, a mitochondrial aminotransferase that synthesizes BCAAs, grow slower, are smaller, and are delayed in the G1 phase, phenocopying cells in which the growth-promoting kinase complex TORC1 is moderately inhibited. Loss of Bat1 lowers the levels of BCAAs and reduces TORC1 activity. Exogenous provision of valine and, to a lesser extent, leucine to cells lacking Bat1 promotes cell division. Valine addition also increases TORC1 activity. In wild-type cells, TORC1 activity is dynamic in the cell cycle, starting low in early G1 but increasing later in the cell cycle. These results suggest a link between BCAA synthesis from glucose to TORC1 activation in the G1 phase of the cell cycle.
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Affiliation(s)
- Heidi M Blank
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Carsten Reuse
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Kerstin Schmidt‐Hohagen
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Staci E Hammer
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Michael Polymenis
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
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8
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Foltman M, Mendez I, Bech-Serra JJ, de la Torre C, Brace JL, Weiss EL, Lucas M, Queralt E, Sanchez-Diaz A. TOR complex 1 negatively regulates NDR kinase Cbk1 to control cell separation in budding yeast. PLoS Biol 2023; 21:e3002263. [PMID: 37647291 PMCID: PMC10468069 DOI: 10.1371/journal.pbio.3002263] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/19/2023] [Indexed: 09/01/2023] Open
Abstract
The target of rapamycin (TOR) signalling pathway plays a key role in the coordination between cellular growth and the cell cycle machinery in eukaryotes. The underlying molecular mechanisms by which TOR might regulate events after anaphase remain unknown. We show for the first time that one of the 2 TOR complexes in budding yeast, TORC1, blocks the separation of cells following cytokinesis by phosphorylation of a member of the NDR (nuclear Dbf2-related) protein-kinase family, the protein Cbk1. We observe that TORC1 alters the phosphorylation pattern of Cbk1 and we identify a residue within Cbk1 activation loop, T574, for which a phosphomimetic substitution makes Cbk1 catalytically inactive and, indeed, reproduces TORC1 control over cell separation. In addition, we identify the exocyst component Sec3 as a key substrate of Cbk1, since Sec3 activates the SNARE complex to promote membrane fusion. TORC1 activity ultimately compromises the interaction between Sec3 and a t-SNARE component. Our data indicate that TORC1 negatively regulates cell separation in budding yeast by participating in Cbk1 phosphorylation, which in turn controls the fusion of secretory vesicles transporting hydrolase at the site of division.
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Affiliation(s)
- Magdalena Foltman
- Mechanisms and Regulation of Cell Division Research Unit, Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, Santander, Spain
| | - Iván Mendez
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, Santander, Spain
- Structural Biology of Macromolecular Complexes Research Unit, Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Joan J. Bech-Serra
- Josep Carreras Leukaemia Research Institute, IJC Building, Campus ICO-Germans Trias i Pujol, Barcelona, Spain
| | - Carolina de la Torre
- Josep Carreras Leukaemia Research Institute, IJC Building, Campus ICO-Germans Trias i Pujol, Barcelona, Spain
| | - Jennifer L. Brace
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois, United States of America
| | - Eric L. Weiss
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois, United States of America
| | - María Lucas
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, Santander, Spain
- Structural Biology of Macromolecular Complexes Research Unit, Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Ethel Queralt
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Alberto Sanchez-Diaz
- Mechanisms and Regulation of Cell Division Research Unit, Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, Santander, Spain
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9
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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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10
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Navarro‐Velasco GY, Di Pietro A, López‐Berges MS. Constitutive activation of TORC1 signalling attenuates virulence in the cross-kingdom fungal pathogen Fusarium oxysporum. MOLECULAR PLANT PATHOLOGY 2023; 24:289-301. [PMID: 36840362 PMCID: PMC10013769 DOI: 10.1111/mpp.13292] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 06/18/2023]
Abstract
The filamentous fungus Fusarium oxysporum causes vascular wilt disease in a wide range of plant species and opportunistic infections in humans. Previous work suggested that invasive growth in this pathogen is controlled by environmental cues such as pH and nutrient status. Here we investigated the role of Target Of Rapamycin Complex 1 (TORC1), a global regulator of eukaryotic cell growth and development. Inactivation of the negative regulator Tuberous Sclerosis Complex 2 (Tsc2), but not constitutive activation of the positive regulator Gtr1, in F. oxysporum resulted in inappropriate activation of TORC1 signalling under nutrient-limiting conditions. The tsc2Δ mutants showed reduced colony growth on minimal medium with different nitrogen sources and increased sensitivity to cell wall or high temperature stress. Furthermore, these mutants were impaired in invasive hyphal growth across cellophane membranes and exhibited a marked decrease in virulence, both on tomato plants and on the invertebrate animal host Galleria mellonella. Importantly, invasive hyphal growth in tsc2Δ strains was rescued by rapamycin-mediated inhibition of TORC1. Collectively, these results reveal a key role of TORC1 signalling in the development and pathogenicity of F. oxysporum and suggest new potential targets for controlling fungal infections.
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Affiliation(s)
- Gesabel Yaneth Navarro‐Velasco
- Departamento de GenéticaUniversidad de CórdobaCórdobaSpain
- Present address:
Centro de Investigación e Información de Medicamentos y Tóxicos, Facultad de MedicinaUniversidad de PanamáPanama CityPanama
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11
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Martins TS, Costa RS, Vilaça R, Lemos C, Teixeira V, Pereira C, Costa V. Iron Limitation Restores Autophagy and Increases Lifespan in the Yeast Model of Niemann–Pick Type C1. Int J Mol Sci 2023; 24:ijms24076221. [PMID: 37047194 PMCID: PMC10094029 DOI: 10.3390/ijms24076221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Niemann–Pick type C1 (NPC1) is an endolysosomal transmembrane protein involved in the export of cholesterol and sphingolipids to other cellular compartments such as the endoplasmic reticulum and plasma membrane. NPC1 loss of function is the major cause of NPC disease, a rare lysosomal storage disorder characterized by an abnormal accumulation of lipids in the late endosomal/lysosomal network, mitochondrial dysfunction, and impaired autophagy. NPC phenotypes are conserved in yeast lacking Ncr1, an orthologue of human NPC1, leading to premature aging. Herein, we performed a phosphoproteomic analysis to investigate the effect of Ncr1 loss on cellular functions mediated by the yeast lysosome-like vacuoles. Our results revealed changes in vacuolar membrane proteins that are associated mostly with vesicle biology (fusion, transport, organization), autophagy, and ion homeostasis, including iron, manganese, and calcium. Consistently, the cytoplasm to vacuole targeting (Cvt) pathway was increased in ncr1∆ cells and autophagy was compromised despite TORC1 inhibition. Moreover, ncr1∆ cells exhibited iron overload mediated by the low-iron sensing transcription factor Aft1. Iron deprivation restored the autophagic flux of ncr1∆ cells and increased its chronological lifespan and oxidative stress resistance. These results implicate iron overload on autophagy impairment, oxidative stress sensitivity, and cell death in the yeast model of NPC1.
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12
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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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13
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Troutman KK, Varlakhanova NV, Tornabene BA, Ramachandran R, Ford MGJ. Conserved Pib2 regions have distinct roles in TORC1 regulation at the vacuole. J Cell Sci 2022; 135:276418. [PMID: 36000409 PMCID: PMC9584352 DOI: 10.1242/jcs.259994] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/15/2022] [Indexed: 12/27/2022] Open
Abstract
TORC1 is a critical controller of cell growth in eukaryotes. In yeast (Saccharomyces cerevisiae), the presence of nutrients is signaled to TORC1 by several upstream regulatory sensors that together coordinate TORC1 activity. TORC1 localizes to both vacuolar and endosomal membranes, where differential signaling occurs. This localization is mimicked by Pib2, a key upstream TORC1 regulator that is essential for TORC1 reactivation after nutrient starvation or pharmacological inhibition. Pib2 has both positive and negative effects on TORC1 activity, but the mechanisms remain poorly understood. Here, we pinpoint the Pib2 inhibitory function on TORC1 to residues within short, conserved N-terminal regions. We also show that the Pib2 C-terminal regions, helical region E and tail, are essential for TORC1 reactivation. Furthermore, the Pib2 FYVE domain plays a role in vacuolar localization, but it is surprisingly unnecessary for recovery from rapamycin exposure. Using chimeric Pib2 targeting constructs, we show that endosomal localization is not necessary for TORC1 reactivation and cell growth after rapamycin treatment. Thus, a comprehensive molecular dissection of Pib2 demonstrates that each of its conserved regions differentially contribute to Pib2-mediated regulation of TORC1 activity.
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Affiliation(s)
- Kayla K. Troutman
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Natalia V. Varlakhanova
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Bryan A. Tornabene
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Rajesh Ramachandran
- Department of Physiology & Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Marijn G. J. Ford
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA,Author for correspondence ()
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14
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Nomura W, Ng SP, Takahara T, Maeda T, Kawada T, Goto T, Inoue Y. Roles of phosphatidylserine and phospholipase C in the activation of TOR complex 2 signaling in Saccharomyces cerevisiae. J Cell Sci 2022; 135:276172. [PMID: 35912799 DOI: 10.1242/jcs.259988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/22/2022] [Indexed: 11/20/2022] Open
Abstract
The target of rapamycin (TOR) forms two distinct complexes, TORC1 and TORC2, to exert its functions essential for cellular growth and homeostasis. TORC1 signaling is regulated in response to nutrients such as amino acids and glucose; however, the mechanisms underlying the activation of TORC2 signaling are still poorly understood compared to TORC1 signaling. In the budding yeast Saccharomyces cerevisiae, TORC2 targets protein kinases Ypk1, Ypk2, and Pkc1 for phosphorylation. Plasma membrane stress is known to activate the TORC2-Ypk1/2 signaling. We have previously reported that methylglyoxal (MG), a metabolite derived from glycolysis, activates TORC2-Pkc1 signaling. In this study, we found that MG activates the TORC2-Ypk1/2 and TORC2-Pkc1 signaling, and that phosphatidylserine is involved in the activation of both signaling pathways. We also demonstrated that the Rho-family GTPase Cdc42 contributes to the plasma membrane stress-induced activation of TORC2-Ypk1/2 signaling. Furthermore, we revealed that phosphatidylinositol-specific phospholipase C, Plc1, contributes to the activation of both TORC2-Ypk1/2 and TORC2-Pkc1 signaling.
