451
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Yerlikaya S, Meusburger M, Kumari R, Huber A, Anrather D, Costanzo M, Boone C, Ammerer G, Baranov PV, Loewith R. TORC1 and TORC2 work together to regulate ribosomal protein S6 phosphorylation in Saccharomyces cerevisiae. Mol Biol Cell 2015; 27:397-409. [PMID: 26582391 PMCID: PMC4713140 DOI: 10.1091/mbc.e15-08-0594] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/09/2015] [Indexed: 11/14/2022] Open
Abstract
Phosphorylation of the S6 protein of the 40S subunit of the eukaryote ribosome downstream of anabolic signals has long been assumed to promote protein synthesis. Both target of rapamycin complexes regulate this modification in yeast, but the use of ribosome profiling shows no role for Rps6 phosphorylation in mRNA translation. Nutrient-sensitive phosphorylation of the S6 protein of the 40S subunit of the eukaryote ribosome is highly conserved. However, despite four decades of research, the functional consequences of this modification remain unknown. Revisiting this enigma in Saccharomyces cerevisiae, we found that the regulation of Rps6 phosphorylation on Ser-232 and Ser-233 is mediated by both TOR complex 1 (TORC1) and TORC2. TORC1 regulates phosphorylation of both sites via the poorly characterized AGC-family kinase Ypk3 and the PP1 phosphatase Glc7, whereas TORC2 regulates phosphorylation of only the N-terminal phosphosite via Ypk1. Cells expressing a nonphosphorylatable variant of Rps6 display a reduced growth rate and a 40S biogenesis defect, but these phenotypes are not observed in cells in which Rps6 kinase activity is compromised. Furthermore, using polysome profiling and ribosome profiling, we failed to uncover a role of Rps6 phosphorylation in either global translation or translation of individual mRNAs. Taking the results together, this work depicts the signaling cascades orchestrating Rps6 phosphorylation in budding yeast, challenges the notion that Rps6 phosphorylation plays a role in translation, and demonstrates that observations made with Rps6 knock-ins must be interpreted cautiously.
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Affiliation(s)
- Seda Yerlikaya
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva, University of Geneva, CH-1211 Geneva, Switzerland
| | - Madeleine Meusburger
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva, University of Geneva, CH-1211 Geneva, Switzerland
| | - Romika Kumari
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Alexandre Huber
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva, University of Geneva, CH-1211 Geneva, Switzerland
| | - Dorothea Anrather
- Max F. Perutz Laboratories, Department of Biochemistry, University of Vienna, A1030 Vienna, Austria
| | - Michael Costanzo
- Banting and Best Department of Medical Research, Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Charles Boone
- Banting and Best Department of Medical Research, Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Gustav Ammerer
- Max F. Perutz Laboratories, Department of Biochemistry, University of Vienna, A1030 Vienna, Austria
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Robbie Loewith
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva, University of Geneva, CH-1211 Geneva, Switzerland Swiss National Centre for Competence in Research Programme Chemical Biology, 1211 Geneva, Switzerland
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452
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Eltschinger S, Loewith R. TOR Complexes and the Maintenance of Cellular Homeostasis. Trends Cell Biol 2015; 26:148-159. [PMID: 26546292 DOI: 10.1016/j.tcb.2015.10.003] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/29/2015] [Accepted: 10/01/2015] [Indexed: 12/30/2022]
Abstract
The Target of Rapamycin (TOR) is a conserved serine/threonine (ser/thr) kinase that functions in two, distinct, multiprotein complexes called TORC1 and TORC2. Each complex regulates different aspects of eukaryote growth: TORC1 regulates cell volume and/or mass by influencing protein synthesis and turnover, while TORC2, as detailed in this review, regulates cell surface area by influencing lipid production and intracellular turgor. TOR complexes function in feedback loops, implying that downstream effectors are also likely to be involved in upstream regulation. In this regard, the notion that TORCs function primarily as mediators of cellular and organismal homeostasis is fundamentally different from the current, predominate view of TOR as a direct transducer of extracellular biotic and abiotic signals.