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Affiliation(s)
- Wataru Nomura
- Laboratory of Molecular Microbiology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Su-Ping Ng
- Laboratory of Molecular Functions of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Terunao Takahara
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Tatsuya Maeda
- Department of Biology, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Teruo Kawada
- Laboratory of Molecular Functions of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tsuyoshi Goto
- Laboratory of Molecular Functions of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yoshiharu Inoue
- Laboratory of Molecular Microbiology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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15
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Stress- and metabolic responses of Candida albicans require Tor1 kinase N-terminal HEAT repeats. PLoS Pathog 2022; 18:e1010089. [PMID: 35687592 PMCID: PMC9223334 DOI: 10.1371/journal.ppat.1010089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 06/23/2022] [Accepted: 05/12/2022] [Indexed: 11/19/2022] Open
Abstract
Whether to commit limited cellular resources toward growth and proliferation, or toward survival and stress responses, is an essential determination made by Target of Rapamycin Complex 1 (TORC1) for a eukaryotic cell in response to favorable or adverse conditions. Loss of TORC1 function is lethal. The TORC1 inhibitor rapamycin that targets the highly conserved Tor kinase domain kills fungal pathogens like Candida albicans, but is also severely toxic to human cells. The least conserved region of fungal and human Tor kinases are the N-terminal HEAT domains. We examined the role of the 8 most N-terminal HEAT repeats of C. albicans Tor1. We compared nutritional- and stress responses of cells that express a message for N-terminally truncated Tor1 from repressible tetO, with cells expressing wild type TOR1 from tetO or from the native promoter. Some but not all stress responses were significantly impaired by loss of Tor1 N-terminal HEAT repeats, including those to oxidative-, cell wall-, and heat stress; in contrast, plasma membrane stress and antifungal agents that disrupt plasma membrane function were tolerated by cells lacking this Tor1 region. Translation was inappropriately upregulated during oxidative stress in cells lacking N-terminal Tor1 HEAT repeats despite simultaneously elevated Gcn2 activity, while activation of the oxidative stress response MAP kinase Hog1 was weak. Conversely, these cells were unable to take advantage of favorable nutritional conditions by accelerating their growth. Consuming oxygen more slowly than cells containing wild type TOR1 alleles during growth in glucose, cells lacking N-terminal Tor1 HEAT repeats additionally were incapable of utilizing non-fermentable carbon sources. They were also hypersensitive to inhibitors of specific complexes within the respiratory electron transport chain, suggesting that inefficient ATP generation and a resulting dearth of nucleotide sugar building blocks for cell wall polysaccharides causes cell wall integrity defects in these mutants. Genome-wide expression analysis of cells lacking N-terminal HEAT repeats showed dysregulation of carbon metabolism, cell wall biosynthetic enzymes, translational machinery biosynthesis, oxidative stress responses, and hyphal- as well as white-opaque cell type-associated genes. Targeting fungal-specific Tor1 N-terminal HEAT repeats with small molecules might selectively abrogate fungal viability, especially when during infection multiple stresses are imposed by the host immune system. Whether growing harmlessly on our mucous membranes in competition with bacterial multitudes, or invading our tissues and bloodstream, the fungus Candida albicans must be capable of rapid growth when it finds abundant nutrients and favorable conditions. It must also be able to switch to stress- and survival mode when encountering host immune cells and when starving for nutrients. Tor1 kinase is the central regulator at the heart of these cellular decisions. As an essential protein, it is an attractive drug target. But the Tor1 kinase domain is very similar to its human counterpart, rendering its inhibitors like rapamycin toxic for humans. We identified a region of helical protein-protein interaction domains, the N-terminal HEAT repeats, as the least conserved part of C. albicans Tor1. Using genetic- and genome-wide expression analysis, we found that 8 N-terminal HEAT repeats are required for growth acceleration in nutrient-rich environments and for decreased translation in starvation- and stress conditions. This Tor1 region contributes to oxidative-, cell wall- and heat stress reponses, to hyphal growth and to respiration, but apparently not to plasma membrane stress endurance or fermentation. Small molecules that disrupt the protein-protein interactions mediated by this region could become fungal-selective inhibitors of Tor kinase.
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16
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Identification of a modulator of the actin cytoskeleton, mitochondria, nutrient metabolism and lifespan in yeast. Nat Commun 2022; 13:2706. [PMID: 35577788 PMCID: PMC9110415 DOI: 10.1038/s41467-022-30045-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 04/06/2022] [Indexed: 11/26/2022] Open
Abstract
In yeast, actin cables are F-actin bundles that are essential for cell division through their function as tracks for cargo movement from mother to daughter cell. Actin cables also affect yeast lifespan by promoting transport and inheritance of higher-functioning mitochondria to daughter cells. Here, we report that actin cable stability declines with age. Our genome-wide screen for genes that affect actin cable stability identified the open reading frame YKL075C. Deletion of YKL075C results in increases in actin cable stability and abundance, mitochondrial fitness, and replicative lifespan. Transcriptome analysis revealed a role for YKL075C in regulating branched-chain amino acid (BCAA) metabolism. Consistent with this, modulation of BCAA metabolism or decreasing leucine levels promotes actin cable stability and function in mitochondrial quality control. Our studies support a role for actin stability in yeast lifespan, and demonstrate that this process is controlled by BCAA and a previously uncharacterized ORF YKL075C, which we refer to as actin, aging and nutrient modulator protein 1 (AAN1). Actin cables affect lifespan by supporting movement and inheritance of fitter mitochondria to daughter cells in yeast. Here the authors show that branched-chain amino acid (BCAA) levels affect actin cable stability and a role for YKL075C/AAN1 in control of BCAA metabolism and actin cable stability and function.
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17
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Casamayor A, Ariño J. When Phosphatases Go Mad: The Molecular Basis for Toxicity of Yeast Ppz1. Int J Mol Sci 2022; 23:ijms23084304. [PMID: 35457140 PMCID: PMC9029398 DOI: 10.3390/ijms23084304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 02/04/2023] Open
Abstract
The fact that overexpression of the yeast Ser/Thr protein phosphatase Ppz1 induces a dramatic halt in cell proliferation was known long ago, but only work in the last few years has provided insight into the molecular basis for this toxicity. Overexpression of Ppz1 causes abundant changes in gene expression and modifies the phosphorylation state of more than 150 proteins, including key signaling protein kinases such as Hog1 or Snf1. Diverse cellular processes are altered: halt in translation, failure to properly adapt to low glucose supply, acidification of the cytosol, or depletion of intracellular potassium content are a few examples. Therefore, the toxicity derived from an excess of Ppz1 appears to be multifactorial, the characteristic cell growth blockage thus arising from the combination of various altered processes. Notably, overexpression of the Ppz1 regulatory subunit Hal3 fully counteracts the toxic effects of the phosphatase, and this process involves intracellular relocation of the phosphatase to internal membranes.
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18
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Sánchez-Adriá IE, Sanmartín G, Prieto JA, Estruch F, Randez-Gil F. Slt2 Is Required to Activate ER-Stress-Protective Mechanisms through TORC1 Inhibition and Hexosamine Pathway Activation. J Fungi (Basel) 2022; 8:jof8020092. [PMID: 35205847 PMCID: PMC8877190 DOI: 10.3390/jof8020092] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 02/07/2023] Open
Abstract
Slt2, the MAPK of the cell wall integrity (CWI) pathway, connects different signaling pathways and performs different functions in the protective response of S. cerevisiae to stress. Previous work has evidenced the relation of the CWI pathway and the unfolded protein response (UPR), a transcriptional program activated upon endoplasmic reticulum (ER) stress. However, the mechanisms of crosstalk between these pathways and the targets regulated by Slt2 under ER stress remain unclear. Here, we demonstrated that ectopic expression of GFA1, the gene encoding the first enzyme in the synthesis of UDP-GlcNAc by the hexosamine biosynthetic pathway (HBP) or supplementation of the growth medium with glucosamine (GlcN), increases the tolerance of slt2 mutant cells to different ER-stress inducers. Remarkably, GlcN also alleviates the sensitivity phenotype of cells lacking IRE1 or HAC1, the main actors in controlling the UPR. The exogenous addition of GlcN reduced the abundance of glycosylated proteins and triggered autophagy. We also found that TORC1, the central stress and growth controller, is inhibited by tunicamycin exposure in cells of the wild-type strain but not in those lacking Slt2. Consistent with this, the tunicamycin-induced activation of autophagy and the increased synthesis of ATP in response to ER stress were absent by knock-out of SLT2. Altogether, our data placed Slt2 as an essential actor of the ER stress response by regulating the HBP activity and the TORC1-dependent signaling.
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Affiliation(s)
- Isabel E. Sánchez-Adriá
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino 7, 46980 Paterna, Valencia, Spain; (I.E.S.-A.); (G.S.); (J.A.P.)
| | - Gemma Sanmartín
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino 7, 46980 Paterna, Valencia, Spain; (I.E.S.-A.); (G.S.); (J.A.P.)
| | - Jose A. Prieto
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino 7, 46980 Paterna, Valencia, Spain; (I.E.S.-A.); (G.S.); (J.A.P.)
| | - Francisco Estruch
- Departament of Biochemistry and Molecular Biology, Universitat de València, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain;
| | - Francisca Randez-Gil
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino 7, 46980 Paterna, Valencia, Spain; (I.E.S.-A.); (G.S.); (J.A.P.)
- Correspondence:
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19
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Segreto R, Bazafkan H, Millinger J, Schenk M, Atanasova L, Doppler M, Büschl C, Boeckstaens M, Soto Diaz S, Schreiner U, Sillo F, Balestrini R, Schuhmacher R, Zeilinger S. The TOR kinase pathway is relevant for nitrogen signaling and antagonism of the mycoparasite Trichoderma atroviride. PLoS One 2022; 16:e0262180. [PMID: 34972198 PMCID: PMC8719763 DOI: 10.1371/journal.pone.0262180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/18/2021] [Indexed: 01/14/2023] Open
Abstract
Trichoderma atroviride (Ascomycota, Sordariomycetes) is a well-known mycoparasite applied for protecting plants against fungal pathogens. Its mycoparasitic activity involves processes shared with plant and human pathogenic fungi such as the production of cell wall degrading enzymes and secondary metabolites and is tightly regulated by environmental cues. In eukaryotes, the conserved Target of Rapamycin (TOR) kinase serves as a central regulator of cellular growth in response to nutrient availability. Here we describe how alteration of the activity of TOR1, the single and essential TOR kinase of T. atroviride, by treatment with chemical TOR inhibitors or by genetic manipulation of selected TOR pathway components affected various cellular functions. Loss of TSC1 and TSC2, that are negative regulators of TOR complex 1 (TORC1) in mammalian cells, resulted in altered nitrogen source-dependent growth of T. atroviride, reduced mycoparasitic overgrowth and, in the case of Δtsc1, a diminished production of numerous secondary metabolites. Deletion of the gene encoding the GTPase RHE2, whose mammalian orthologue activates mTORC1, led to rapamycin hypersensitivity and altered secondary metabolism, but had an only minor effect on vegetative growth and mycoparasitic overgrowth. The latter also applied to mutants missing the npr1-1 gene that encodes a fungus-specific kinase known as TOR target in yeast. Genome-wide transcriptome analysis confirmed TOR1 as a regulatory hub that governs T. atroviride metabolism and processes associated to ribosome biogenesis, gene expression and translation. In addition, mycoparasitism-relevant genes encoding terpenoid and polyketide synthases, peptidases, glycoside hydrolases, small secreted cysteine-rich proteins, and G protein coupled receptors emerged as TOR1 targets. Our results provide the first in-depth insights into TOR signaling in a fungal mycoparasite and emphasize its importance in the regulation of processes that critically contribute to the antagonistic activity of T. atroviride.
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Affiliation(s)
- Rossana Segreto
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Hoda Bazafkan
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Julia Millinger
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Martina Schenk
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Lea Atanasova
- Institute of Food Technology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Maria Doppler
- Department of Agrobiotechnology IFA-Tulln, Center for Analytical Chemistry, University of Natural, Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Christoph Büschl
- Department of Agrobiotechnology IFA-Tulln, Center for Analytical Chemistry, University of Natural, Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Mélanie Boeckstaens
- Département de Biologie Moléculaire, Laboratory of Biology of Membrane Transport, Université Libre de Bruxelles, Gosselies, Belgium
| | - Silvia Soto Diaz
- Département de Biologie Moléculaire, Laboratory of Biology of Membrane Transport, Université Libre de Bruxelles, Gosselies, Belgium
| | - Ulrike Schreiner
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | | | | | - Rainer Schuhmacher
- Department of Agrobiotechnology IFA-Tulln, Center for Analytical Chemistry, University of Natural, Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Susanne Zeilinger
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
- * E-mail:
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20
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Phosphoproteomic responses of TORC1 target kinases reveal discrete and convergent mechanisms that orchestrate the quiescence program in yeast. Cell Rep 2021; 37:110149. [PMID: 34965436 DOI: 10.1016/j.celrep.2021.110149] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/19/2021] [Accepted: 11/30/2021] [Indexed: 01/18/2023] Open
Abstract
The eukaryotic TORC1 kinase assimilates diverse environmental cues, including growth factors and nutrients, to control growth by tuning anabolic and catabolic processes. In yeast, TORC1 stimulates protein synthesis in response to abundant nutrients primarily through its proximal effector kinase Sch9. Conversely, TORC1 inhibition following nutrient limitation unlocks various distally controlled kinases (e.g., Atg1, Gcn2, Npr1, Rim15, Slt2/Mpk1, and Yak1), which cooperate through poorly defined circuits to orchestrate the quiescence program. To better define the signaling landscape of the latter kinases, we use in vivo quantitative phosphoproteomics. Through pinpointing known and uncharted Npr1, Rim15, Slt2/Mpk1, and Yak1 effectors, our study examines the architecture of the distally controlled TORC1 kinase network. Accordingly, this is built on a combination of discrete, convergent, and multilayered feedback regulatory mechanisms, which likely ensure homeostatic control of and/or robust responses by TORC1 and its effector kinases under fluctuating nutritional conditions.
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21
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Morozumi Y, Hishinuma A, Furusawa S, Sofyantoro F, Tatebe H, Shiozaki K. Fission yeast TOR complex 1 phosphorylates Psk1 through an evolutionarily conserved interaction mediated by the TOS motif. J Cell Sci 2021; 134:272450. [PMID: 34499159 PMCID: PMC8542387 DOI: 10.1242/jcs.258865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/03/2021] [Indexed: 12/28/2022] Open
Abstract
TOR complex 1 (TORC1) is a multi-subunit protein kinase complex that controls cellular growth in response to environmental cues. The regulatory subunits of mammalian TORC1 (mTORC1) include RAPTOR (also known as RPTOR), which recruits mTORC1 substrates, such as S6K1 (also known as RPS6KB1) and 4EBP1 (EIF4EBP1), by interacting with their TOR signaling (TOS) motif. Despite the evolutionary conservation of TORC1, no TOS motif has been described in lower eukaryotes. In the present study, we show that the fission yeast S6 kinase Psk1 contains a TOS motif that interacts with Mip1, a RAPTOR ortholog. The TOS motif in Psk1 resembles those in mammals, including the conserved phenylalanine and aspartic acid residues essential for the Mip1 interaction and TORC1-dependent phosphorylation of Psk1. The binding of the TOS motif to Mip1 is dependent on Mip1 Tyr-533, whose equivalent in RAPTOR is known to interact with the TOS motif in their co-crystals. Furthermore, we utilized the mip1-Y533A mutation to screen the known TORC1 substrates in fission yeast and successfully identified Atg13 as a novel TOS-motif-containing substrate. These results strongly suggest that the TOS motif represents an evolutionarily conserved mechanism of the substrate recognition by TORC1. Summary: By analyzing S6 kinase in fission yeast, we have demonstrated that the TOR signaling (TOS) motif-mediated substrate recognition by TOR complex 1 is conserved from yeast to humans.
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Affiliation(s)
- Yuichi Morozumi
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Ai Hishinuma
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.,Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, Daisen, Akita 019-2112, Japan
| | - Suguru Furusawa
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Fajar Sofyantoro
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.,Department of Animal Physiology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Hisashi Tatebe
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Kazuhiro Shiozaki
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.,Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
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22
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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: 8] [Impact Index Per Article: 2.7] [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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23
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Anton-Plagaro C, Sanchez N, Valle R, Mulet JM, Duncan MC, Roncero C. Exomer complex regulates protein traffic at the TGN through differential interactions with cargos and clathrin adaptor complexes. FASEB J 2021; 35:e21615. [PMID: 33978245 DOI: 10.1096/fj.202002610r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 12/16/2022]
Abstract
Protein sorting at the trans-Golgi network (TGN) usually requires the assistance of cargo adaptors. However, it remains to be examined how the same complex can mediate both the export and retention of different proteins or how sorting complexes interact among themselves. In Saccharomyces cerevisiae, the exomer complex is involved in the polarized transport of some proteins from the TGN to the plasma membrane (PM). Intriguingly, exomer and its cargos also show a sort of functional relationship with TGN clathrin adaptors that is still unsolved. Here, using a wide range of techniques, including time-lapse and BIFC microscopy, we describe new molecular implications of the exomer complex in protein sorting and address its different layers of functional interaction with clathrin adaptor complexes. Exomer mutants show impaired amino acid uptake because it facilitates not only the polarized delivery of amino acid permeases to the PM but also participates in their endosomal traffic. We propose a model for exomer where it modulates the recruitment of TGN clathrin adaptors directly or indirectly through the Arf1 function. Moreover, we describe an in vivo competitive relationship between the exomer and AP-1 complexes for the model cargo Chs3. These results highlight a broad role for exomer in regulating protein sorting at the TGN that is complementary to its role as cargo adaptor and present a model to understand the complexity of TGN protein sorting.