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Affiliation(s)
- Sandra Eltschinger
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland; iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
| | - Robbie Loewith
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland; iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland; National Centre for Competence in Research in Chemical Biology, Geneva, Switzerland.
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453
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Shimizu Y, Nagai M, Yeasmin AMST, Koike N, Talukdar MW, Ushimaru T. Elucidation of novel budding yeast separase mutants. Biosci Biotechnol Biochem 2015; 80:473-8. [PMID: 26523765 DOI: 10.1080/09168451.2015.1101337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The mitotic separase cleaves Scc1 in cohesin to allow sister chromatids to separate from each other upon anaphase onset. Separase is also required for DNA damage repair. Here, we isolated and characterized 10 temperature-sensitive (ts) mutants of separase ESP1 in the budding yeast Saccharomyces cerevisiae. All mutants were defective in sister chromatid separation at the restricted temperature. Some esp1-ts mutants were hypersensitive to the microtubule poison benomyl and/or the DNA-damaging agent bleomycin. Overexpression of securin alleviated the growth defect in some esp1-ts mutants, whereas it rather exacerbated it in others. The Drosophila Pumilio homolog MPT5 was isolated as a high-dosage suppressor of esp1-ts cells. We discuss various features of separase based on these findings.
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Affiliation(s)
- Yoshihito Shimizu
- a Graduate School of Science and Technology , Shizuoka University , Shizuoka , Japan
| | - Masayoshi Nagai
- a Graduate School of Science and Technology , Shizuoka University , Shizuoka , Japan
| | - Akter M S T Yeasmin
- b Faculty of Science, Graduate School of Science , Shizuoka University , Shizuoka , Japan
| | - Naoki Koike
- a Graduate School of Science and Technology , Shizuoka University , Shizuoka , Japan
| | | | - Takashi Ushimaru
- a Graduate School of Science and Technology , Shizuoka University , Shizuoka , Japan.,b Faculty of Science, Graduate School of Science , Shizuoka University , Shizuoka , Japan
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454
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Kim A, Cunningham KW. A LAPF/phafin1-like protein regulates TORC1 and lysosomal membrane permeabilization in response to endoplasmic reticulum membrane stress. Mol Biol Cell 2015; 26:4631-45. [PMID: 26510498 PMCID: PMC4678020 DOI: 10.1091/mbc.e15-08-0581] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/19/2015] [Indexed: 01/13/2023] Open
Abstract
The controlled permeabilization of lysosomes and vacuoles may represent an ancient manner of programmed cell death. It is shown that TORC1 is required for lysosomal membrane permeabilization and death of yeast cells that have been exposed to antifungals, and that a novel FYVE-domain protein regulates TORC1 signaling in these conditions. Lysosomal membrane permeabilization (LMP) is a poorly understood regulator of programmed cell death that involves leakage of luminal lysosomal or vacuolar hydrolases into the cytoplasm. In Saccharomyces cerevisiae, LMP can be induced by antifungals and endoplasmic reticulum stressors when calcineurin also has been inactivated. A genome-wide screen revealed Pib2, a relative of LAPF/phafin1 that regulates LMP in mammals, as a pro-LMP protein in yeast. Pib2 associated with vacuolar and endosomal limiting membranes in unstressed cells in a manner that depended on its FYVE domain and on phosphatidylinositol 3-phosphate (PI(3)P) biosynthesis. Genetic experiments suggest that Pib2 stimulates the activity of TORC1, a vacuole-associated protein kinase that is sensitive to rapamycin, in a pathway parallel to the Ragulator/EGO complex containing the GTPases Gtr1 and Gtr2. A hyperactivating mutation in the catalytic subunit of TORC1 restored LMP to the gtr1∆ and pib2∆ mutants and also prevented the synthetic lethality of the double mutants. These findings show novel roles of PI(3)P and Pib2 in the regulation of TORC1, which in turn promoted LMP and nonapoptotic death of stressed cells. Rapamycin prevented the death of the pathogenic yeast Candida albicans during exposure to fluconazole plus a calcineurin inhibitor, suggesting that TORC1 broadly promotes sensitivity to fungistats in yeasts.