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Affiliation(s)
- Carlos Anton-Plagaro
- Instituto de Biología Funcional y Genómica (IBFG) and Departamento de Microbiología y Genética, CSIC-Universidad de Salamanca, Salamanca, Spain
| | - Noelia Sanchez
- Instituto de Biología Funcional y Genómica (IBFG) and Departamento de Microbiología y Genética, CSIC-Universidad de Salamanca, Salamanca, Spain
| | - Rosario Valle
- Instituto de Biología Funcional y Genómica (IBFG) and Departamento de Microbiología y Genética, CSIC-Universidad de Salamanca, Salamanca, Spain
| | - Jose Miguel Mulet
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universitat Politècnica de València, Valencia, Spain
| | - Mara C Duncan
- Cell and Developmental Biology Department, University of Michigan, Ann Arbor, MI, USA
| | - Cesar Roncero
- Instituto de Biología Funcional y Genómica (IBFG) and Departamento de Microbiología y Genética, CSIC-Universidad de Salamanca, Salamanca, Spain
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24
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Zhang S, Khalid AR, Guo D, Zhang J, Xiong F, Ren M. TOR Inhibitors Synergistically Suppress the Growth and Development of Phytophthora infestans, a Highly Destructive Pathogenic Oomycete. Front Microbiol 2021; 12:596874. [PMID: 33935983 PMCID: PMC8086431 DOI: 10.3389/fmicb.2021.596874] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 03/22/2021] [Indexed: 11/25/2022] Open
Abstract
Phytophthora infestans, one of most famous pathogenic oomycetes, triggered the Great Irish Famine from 1845 to 1852. The target of rapamycin (TOR) is well known as a key gene in eukaryotes that controls cell growth, survival and development. However, it is unclear about its function in controlling the mycelial growth, sporulation capacity, spore germination and virulence of Phytophthora infestans. In this study, key components of the TOR signaling pathway are analyzed in detail. TOR inhibitors, including rapamycin (RAP), AZD8055 (AZD), KU-0063794 (KU), and Torin1, inhibit the mycelial growth, sporulation capacity, spore germination, and virulence of Phytophthora infestans with AZD showing the best inhibitory effects on Phytophthora infestans. Importantly, compared with a combination of RAP + KU or RAP + Torin1, the co-application of RAP and AZD show the best synergistic inhibitory effects on P. infestans, resulting in the reduced dosage and increased efficacy of drugs. Transcriptome analysis supports the synergistic effects of the combination of RAP and AZD on gene expression, functions and pathways related to the TOR signaling pathway. Thus, TOR is an important target for controlling Phytophthora infestans, and synergism based on the application of TOR inhibitors exhibit the potential for controlling the growth of Phytophthora infestans.
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Affiliation(s)
- Shumin Zhang
- School of Preclinical Medicine, North Sichuan Medical College, Nanchong, China.,Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China.,School of Life Sciences, Chongqing University, Chongqing, China
| | - A Rehman Khalid
- Department of Plant Pathology, University of Poonch Rawalakot, Rawalkot, Pakistan
| | - Dongmei Guo
- School of Preclinical Medicine, North Sichuan Medical College, Nanchong, China
| | - Jingping Zhang
- School of Preclinical Medicine, North Sichuan Medical College, Nanchong, China
| | - Fangjie Xiong
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Maozhi Ren
- School of Preclinical Medicine, North Sichuan Medical College, Nanchong, China.,Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
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25
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Indole-3-acetic acid is a physiological inhibitor of TORC1 in yeast. PLoS Genet 2021; 17:e1009414. [PMID: 33690632 PMCID: PMC7978357 DOI: 10.1371/journal.pgen.1009414] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/19/2021] [Accepted: 02/11/2021] [Indexed: 01/13/2023] Open
Abstract
Indole-3-acetic acid (IAA) is the most common, naturally occurring phytohormone that regulates cell division, differentiation, and senescence in plants. The capacity to synthesize IAA is also widespread among plant-associated bacterial and fungal species, which may use IAA as an effector molecule to define their relationships with plants or to coordinate their physiological behavior through cell-cell communication. Fungi, including many species that do not entertain a plant-associated life style, are also able to synthesize IAA, but the physiological role of IAA in these fungi has largely remained enigmatic. Interestingly, in this context, growth of the budding yeast Saccharomyces cerevisiae is sensitive to extracellular IAA. Here, we use a combination of various genetic approaches including chemical-genetic profiling, SAturated Transposon Analysis in Yeast (SATAY), and genetic epistasis analyses to identify the mode-of-action by which IAA inhibits growth in yeast. Surprisingly, these analyses pinpointed the target of rapamycin complex 1 (TORC1), a central regulator of eukaryotic cell growth, as the major growth-limiting target of IAA. Our biochemical analyses further demonstrate that IAA inhibits TORC1 both in vivo and in vitro. Intriguingly, we also show that yeast cells are able to synthesize IAA and specifically accumulate IAA upon entry into stationary phase. Our data therefore suggest that IAA contributes to proper entry of yeast cells into a quiescent state by acting as a metabolic inhibitor of TORC1. Auxins are a major group of plant phytohormones that are critical for growth and development. Amongst the auxins, indole-3-acetic acid (IAA) is the most common, naturally occurring phytohormone that regulates cell division, differentiation, and senescence in plants. Interestingly, the capacity to synthesize and secrete IAA is also widespread among fungi, including the budding yeast Saccharomyces cerevisiae, but the role of IAA in fungi has largely remained unknown. Here, we confirm an earlier observation that IAA inhibits growth of budding yeast and show by diverse genetic and biochemical means that IAA restrains budding yeast growth by inhibiting the target of rapamycin complex 1 (TORC1), a highly conserved eukaryotic regulator of growth. Intriguingly, budding yeast cells accumulate IAA specifically when limited for nutrients, which suggests that IAA plays a hitherto unknown physiological role in contributing to the establishment of cellular quiescence by acting as a metabolic inhibitor of TORC1.
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26
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Hu Z, Raucci S, Jaquenoud M, Hatakeyama R, Stumpe M, Rohr R, Reggiori F, De Virgilio C, Dengjel J. Multilayered Control of Protein Turnover by TORC1 and Atg1. Cell Rep 2020; 28:3486-3496.e6. [PMID: 31553916 DOI: 10.1016/j.celrep.2019.08.069] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/19/2019] [Accepted: 08/22/2019] [Indexed: 12/13/2022] Open
Abstract
The target of rapamycin complex 1 (TORC1) is a master regulator of cell homeostasis, which promotes anabolic reactions and synchronously inhibits catabolic processes such as autophagy-mediated protein degradation. Its prime autophagy target is Atg13, a subunit of the Atg1 kinase complex that acts as the gatekeeper of canonical autophagy. To study whether the activities of TORC1 and Atg1 are coupled through additional, more intricate control mechanisms than simply this linear pathway, we analyzed the epistatic relationship between TORC1 and Atg1 by using quantitative phosphoproteomics. Our in vivo data, combined with targeted in vitro TORC1 and Atg1 kinase assays, not only uncover numerous TORC1 and Atg1 effectors, but also suggest distinct bi-directional regulatory feedback loops and characterize Atg29 as a commonly regulated downstream target of both TORC1 and Atg1. Thus, an exquisitely multilayered regulatory network appears to coordinate TORC1 and Atg1 activities to robustly tune autophagy in response to nutritional cues.
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Affiliation(s)
- Zehan Hu
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Serena Raucci
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Malika Jaquenoud
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Riko Hatakeyama
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Michael Stumpe
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Rudolf Rohr
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells & Systems, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
| | | | - Jörn Dengjel
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland.
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27
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Petibon C, Malik Ghulam M, Catala M, Abou Elela S. Regulation of ribosomal protein genes: An ordered anarchy. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1632. [PMID: 33038057 PMCID: PMC8047918 DOI: 10.1002/wrna.1632] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023]
Abstract
Ribosomal protein genes are among the most highly expressed genes in most cell types. Their products are generally essential for ribosome synthesis, which is the cornerstone for cell growth and proliferation. Many cellular resources are dedicated to producing ribosomal proteins and thus this process needs to be regulated in ways that carefully balance the supply of nascent ribosomal proteins with the demand for new ribosomes. Ribosomal protein genes have classically been viewed as a uniform interconnected regulon regulated in eukaryotic cells by target of rapamycin and protein kinase A pathway in response to changes in growth conditions and/or cellular status. However, recent literature depicts a more complex picture in which the amount of ribosomal proteins produced varies between genes in response to two overlapping regulatory circuits. The first includes the classical general ribosome‐producing program and the second is a gene‐specific feature responsible for fine‐tuning the amount of ribosomal proteins produced from each individual ribosomal gene. Unlike the general pathway that is mainly controlled at the level of transcription and translation, this specific regulation of ribosomal protein genes is largely achieved through changes in pre‐mRNA splicing efficiency and mRNA stability. By combining general and specific regulation, the cell can coordinate ribosome production, while allowing functional specialization and diversity. Here we review the many ways ribosomal protein genes are regulated, with special focus on the emerging role of posttranscriptional regulatory events in fine‐tuning the expression of ribosomal protein genes and its role in controlling the potential variation in ribosome functions. This article is categorized under:Translation > Ribosome Biogenesis Translation > Ribosome Structure/Function Translation > Translation Regulation
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Affiliation(s)
- Cyrielle Petibon
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Mustafa Malik Ghulam
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Mathieu Catala
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Sherif Abou Elela
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
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28
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Martínez-Fernández V, Cuevas-Bermúdez A, Gutiérrez-Santiago F, Garrido-Godino AI, Rodríguez-Galán O, Jordán-Pla A, Lois S, Triviño JC, de la Cruz J, Navarro F. Prefoldin-like Bud27 influences the transcription of ribosomal components and ribosome biogenesis in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2020; 26:1360-1379. [PMID: 32503921 PMCID: PMC7491330 DOI: 10.1261/rna.075507.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/28/2020] [Indexed: 05/08/2023]
Abstract
Understanding the functional connection that occurs for the three nuclear RNA polymerases to synthesize ribosome components during the ribosome biogenesis process has been the focal point of extensive research. To preserve correct homeostasis on the production of ribosomal components, cells might require the existence of proteins that target a common subunit of these RNA polymerases to impact their respective activities. This work describes how the yeast prefoldin-like Bud27 protein, which physically interacts with the Rpb5 common subunit of the three RNA polymerases, is able to modulate the transcription mediated by the RNA polymerase I, likely by influencing transcription elongation, the transcription of the RNA polymerase III, and the processing of ribosomal RNA. Bud27 also regulates both RNA polymerase II-dependent transcription of ribosomal proteins and ribosome biogenesis regulon genes, likely by occupying their DNA ORFs, and the processing of the corresponding mRNAs. With RNA polymerase II, this association occurs in a transcription rate-dependent manner. Our data also indicate that Bud27 inactivation alters the phosphorylation kinetics of ribosomal protein S6, a readout of TORC1 activity. We conclude that Bud27 impacts the homeostasis of the ribosome biogenesis process by regulating the activity of the three RNA polymerases and, in this way, the synthesis of ribosomal components. This quite likely occurs through a functional connection of Bud27 with the TOR signaling pathway.
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Affiliation(s)
- Verónica Martínez-Fernández
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Abel Cuevas-Bermúdez
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Francisco Gutiérrez-Santiago
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Ana I Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Olga Rodríguez-Galán
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain
- Departamento de Genética, Universidad de Sevilla, E-41012 Seville, Spain
| | - Antonio Jordán-Pla
- ERI Biotecmed, Facultad de Biológicas, Universitat de València, E-46100 Burjassot, Valencia, Spain
| | - Sergio Lois
- Sistemas Genómicos. Ronda de Guglielmo Marconi, 6, 46980 Paterna, Valencia, Spain
| | - Juan C Triviño
- Sistemas Genómicos. Ronda de Guglielmo Marconi, 6, 46980 Paterna, Valencia, Spain
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain
- Departamento de Genética, Universidad de Sevilla, E-41012 Seville, Spain
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
- Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
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29
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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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30
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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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31
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Shu WJ, Chen R, Yin ZH, Li F, Zhang H, Du HN. Rph1 coordinates transcription of ribosomal protein genes and ribosomal RNAs to control cell growth under nutrient stress conditions. Nucleic Acids Res 2020; 48:8360-8373. [PMID: 32619236 PMCID: PMC7470948 DOI: 10.1093/nar/gkaa558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 06/17/2020] [Accepted: 06/21/2020] [Indexed: 12/24/2022] Open
Abstract
Coordinated regulation of ribosomal RNA (rRNA) synthesis and ribosomal protein gene (RPG) transcription by eukaryotic RNA polymerases (RNAP) is a key requirement for growth control. Although evidence for balance between RNPI-dependent 35S rRNA production and RNAPII-mediated RPG transcription have been described, the molecular basis is still obscure. Here, we found that Rph1 modulates the transcription status of both rRNAs and RPGs in yeast. We show that Rph1 widely associates with RNAPI and RNAPII-transcribed genes. Deletion of RPH1 remarkably alleviates cell slow growth caused by TORC1 inhibition via derepression of rRNA and RPG transcription under nutrient stress conditions. Mechanistically, Rim15 kinase phosphorylates Rph1 upon rapamycin treatment. Phosphorylation-mimetic mutant of Rph1 exhibited more resistance to rapamycin treatment, decreased association with ribosome-related genes, and faster cell growth compared to the wild-type, indicating that Rph1 dissociation from chromatin ensures cell survival upon nutrient stress. Our results uncover the role of Rph1 in coordination of RNA polymerases-mediated transcription to control cell growth under nutrient stress conditions.
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Affiliation(s)
- Wen-Jie Shu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072 China
| | - Runfa Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072 China
| | - Zhao-Hong Yin
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072 China
| | - Feng Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072 China
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, 3888 Chenhua Road, Shanghai, 201062, China
| | - Hai-Ning Du
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072 China
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32
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Qian B, Liu X, Ye Z, Zhou Q, Liu P, Yin Z, Wang W, Zheng X, Zhang H, Zhang Z. Phosphatase-associated protein MoTip41 interacts with the phosphatase MoPpe1 to mediate crosstalk between TOR and cell wall integrity signalling during infection by the rice blast fungus Magnaporthe oryzae. Environ Microbiol 2020; 23:791-809. [PMID: 32564502 DOI: 10.1111/1462-2920.15136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/26/2022]
Abstract
The type 2A (PP2A) and type 2A-like (PP4 and PP6) serine/threonine phosphatases participate in a variety of cellular processes, such as cell cycle progression, signal transduction and apoptosis. Previously, we reported that the PP6 catalytic subunit MoPpe1, which interacts with and is suppressed by type 2A associated protein of 42 kDa (MoTap42), an essential protein involved in the target of rapamycin (TOR) signalling pathway, has important roles in development, virulence and activation of the cell wall integrity (CWI) pathway in the rice blast fungus Magnaporthe oryzae. Here, we show that Tap42-interacting protein 41 (MoTip41) mediates crosstalk between the TOR and CWI signalling pathways; and participates in the TOR pathway via interaction with MoPpe1, but not MoTap42. The deletion of MoTIP41 resulted in disruption of CWI signalling, autophagy, vegetative growth, appressorium function and plant infection, as well as increased sensitivity to rapamycin. Further investigation revealed that MoTip41 modulates activation of the CWI pathway in response to infection by interfering with the interaction between MoTap42 and MoPpe1. These findings enhance our understanding of how crosstalk between TOR and CWI signalling modulates the development and pathogenicity of M. oryzae.
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Affiliation(s)
- Bin Qian
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Xinyu Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Ziyuan Ye
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Qikun Zhou
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Peng Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Ziyi Yin
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Wenhao Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Xiaobo Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Haifeng Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
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33
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Vallejo B, Matallana E, Aranda A. Saccharomyces cerevisiae nutrient signaling pathways show an unexpected early activation pattern during winemaking. Microb Cell Fact 2020; 19:124. [PMID: 32505207 PMCID: PMC7275465 DOI: 10.1186/s12934-020-01381-6] [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: 01/02/2020] [Accepted: 05/27/2020] [Indexed: 12/28/2022] Open
Abstract
Background Saccharomyces cerevisiae wine strains can develop stuck or sluggish fermentations when nutrients are scarce or suboptimal. Nutrient sensing and signaling pathways, such as PKA, TORC1 and Snf1, work coordinately to adapt growth and metabolism to the amount and balance of the different nutrients in the medium. This has been exhaustively studied in laboratory strains of S. cerevisiae and laboratory media, but much less under industrial conditions. Results Inhibitors of such pathways, like rapamycin or 2-deoxyglucose, failed to discriminate between commercial wine yeast strains with different nutritional requirements, but evidenced genetic variability among industrial isolates, and between laboratory and commercial strains. Most signaling pathways involve events of protein phosphorylation that can be followed as markers of their activity. The main pathway to promote growth in the presence of nitrogen, the TORC1 pathway, measured by the phosphorylation of Rps6 and Par32, proved active at the very start of fermentation, mainly on day 1, and ceased soon afterward, even before cellular growth stopped. Transcription factor Gln3, which activates genes subject to nitrogen catabolite repression, was also active for the first hours, even when ammonium and amino acids were still present in media. Snf1 kinase was activated only when glucose was exhausted under laboratory conditions, but was active from early fermentation stages. The same results were generally obtained when nitrogen was limiting, which indicates a unique pathway activation pattern in winemaking. As PKA remained active throughout fermentation, it could be the central pathway that controls others, provided sugars are present. Conclusions Wine fermentation is a distinct environmental situation from growth in laboratory media in molecular terms. The mechanisms involved in glucose and nitrogen repression respond differently under winemaking conditions.
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Affiliation(s)
- Beatriz Vallejo
- Institute for Integrative Systems Biology, I2SysBio, University of Valencia-CSIC, Parc Cientific UV. Av. Agustín Escardino 9, Paterna, 46980, Valencia, Spain
| | - Emilia Matallana
- Institute for Integrative Systems Biology, I2SysBio, University of Valencia-CSIC, Parc Cientific UV. Av. Agustín Escardino 9, Paterna, 46980, Valencia, Spain
| | - Agustín Aranda
- Institute for Integrative Systems Biology, I2SysBio, University of Valencia-CSIC, Parc Cientific UV. Av. Agustín Escardino 9, Paterna, 46980, Valencia, Spain.
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34
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Yaguchi M, Ikeya S, Kozaki A. The activation mechanism of plant S6 kinase (S6K), a substrate of TOR kinase, is different from that of mammalian S6K. FEBS Lett 2019; 594:776-787. [PMID: 31705659 DOI: 10.1002/1873-3468.13661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 11/06/2022]
Abstract
The S6 kinases (S6Ks) are known to be activated by the target of rapamycin through phosphorylation of their hydrophobic motif (HM). However, our previous research showed that the HM site of plant S6Ks is not phosphorylated and is not essential for their activity in yeast cells lacking Ypk3, an ortholog of mammalian S6K. Here, we demonstrate that the HM site of mammalian S6Ks is phosphorylated and is indispensable for their activity in yeast ypk3∆ cells. Furthermore, pseudo-phosphorylation at the HM site of plant S6Ks results in regaining of activity that is lost due to mutation in the conserved phosphorylation sites, namely the T-loop and Turn motif. These results indicate the activation mechanism of plant S6Ks is different from that of mammals.
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Affiliation(s)
| | - Shun Ikeya
- Department of Biology, Shizuoka University, Japan
| | - Akiko Kozaki
- Department of Biology, Shizuoka University, Japan
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35
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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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36
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Romero AM, Ramos-Alonso L, Montellá-Manuel S, García-Martínez J, de la Torre-Ruiz MÁ, Pérez-Ortín JE, Martínez-Pastor MT, Puig S. A genome-wide transcriptional study reveals that iron deficiency inhibits the yeast TORC1 pathway. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194414. [PMID: 31394264 DOI: 10.1016/j.bbagrm.2019.194414] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/29/2019] [Accepted: 07/29/2019] [Indexed: 12/20/2022]
Abstract
Iron is an essential micronutrient that participates as a cofactor in a broad range of metabolic processes including mitochondrial respiration, DNA replication, protein translation and lipid biosynthesis. Adaptation to iron deficiency requires the global reorganization of cellular metabolism directed to optimize iron utilization. The budding yeast Saccharomyces cerevisiae has been widely used to characterize the responses of eukaryotic microorganisms to iron depletion. In this report, we used a genomic approach to investigate the contribution of transcription rates to the modulation of mRNA levels during adaptation of yeast cells to iron starvation. We reveal that a decrease in the activity of all RNA polymerases contributes to the down-regulation of many mRNAs, tRNAs and rRNAs. Opposite to the general expression pattern, many genes including components of the iron deficiency response, the mitochondrial retrograde pathway and the general stress response display a remarkable increase in both transcription rates and mRNA levels upon iron limitation, whereas genes encoding ribosomal proteins or implicated in ribosome biogenesis exhibit a pronounced fall. This expression profile is consistent with an activation of the environmental stress response. The phosphorylation stage of multiple regulatory factors strongly suggests that the conserved nutrient signaling pathway TORC1 is inhibited during the progress of iron deficiency. These results suggest an intricate crosstalk between iron metabolism and the TORC1 pathway that should be considered in many disorders.