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Affiliation(s)
- Adam Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Kyle W Cunningham
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
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455
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Abstract
Although the eukaryotic TOR (target of rapamycin) kinase signalling pathway has emerged as a key player for integrating nutrient-, energy- and stress-related cues with growth and metabolic outputs, relatively little is known of how this ancient regulatory mechanism has been adapted in higher plants. Drawing comparisons with the substantial knowledge base around TOR kinase signalling in fungal and animal systems, functional aspects of this pathway in plants are reviewed. Both conserved and divergent elements are discussed in relation to unique aspects associated with an autotrophic mode of nutrition and adaptive strategies for multicellular development exhibited by plants.
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456
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Teixeira V, Medeiros TC, Vilaça R, Ferreira J, Moradas-Ferreira P, Costa V. Ceramide signaling targets the PP2A-like protein phosphatase Sit4p to impair vacuolar function, vesicular trafficking and autophagy in Isc1p deficient cells. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1861:21-33. [PMID: 26477382 DOI: 10.1016/j.bbalip.2015.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 09/09/2015] [Accepted: 10/14/2015] [Indexed: 02/02/2023]
Abstract
The vacuoles play important roles in cellular homeostasis and their functions include the digestion of cytoplasmic material and organelles derived from autophagy. Conserved nutrient signaling pathways regulate vacuolar function and autophagy, ensuring normal cell and organismal development and aging. Recent evidence implicates sphingolipids in the modulation of these processes, but the impact of ceramide signaling on vacuolar dynamics and autophagy remains largely unknown. Here, we show that yeast cells lacking Isc1p, an orthologue of mammalian neutral sphingomyelinase type 2, exhibit vacuolar fragmentation and dysfunctions, namely decreased Pep4p-mediated proteolysis and V-ATPase activity, which impairs vacuolar acidification. Moreover, these phenotypes are suppressed by downregulation of the ceramide-activated protein phosphatase Sit4p. The isc1Δ cells also exhibit defective Cvt and vesicular trafficking in a Sit4p-dependent manner, ultimately contributing to a reduced autophagic flux. Importantly, these phenotypes are also suppressed by downregulation of the nutrient signaling kinase TORC1, which is known to inhibit Sit4p and autophagy, or Sch9p. These results support a model in which Sit4p functions downstream of Isc1p in a TORC1-independent, ceramide-dependent signaling branch that impairs vacuolar function and vesicular trafficking, leading to autophagic defects in yeast.