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Affiliation(s)
- Antonia María Romero
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), E-46980 Paterna, Valencia, Spain
| | - Lucía Ramos-Alonso
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), E-46980 Paterna, Valencia, Spain
| | - Sandra Montellá-Manuel
- Department of Basic Medical Sciences, IRB-Lleida, University of Lleida, E-25198 Lleida, Spain
| | - José García-Martínez
- Departamento de Genética, Universitat de València, E-46100 Burjassot, Valencia, Spain; ERI Biotecmed, Universitat de València, E-46100 Burjassot, Valencia, Spain
| | | | - José Enrique Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular, Universitat de València, E-46100 Burjassot, Valencia, Spain; ERI Biotecmed, Universitat de València, E-46100 Burjassot, Valencia, Spain
| | | | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), E-46980 Paterna, Valencia, Spain.
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37
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Kessi-Pérez EI, Salinas F, González A, Su Y, Guillamón JM, Hall MN, Larrondo LF, Martínez C. KAE1 Allelic Variants Affect TORC1 Activation and Fermentation Kinetics in Saccharomyces cerevisiae. Front Microbiol 2019; 10:1686. [PMID: 31417508 PMCID: PMC6685402 DOI: 10.3389/fmicb.2019.01686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/09/2019] [Indexed: 12/17/2022] Open
Abstract
The eukaryotic domain-conserved TORC1 signalling pathway connects growth with nutrient sufficiency, promoting anabolic processes such as ribosomal biogenesis and protein synthesis. In Saccharomyces cerevisiae, TORC1 is activated mainly by the nitrogen sources. Recently, this pathway has gotten renewed attention but now in the context of the alcoholic fermentation, due to its key role in nitrogen metabolism regulation. Although the distal and proximal effectors downstream TORC1 are well characterised in yeast, the mechanism by which TORC1 is activated by nitrogen sources is not fully understood. In this work, we took advantage of a previously developed microculture-based methodology, which indirectly evaluates TORC1 activation in a nitrogen upshift experiment, to identify genetic variants affecting the activation of this pathway. We used this method to phenotype a recombinant population derived from two strains (SA and WE) with different geographic origins, which show opposite phenotypes for TORC1 activation by glutamine. Using this phenotypic information, we performed a QTL mapping that allowed us to identify several QTLs for TORC1 activation. Using a reciprocal hemizygous analysis, we validated GUS1, KAE1, PIB2, and UTH1 as genes responsible for the natural variation in the TORC1 activation. We observed that reciprocal hemizygous strains for KAE1 (ATPase required for t6A tRNA modification) gene showed the greatest phenotypic differences for TORC1 activation, with the hemizygous strain carrying the SA allele (KAE1SA) showing the higher TORC1 activation. In addition, we evaluated the fermentative capacities of the hemizygous strains under low nitrogen conditions, observing an antagonistic effect for KAE1SA allele, where the hemizygous strain containing this allele presented the lower fermentation rate. Altogether, these results highlight the importance of the tRNA processing in TORC1 activation and connects this pathway with the yeasts fermentation kinetics under nitrogen-limited conditions.
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Affiliation(s)
- Eduardo I Kessi-Pérez
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile.,Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Francisco Salinas
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile (UACH), Valdivia, Chile
| | | | - Ying Su
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - José M Guillamón
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | | | - Luis F Larrondo
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudio Martínez
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile.,Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
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38
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INO80 Chromatin Remodeling Coordinates Metabolic Homeostasis with Cell Division. Cell Rep 2019; 22:611-623. [PMID: 29346761 PMCID: PMC5949282 DOI: 10.1016/j.celrep.2017.12.079] [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: 08/07/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 12/13/2022] Open
Abstract
Adaptive survival requires the coordination of nutrient availability with expenditure of cellular resources. For example, in nutrient-limited environments, 50% of all S. cerevisiae genes synchronize and exhibit periodic bursts of expression in coordination with respiration and cell division in the yeast metabolic cycle (YMC). Despite the importance of metabolic and proliferative synchrony, the majority of YMC regulators are currently unknown. Here, we demonstrate that the INO80 chromatin-remodeling complex is required to coordinate respiration and cell division with periodic gene expression. Specifically, INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. In mutant cells, chromatin accessibility of periodic genes, including TORC1-responsive genes, is relatively static, concomitant with severely attenuated gene expression. Collectively, these results reveal that the INO80 complex mediates metabolic signaling to chromatin to restrict proliferation to metabolically optimal states.
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39
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Li J, Vázquez-García I, Persson K, González A, Yue JX, Barré B, Hall MN, Long A, Warringer J, Mustonen V, Liti G. Shared Molecular Targets Confer Resistance over Short and Long Evolutionary Timescales. Mol Biol Evol 2019; 36:691-708. [PMID: 30657986 DOI: 10.1093/molbev/msz006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Pre-existing and de novo genetic variants can both drive adaptation to environmental changes, but their relative contributions and interplay remain poorly understood. Here we investigated the evolutionary dynamics in drug-treated yeast populations with different levels of pre-existing variation by experimental evolution coupled with time-resolved sequencing and phenotyping. We found a doubling of pre-existing variation alone boosts the adaptation by 64.1% and 51.5% in hydroxyurea and rapamycin, respectively. The causative pre-existing and de novo variants were selected on shared targets: RNR4 in hydroxyurea and TOR1, TOR2 in rapamycin. Interestingly, the pre-existing and de novo TOR variants map to different functional domains and act via distinct mechanisms. The pre-existing TOR variants from two domesticated strains exhibited opposite rapamycin resistance effects, reflecting lineage-specific functional divergence. This study provides a dynamic view on how pre-existing and de novo variants interactively drive adaptation and deepens our understanding of clonally evolving populations.
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Affiliation(s)
- Jing Li
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
| | - Ignacio Vázquez-García
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom.,Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Statistics, Columbia University, New York, NY
| | - Karl Persson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | | | - Jia-Xing Yue
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
| | - Benjamin Barré
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
| | | | - Anthony Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Gianni Liti
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
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40
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Ahmed K, Carter DE, Lajoie P. Hyperactive
TORC
1 sensitizes yeast cells to endoplasmic reticulum stress by compromising cell wall integrity. FEBS Lett 2019; 593:1957-1973. [DOI: 10.1002/1873-3468.13463] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 05/17/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Khadija Ahmed
- Department of Anatomy and Cell Biology The University of Western Ontario London Canada
| | - David E. Carter
- Robarts Research Institute The University of Western Ontario London Canada
| | - Patrick Lajoie
- Department of Anatomy and Cell Biology The University of Western Ontario London Canada
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41
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Auxin-Inducible Depletion of the Essentialome Suggests Inhibition of TORC1 by Auxins and Inhibition of Vrg4 by SDZ 90-215, a Natural Antifungal Cyclopeptide. G3-GENES GENOMES GENETICS 2019; 9:829-840. [PMID: 30670608 PMCID: PMC6404609 DOI: 10.1534/g3.118.200748] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Gene knockout and knockdown strategies have been immensely successful probes of gene function, but small molecule inhibitors (SMIs) of gene products allow much greater time resolution and are particularly useful when the targets are essential for cell replication or survival. SMIs also serve as lead compounds for drug discovery. However, discovery of selective SMIs is costly and inefficient. The action of SMIs can be modeled simply by tagging gene products with an auxin-inducible degron (AID) that triggers rapid ubiquitylation and proteasomal degradation of the tagged protein upon exposure of live cells to auxin. To determine if this approach is broadly effective, we AID-tagged over 750 essential proteins in Saccharomyces cerevisiae and observed growth inhibition by low concentrations of auxin in over 66% of cases. Polytopic transmembrane proteins in the plasma membrane, Golgi complex, and endoplasmic reticulum were efficiently depleted if the AID-tag was exposed to cytoplasmic OsTIR1 ubiquitin ligase. The auxin analog 1-napthylacetic acid (NAA) was as potent as auxin on AID-tags, but surprisingly NAA was more potent than auxin at inhibiting target of rapamycin complex 1 (TORC1) function. Auxin also synergized with known SMIs when acting on the same essential protein, indicating that AID-tagged strains can be useful for SMI screening. Auxin synergy, resistance mutations, and cellular assays together suggest the essential GMP/GDP-mannose exchanger in the Golgi complex (Vrg4) as the target of a natural cyclic peptide of unknown function (SDZ 90-215). These findings indicate that AID-tagging can efficiently model the action of SMIs before they are discovered and can facilitate SMI discovery.
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42
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Tye BW, Commins N, Ryazanova LV, Wühr M, Springer M, Pincus D, Churchman LS. Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness. eLife 2019; 8:43002. [PMID: 30843788 PMCID: PMC6453566 DOI: 10.7554/elife.43002] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/06/2019] [Indexed: 12/31/2022] Open
Abstract
To achieve maximal growth, cells must manage a massive economy of ribosomal proteins (r-proteins) and RNAs (rRNAs) to produce thousands of ribosomes every minute. Although ribosomes are essential in all cells, natural disruptions to ribosome biogenesis lead to heterogeneous phenotypes. Here, we model these perturbations in Saccharomyces cerevisiae and show that challenges to ribosome biogenesis result in acute loss of proteostasis. Imbalances in the synthesis of r-proteins and rRNAs lead to the rapid aggregation of newly synthesized orphan r-proteins and compromise essential cellular processes, which cells alleviate by activating proteostasis genes. Exogenously bolstering the proteostasis network increases cellular fitness in the face of challenges to ribosome assembly, demonstrating the direct contribution of orphan r-proteins to cellular phenotypes. We propose that ribosome assembly is a key vulnerability of proteostasis maintenance in proliferating cells that may be compromised by diverse genetic, environmental, and xenobiotic perturbations that generate orphan r-proteins. Cells are made up of thousands of different proteins that perform unique roles required for life. To create all of these proteins, cells use machines called ribosomes that are partly formed of elements known as r-proteins. When cells grow and divide, the ribosomes have to make copies of themselves through a process called ribosome biogenesis. Although all cells need ribosomes, certain types of cells are especially sensitive to events that interfere with ribosome biogenesis. For example, patients that have mutations in genes needed for ribosome biogenesis produce fewer red blood cells, but their other cells and tissues are mostly healthy. It is not clear why some cells are more sensitive than others. Ribosome biogenesis is very similar between different organisms, so researchers often use budding yeast as a model to study the process. Here, Tye et al. used genetic and chemical tools to interfere with ribosome biogenesis on short time scales, which made it possible to detect early on what was going wrong in the cells. The experiments found that when ribosome biogenesis was disrupted, r-proteins that were waiting to be assembled into ribosomes quickly stuck to one another and formed clumps that reduced the ability of the yeast cells to grow. The cells responded by switching on a protein called Hsf1, which restored their ability to grow. Yeast cells that were growing quickly, and therefore making more ribosomes, were more sensitive to abnormal ribosome biogenesis than slow-growing cells. These results indicate that how actively a cell is growing, and its ability to cope with r-proteins sticking together, may in part explain why certain cells are more vulnerable to events that interfere with ribosome biogenesis. Since human cells also have Hsf1, future experiments could investigate whether turning it on might also protect fast-growing human cells from such events.
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Affiliation(s)
- Blake W Tye
- Department of Genetics, Harvard Medical School, Boston, United States.,Program in Chemical Biology, Harvard University, Cambridge, United States
| | - Nicoletta Commins
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Lillia V Ryazanova
- Department of Molecular Biology, Princeton University, Princeton, United States.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
| | - Martin Wühr
- Department of Molecular Biology, Princeton University, Princeton, United States.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - David Pincus
- Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, United States.,Center for Physics of Evolving Systems, University of Chicago, Chicago, United States
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43
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Bakshi A, Moin M, Madhav MS, Kirti PB. Target of rapamycin, a master regulator of multiple signalling pathways and a potential candidate gene for crop improvement. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:190-205. [PMID: 30411830 DOI: 10.1111/plb.12935] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/05/2018] [Indexed: 06/08/2023]
Abstract
The target of rapamycin (TOR) protein regulates growth and development in photosynthetic and non-photosynthetic eukaryotes. Although the TOR regulatory networks are involved in nutrient and energy signalling, and transcriptional and translational control of multiple signalling pathways, the molecular mechanism of TOR regulation of plant abiotic stress responses is still unclear. The TOR-mediated transcriptional regulation of genes encoding ribosomal proteins (RP) is a necessity under stress conditions for balanced growth and productivity in plants. The activation of SnRKs (sucrose non-fermenting-related kinases) and the inactivation of TOR signalling in abiotic stresses is in line with the accumulation of ABA and transcriptional activation of stress responsive genes. Autophagy is induced under abiotic stress conditions, which results in degradation of proteins and the release of amino acids, which might possibly induce phosphorylation of TOR and, hence, its activation. TOR signalling also has a role in regulating ABA biosynthesis for transcriptional regulation of stress-related genes. The switch between activation and inactivation of TOR by its phosphorylation and de-phosphorylation maintains balanced growth in response to stresses. In the present review, we discuss the important signalling pathways that are regulated by TOR and try to assess the relationship between TOR signalling and tolerance to abiotic stresses in plants. The review also discusses possible cross-talk between TOR and RP genes in response to abiotic stresses.
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Affiliation(s)
- A Bakshi
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - M Moin
- Department of Biotechnology, Indian Institute of Rice Research, Hyderabad, India
| | - M S Madhav
- Department of Biotechnology, Indian Institute of Rice Research, Hyderabad, India
| | - P B Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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44
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Carmona-Gutierrez D, Zimmermann A, Kainz K, Pietrocola F, Chen G, Maglioni S, Schiavi A, Nah J, Mertel S, Beuschel CB, Castoldi F, Sica V, Trausinger G, Raml R, Sommer C, Schroeder S, Hofer SJ, Bauer MA, Pendl T, Tadic J, Dammbrueck C, Hu Z, Ruckenstuhl C, Eisenberg T, Durand S, Bossut N, Aprahamian F, Abdellatif M, Sedej S, Enot DP, Wolinski H, Dengjel J, Kepp O, Magnes C, Sinner F, Pieber TR, Sadoshima J, Ventura N, Sigrist SJ, Kroemer G, Madeo F. The flavonoid 4,4'-dimethoxychalcone promotes autophagy-dependent longevity across species. Nat Commun 2019; 10:651. [PMID: 30783116 PMCID: PMC6381180 DOI: 10.1038/s41467-019-08555-w] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/11/2019] [Indexed: 01/08/2023] Open
Abstract
Ageing constitutes the most important risk factor for all major chronic ailments, including malignant, cardiovascular and neurodegenerative diseases. However, behavioural and pharmacological interventions with feasible potential to promote health upon ageing remain rare. Here we report the identification of the flavonoid 4,4'-dimethoxychalcone (DMC) as a natural compound with anti-ageing properties. External DMC administration extends the lifespan of yeast, worms and flies, decelerates senescence of human cell cultures, and protects mice from prolonged myocardial ischaemia. Concomitantly, DMC induces autophagy, which is essential for its cytoprotective effects from yeast to mice. This pro-autophagic response induces a conserved systemic change in metabolism, operates independently of TORC1 signalling and depends on specific GATA transcription factors. Notably, we identify DMC in the plant Angelica keiskei koidzumi, to which longevity- and health-promoting effects are ascribed in Asian traditional medicine. In summary, we have identified and mechanistically characterised the conserved longevity-promoting effects of a natural anti-ageing drug.
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Affiliation(s)
| | - Andreas Zimmermann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- Division of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, Graz, 8036, Austria
| | - Katharina Kainz
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Federico Pietrocola
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM U 1138, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Center, Villejuif, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Université Pierre et Marie Curie, Paris, France
| | - Guo Chen
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM U 1138, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Center, Villejuif, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Université Pierre et Marie Curie, Paris, France
| | - Silvia Maglioni
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
| | - Alfonso Schiavi
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
| | - Jihoon Nah
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Sara Mertel
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, 14195, Germany
| | - Christine B Beuschel
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, 14195, Germany
| | - Francesca Castoldi
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM U 1138, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Center, Villejuif, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Université Pierre et Marie Curie, Paris, France
- Sotio a.c, 17000, Prague, Czech Republic
| | - Valentina Sica
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM U 1138, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Center, Villejuif, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Université Pierre et Marie Curie, Paris, France
| | - Gert Trausinger
- Joanneum Research Forschungsgesellschaft m.b.H., HEALTH, Institute for Biomedicine and Health Sciences, Graz, 8010, Austria
| | - Reingard Raml
- Joanneum Research Forschungsgesellschaft m.b.H., HEALTH, Institute for Biomedicine and Health Sciences, Graz, 8010, Austria
| | - Cornelia Sommer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Sabrina Schroeder
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Sebastian J Hofer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Maria A Bauer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Tobias Pendl
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Jelena Tadic
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | | | - Zehan Hu
- Department of Cardiology, Medical University of Graz, Graz, 8036, Austria
| | - Christoph Ruckenstuhl
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Tobias Eisenberg
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Sylvere Durand
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM U 1138, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Center, Villejuif, France
| | - Noélie Bossut
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM U 1138, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Center, Villejuif, France
| | - Fanny Aprahamian
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM U 1138, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Center, Villejuif, France
| | - Mahmoud Abdellatif
- Department of Cardiology, Medical University of Graz, Graz, 8036, Austria
| | - Simon Sedej
- Department of Cardiology, Medical University of Graz, Graz, 8036, Austria
- BioTechMed Graz, Graz, 8010, Austria
| | - David P Enot
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM U 1138, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Center, Villejuif, France
| | - Heimo Wolinski
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Jörn Dengjel
- Department of Biology, Université de Fribourg, Chemin du Musée 10, 1700, Fribourg, Switzerland
| | - Oliver Kepp
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM U 1138, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Center, Villejuif, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Université Pierre et Marie Curie, Paris, France
| | - Christoph Magnes
- Joanneum Research Forschungsgesellschaft m.b.H., HEALTH, Institute for Biomedicine and Health Sciences, Graz, 8010, Austria
| | - Frank Sinner
- Division of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, Graz, 8036, Austria
- Joanneum Research Forschungsgesellschaft m.b.H., HEALTH, Institute for Biomedicine and Health Sciences, Graz, 8010, Austria
| | - Thomas R Pieber
- Division of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, Graz, 8036, Austria
- Joanneum Research Forschungsgesellschaft m.b.H., HEALTH, Institute for Biomedicine and Health Sciences, Graz, 8010, Austria
| | - Junichi Sadoshima
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Natascia Ventura
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
- Institute for Clinical Chemistry and Laboratory Diagnostic, Medical Faculty of the Heinrich Heine University, Moorenstrasse 5, 40225, Düsseldorf, Germany
| | - Stephan J Sigrist
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, 14195, Germany
- NeuroCure, Charité, Berlin, 10117, Germany
| | - Guido Kroemer
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM U 1138, Paris, France.
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Center, Villejuif, France.
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
- Université Pierre et Marie Curie, Paris, France.
- Pôle de Biologie, Hôpital Européen Georges Pompidou, Paris, France.
- Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden.
| | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria.
- BioTechMed Graz, Graz, 8010, Austria.