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Affiliation(s)
- Vitor Teixeira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen s/n, 4200-135 Porto, Portugal; IBMC, Instituto de Biologia Molecular e Celular, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Departamento de Biologia Molecular, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Tânia C Medeiros
- IBMC, Instituto de Biologia Molecular e Celular, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Rita Vilaça
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen s/n, 4200-135 Porto, Portugal; IBMC, Instituto de Biologia Molecular e Celular, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - João Ferreira
- IBMC, Instituto de Biologia Molecular e Celular, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Pedro Moradas-Ferreira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen s/n, 4200-135 Porto, Portugal; IBMC, Instituto de Biologia Molecular e Celular, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Departamento de Biologia Molecular, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Vítor Costa
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen s/n, 4200-135 Porto, Portugal; IBMC, Instituto de Biologia Molecular e Celular, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Departamento de Biologia Molecular, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
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457
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Russell CW, Poliakov A, Haribal M, Jander G, van Wijk KJ, Douglas AE. Matching the supply of bacterial nutrients to the nutritional demand of the animal host. Proc Biol Sci 2015; 281:20141163. [PMID: 25080346 DOI: 10.1098/rspb.2014.1163] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Various animals derive nutrients from symbiotic microorganisms with much-reduced genomes, but it is unknown whether, and how, the supply of these nutrients is regulated. Here, we demonstrate that the production of essential amino acids (EAAs) by the bacterium Buchnera aphidicola in the pea aphid Acyrthosiphon pisum is elevated when aphids are reared on diets from which that EAA are omitted, demonstrating that Buchnera scale EAA production to host demand. Quantitative proteomics of bacteriocytes (host cells bearing Buchnera) revealed that these metabolic changes are not accompanied by significant change in Buchnera or host proteins, suggesting that EAA production is regulated post-translationally. Bacteriocytes in aphids reared on diet lacking the EAA methionine had elevated concentrations of both methionine and the precursor cystathionine, indicating that methionine production is promoted by precursor supply and is not subject to feedback inhibition by methionine. Furthermore, methionine production by isolated Buchnera increased with increasing cystathionine concentration. We propose that Buchnera metabolism is poised for EAA production at certain maximal rates, and the realized release rate is determined by precursor supply from the host. The incidence of host regulation of symbiont nutritional function via supply of key nutritional inputs in other symbioses remains to be investigated.
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Affiliation(s)
- Calum W Russell
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA
| | - Anton Poliakov
- Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Meena Haribal
- Boyce Thompson Institute, Tower Road, Ithaca, NY 14853, USA
| | - Georg Jander
- Boyce Thompson Institute, Tower Road, Ithaca, NY 14853, USA
| | - Klaas J van Wijk
- Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Angela E Douglas
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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458
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Stauffer B, Powers T. Target of rapamycin signaling mediates vacuolar fission caused by endoplasmic reticulum stress in Saccharomyces cerevisiae. Mol Biol Cell 2015; 26:4618-30. [PMID: 26466677 PMCID: PMC4678019 DOI: 10.1091/mbc.e15-06-0344] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 10/07/2015] [Indexed: 01/15/2023] Open
Abstract
The yeast vacuole is equivalent to the mammalian lysosome and, in response to diverse physiological and environmental stimuli, undergoes alterations both in size and number. Here we demonstrate that vacuoles fragment in response to stress within the endoplasmic reticulum (ER) caused by chemical or genetic perturbations. We establish that this response does not involve known signaling pathways linked previously to ER stress but instead requires the rapamycin-sensitive TOR Complex 1 (TORC1), a master regulator of cell growth, together with its downstream effectors, Tap42/Sit4 and Sch9. To identify additional factors required for ER stress-induced vacuolar fragmentation, we conducted a high-throughput, genome-wide visual screen for yeast mutants that are refractory to ER stress-induced changes in vacuolar morphology. We identified several genes shown previously to be required for vacuolar fusion and/or fission, validating the utility of this approach. We also identified a number of new components important for fragmentation, including a set of proteins involved in assembly of the V-ATPase. Remarkably, we find that one of these, Vph2, undergoes a change in intracellular localization in response to ER stress and, moreover, in a manner that requires TORC1 activity. Together these results reveal a new role for TORC1 in the regulation of vacuolar behavior.