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Parenteau J, Maignon L, Berthoumieux M, Catala M, Gagnon V, Abou Elela S. Introns are mediators of cell response to starvation. Nature 2019; 565:612-617. [DOI: 10.1038/s41586-018-0859-7] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 12/07/2018] [Indexed: 11/09/2022]
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Padilla CA, Bárcena JA, López-Grueso MJ, Requejo-Aguilar R. The regulation of TORC1 pathway by the yeast chaperones Hsp31 is mediated by SFP1 and affects proteasomal activity. Biochim Biophys Acta Gen Subj 2018; 1863:534-546. [PMID: 30578832 DOI: 10.1016/j.bbagen.2018.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/05/2018] [Accepted: 12/17/2018] [Indexed: 12/25/2022]
Abstract
The Saccharomyces cerevisiae heat shock proteins Hsp31-34 are members of DJ-1/ThiJ/Pfpl superfamily that includes human DJ-1 (Park7), a protein involved in heritable Parkinsonism. Although, homologs of these proteins can be found in most organisms their functions are unclear. We have carried out a quantitative proteomics analysis of yeast cells devoid of the whole set of Hsp31 family of proteins, as a model of Parkinson Disease (PD), under conditions of glucose availability and starvation. The protein profile indicates a constitutive activation of the enzyme TORC1 that makes the cells more sensitive to stress conditions. TORC1 activation prevents the cells from diauxic shift and entry into the stationary phase inducing cell death. Sfp1 stays at the helm among the several transcription factors governing the cell adaptation to Hsp31-34 deficiency. We show that Sfp1 remains mainly in the nucleus likely releasing TORC1 from inhibition by cytosolic Sfp1. Impairment of glycolysis leads to increased levels of methylglyoxal and accumulation of glycated proteins. We also show an increase in proteasome subunits in the Hsp31-34 mutant, under the control of Rpn4 transcription factor. This increase is abnormally accompanied by a decrease in proteasomal activity which could lead to accumulation of aberrant proteins and contributing to cell death.
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Affiliation(s)
- C A Padilla
- Departament of Biochemistry and Molecular Biology, University of Cordoba, 14071 Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Avda. Menéndez Pidal s/n Córdoba, Spain
| | - J A Bárcena
- Departament of Biochemistry and Molecular Biology, University of Cordoba, 14071 Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Avda. Menéndez Pidal s/n Córdoba, Spain
| | - M J López-Grueso
- Departament of Biochemistry and Molecular Biology, University of Cordoba, 14071 Córdoba, Spain
| | - R Requejo-Aguilar
- Departament of Biochemistry and Molecular Biology, University of Cordoba, 14071 Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Avda. Menéndez Pidal s/n Córdoba, Spain.
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Teng X, Yau E, Sing C, Hardwick JM. Whi2 signals low leucine availability to halt yeast growth and cell death. FEMS Yeast Res 2018; 18:5083179. [PMID: 30165592 PMCID: PMC6149368 DOI: 10.1093/femsyr/foy095] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/26/2018] [Indexed: 12/16/2022] Open
Abstract
Cells are exquisitely tuned to environmental ques. Amino acid availability is rapidly sensed, allowing cells to adjust molecular processes and implement short or long-term metabolic shifts accordingly. How levels of most individual amino acids may be sensed and subsequently signaled to inform cells of their nutrient status is largely unknown. We made the unexpected observation that small changes in the levels of specific amino acids can have a profound effect on yeast cell growth, leading to the identification of yeast Whi2 as a negative regulator of cell growth in low amino acids. Although Whi2 was originally thought to be fungi-specific, Whi2 appears to share a conserved structural domain found in a family of 25 largely uncharacterized human genes encoding the KCTD (potassium channel tetramerization domain) protein family. Insights gained from yeast Whi2 are likely to be revealing about human KCTDs, many of which have been implicated or demonstrated to cause disease when mutated. Here we report new evidence that Whi2 responds to specific amino acids in the medium, particularly low leucine levels. We also discuss the known pathways of amino acid signaling and potential points of regulation by Whi2 in nutrient signaling in yeast and mammals.
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Affiliation(s)
- Xinchen Teng
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205-2103, USA
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu Province, People's Republic of China
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2103, USA
| | - Eric Yau
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205-2103, USA
| | - Cierra Sing
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205-2103, USA
| | - J Marie Hardwick
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205-2103, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2103, USA
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Yeast thioredoxin reductase Trr1p controls TORC1-regulated processes. Sci Rep 2018; 8:16500. [PMID: 30405153 PMCID: PMC6220292 DOI: 10.1038/s41598-018-34908-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/26/2018] [Indexed: 11/08/2022] Open
Abstract
The thioredoxin system plays a predominant role in the control of cellular redox status. Thioredoxin reductase fuels the system with reducing power in the form of NADPH. The TORC1 complex promotes growth and protein synthesis when nutrients, particularly amino acids, are abundant. It also represses catabolic processes, like autophagy, which are activated during starvation. We analyzed the impact of yeast cytosolic thioredoxin reductase TRR1 deletion under different environmental conditions. It shortens chronological life span and reduces growth in grape juice fermentation. TRR1 deletion has a global impact on metabolism during fermentation. As expected, it reduces oxidative stress tolerance, but a compensatory response is triggered, with catalase and glutathione increasing. Unexpectedly, TRR1 deletion causes sensitivity to the inhibitors of the TORC1 pathway, such as rapamycin. This correlates with low Tor2p kinase levels and indicates a direct role of Trr1p in its stability. Markers of TORC1 activity, however, suggest increased TORC1 activity. The autophagy caused by nitrogen starvation is reduced in the trr1Δ mutant. Ribosomal protein Rsp6p is dephosphorylated in the presence of rapamycin. This dephosphorylation diminishes in the TRR1 deletion strain. These results show a complex network of interactions between thioredoxin reductase Trr1p and the processes controlled by TOR.
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Qian B, Liu X, Jia J, Cai Y, Chen C, Zhang H, Zheng X, Wang P, Zhang Z. MoPpe1 partners with MoSap1 to mediate TOR and cell wall integrity signalling in growth and pathogenicity of the rice blast fungus Magnaporthe oryzae. Environ Microbiol 2018; 20:3964-3979. [PMID: 30246284 DOI: 10.1111/1462-2920.14421] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/14/2018] [Accepted: 09/17/2018] [Indexed: 12/25/2022]
Abstract
In the rice blast fungus Magnaporthe oryzae, the cell wall integrity (CWI) signalling pathway governs cell wall changes in response to external cues and normal CWI signalling is critical for appressorium function and pathogenicity. We previously characterized the mitogen-activated protein kinase (MAPK) kinase MoMkk1 as an integral component of the CWI pathway. Using the affinity purification approach, we have identified MoMkk1-interacting MoPpe1 as a homologue of Saccharomyces cerevisiae serine/threonine protein phosphatase Sit4/Ppe1. We found that MoPpe1 is required for vegetative growth, conidiation and full virulence. In addition, we found that MoPpe1 interacts with MoSap1, a protein with functions similar to MoPpe1. Intriguingly, we found that MoPpe1-MoSap1 interaction is related to CWI and target of rapamycin (TOR) pathways. We presented evidence suggesting that MoPpe1 and MoSap1 function as an adaptor complex linking CWI and TOR signalling and that the activation of the TOR pathway leads to suppression of CWI signalling, resulting in defects in appressorium function and pathogenicity. Taken together, our studies not only reveal important functions of MoMkk1-MoPpe1-MoSap1 interactions in growth and pathogenicity of the blast fungus, but also highlight the complexity of regulatory networks involving conserved yet novel regulatory mechanisms of CWI and TOR signalling.
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Affiliation(s)
- Bin Qian
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China
| | - Xinyu Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China
| | - Jia Jia
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China
| | - Yongchao Cai
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China
| | - Chen Chen
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China
| | - Haifeng Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China
| | - Xiaobo Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China
| | - Ping Wang
- Departments of Pediatrics, and Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, 70112, USA
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China
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Laribee RN. Transcriptional and Epigenetic Regulation by the Mechanistic Target of Rapamycin Complex 1 Pathway. J Mol Biol 2018; 430:4874-4890. [PMID: 30359581 DOI: 10.1016/j.jmb.2018.10.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/09/2018] [Accepted: 10/15/2018] [Indexed: 11/28/2022]
Abstract
Nutrient availability impacts health such that nutrient excess states can dysregulate epigenetic and transcriptional pathways to cause many diseases. Increasing evidence implicates aberrant regulation of nutrient signaling cascades as one means of communicating nutrient information to the epigenetic and transcriptional regulatory machinery. One such signaling cascade, the mechanistic target of rapamycin complex 1 (mTORC1), is conserved from yeast to man, and it is deregulated in diverse disease states. The catalytic subunit of the mTORC1 kinase complex (Tor1 or Tor2 in budding yeast and mTor in mammals) phosphorylates several downstream effectors regulating transcriptional and translational responses controlling growth and proliferation. Delineating mechanisms of cytoplasmic nutrient mTORC1 activation continues to be a major research focus. However, Tor kinases not only localize to the cytoplasm but also are found in the nucleus where they selectively bind and regulate genes controlling cellular metabolism and anabolism. The nuclear mTORC1 functions are now beginning to be defined, and they suggest that mTORC1 has a critical role in regulating the complex transcriptional activities required for ribosomal biogenesis. The mTORC1 pathway also interacts with epigenetic regulators required for modifying chromatin structure and function to control gene expression. Because altered nutrient states exert both individual and transgenerational phenotypic changes, mTORC1 signaling to chromatin effectors may have a significant role in mediating the effects of diet and nutrients on the epigenome. This article will discuss the recent inroads into the function of nuclear mTORC1 and its role in epigenetic and transcriptional regulation.
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Affiliation(s)
- R Nicholas Laribee
- Department of Pathology and Laboratory Medicine, and Center for Cancer Research, University of Tennessee Health Science Center, 19 South Manassas, Cancer Research Building Rm 318, Memphis, TN 38163, USA.
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