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Affiliation(s)
- Bobbiejane Stauffer
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, CA 95616
| | - Ted Powers
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, CA 95616 )
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459
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Hughes Hallett JE, Luo X, Capaldi AP. Snf1/AMPK promotes the formation of Kog1/Raptor-bodies to increase the activation threshold of TORC1 in budding yeast. eLife 2015; 4. [PMID: 26439012 PMCID: PMC4686425 DOI: 10.7554/elife.09181] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/05/2015] [Indexed: 01/01/2023] Open
Abstract
The target of rapamycin complex I (TORC1) regulates cell growth and metabolism in eukaryotes. Previous studies have shown that nitrogen and amino acid signals activate TORC1 via the small GTPases, Gtr1/2. However, little is known about the way that other nutrient signals are transmitted to TORC1. Here we report that glucose starvation triggers disassembly of TORC1, and movement of the key TORC1 component Kog1/Raptor to a single body near the edge of the vacuole. These events are driven by Snf1/AMPK-dependent phosphorylation of Kog1 at Ser 491/494 and two nearby prion-like motifs. Kog1-bodies then serve to increase the threshold for TORC1 activation in cells that have been starved for a significant period of time. Together, our data show that Kog1-bodies create hysteresis (memory) in the TORC1 pathway and help ensure that cells remain committed to a quiescent state under suboptimal conditions. We suggest that other protein bodies formed in starvation conditions have a similar function. DOI:http://dx.doi.org/10.7554/eLife.09181.001 In humans, yeast and other eukaryotes, a group of proteins called the Target of Rapamycin Complex I (TORC1) promote cell growth and increase metabolic activity when nutrients are plentiful. Previous studies have shown how molecules that contain the nutrient nitrogen – which is needed to make proteins – activate TORC1. However, it is not clear how other nutrients regulate this complex. Bakers yeast is a simple, single celled organism that researchers often use as a model to study how cells work. The yeast TORC1 is made up of three core proteins, including Kog1 and Tor1. Kog1 selectively recruits proteins to the complex, where they are modified by Tor1 to regulate their activity. Here, Hughes Hallett et al. used microscopy to study what effect sugar starvation has on the complex. In the experiments, yeast cells were genetically engineered so that Kog1 and Tor1 appeared fluorescent under the microscope. The experiments reveal that, when sugar is in short supply, Kog1 breaks away from the rest of the TORC1 and moves to another part of the cell where it accumulates to form a cluster called a “body”. This movement is driven by a “kinase” enzyme that adds chemical groups called phosphates to Kog1, and by regions within the Kog1 protein known as prion like domains. When sugar first becomes available again, Kog1 is still in the body so Tor1 cannot immediately trigger cell growth. However, once a steady supply of sugar resumes, Kog1 rejoins the rest of the complex and the cells start to grow. Together, Hughes Hallett et al.’s findings reveal that the formation of Kog1 bodies during sugar starvation creates a “memory” that prevents TORC1 from reactivating cell growth if sugar is only temporarily available. Humans have over 100 proteins that contain prion like domains. Therefore a future challenge is to find out whether any of these proteins form similar bodies that enable our cells to remember past events. DOI:http://dx.doi.org/10.7554/eLife.09181.002
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Affiliation(s)
- James E Hughes Hallett
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, United States
| | - Xiangxia Luo
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, United States
| | - Andrew P Capaldi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, United States
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460
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Imamura S, Kawase Y, Kobayashi I, Sone T, Era A, Miyagishima SY, Shimojima M, Ohta H, Tanaka K. Target of rapamycin (TOR) plays a critical role in triacylglycerol accumulation in microalgae. PLANT MOLECULAR BIOLOGY 2015; 89:309-18. [PMID: 26350402 DOI: 10.1007/s11103-015-0370-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/24/2015] [Indexed: 05/18/2023]
Abstract
Most microalgae produce triacylglycerol (TAG) under stress conditions such as nitrogen depletion, but the underlying molecular mechanism remains unclear. In this study, we focused on the role of target of rapamycin (TOR) in TAG accumulation. TOR is a serine/threonine protein kinase that is highly conserved and plays pivotal roles in nitrogen and other signaling pathways in eukaryotes. We previously constructed a rapamycin-susceptible Cyanidioschyzon merolae, a unicellular red alga, by expressing yeast FKBP12 protein to evaluate the results of TOR inhibition (Imamura et al. in Biochem Biophys Res Commun 439:264-269, 2013). By using this strain, we here report that rapamycin-induced TOR inhibition results in accumulation of cytoplasmic lipid droplets containing TAG. Transcripts for TAG synthesis-related genes, such as glycerol-3-phosphate acyltransferase and acyl-CoA:diacylglycerol acyltransferase (DGAT), were increased by rapamycin treatment. We also found that fatty acid synthase-dependent de novo fatty acid synthesis was required for the accumulation of lipid droplets. Induction of TAG and up-regulation of DGAT gene expression by rapamycin were similarly observed in the unicellular green alga, Chlamydomonas reinhardtii. These results suggest the general involvement of TOR signaling in TAG accumulation in divergent microalgae.
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Affiliation(s)
- Sousuke Imamura
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan.
| | - Yasuko Kawase
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Ikki Kobayashi
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Toshiyuki Sone
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Atsuko Era
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan
- Department of Cell Genetics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Shin-Ya Miyagishima
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan
- Department of Cell Genetics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Mie Shimojima
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B1 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan
| | - Hiroyuki Ohta
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B1 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Kan Tanaka
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan.
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461
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Smykal V, Raikhel AS. Nutritional Control of Insect Reproduction. CURRENT OPINION IN INSECT SCIENCE 2015; 11:31-38. [PMID: 26644995 PMCID: PMC4669899 DOI: 10.1016/j.cois.2015.08.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The amino acid-Target of Rapamycin (AA/TOR) and insulin pathways play a pivotal role in reproduction of female insects, serving as regulatory checkpoints that guarantee the sufficiency of nutrients for developing eggs. Being evolutionary older, the AA/TOR pathway functions as an initial nutritional sensor that not only activates nutritional responses in a tissue-specific manner, but is also involved in the control of insect insulin-like peptides (ILPs) secretion. Insulin and AA/TOR pathways also assert their nutritionally linked influence on reproductive events by contributing to the control of biosynthesis and secretion of juvenile hormone and ecdysone. This review covers the present status of our understanding of the contributions of AA/TOR and insulin pathways in insect reproduction.
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Affiliation(s)
| | - Alexander S. Raikhel
- Corresponding author. Department of Entomology, University of California Riverside, Riverside, CA 92521, USA. Tel.: 951 827 2129
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462
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Katz ME, Buckland R, Hunter CC, Todd RB. Distinct roles for the p53-like transcription factor XprG and autophagy genes in the response to starvation. Fungal Genet Biol 2015; 83:10-18. [DOI: 10.1016/j.fgb.2015.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 08/13/2015] [Accepted: 08/17/2015] [Indexed: 12/21/2022]
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463
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Liko D, Hall MN. mTOR in health and in sickness. J Mol Med (Berl) 2015; 93:1061-73. [DOI: 10.1007/s00109-015-1326-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/14/2015] [Accepted: 07/22/2015] [Indexed: 01/12/2023]
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464
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Mohindra NA, Platanias LC. Catalytic mammalian target of rapamycin inhibitors as antineoplastic agents. Leuk Lymphoma 2015; 56:2518-23. [DOI: 10.3109/10428194.2015.1026816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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465
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Gil-Bona A, Monteoliva L, Gil C. Global Proteomic Profiling of the Secretome of Candida albicans ecm33 Cell Wall Mutant Reveals the Involvement of Ecm33 in Sap2 Secretion. J Proteome Res 2015; 14:4270-81. [DOI: 10.1021/acs.jproteome.5b00411] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Ana Gil-Bona
- Departamento de
Microbiología
II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón
y Cajal s/n, 28040 Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. de Colmenar Viejo, 28034 Madrid, Spain
| | - Lucía Monteoliva
- Departamento de
Microbiología
II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón
y Cajal s/n, 28040 Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. de Colmenar Viejo, 28034 Madrid, Spain
| | - Concha Gil
- Departamento de
Microbiología
II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón
y Cajal s/n, 28040 Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. de Colmenar Viejo, 28034 Madrid, Spain
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466
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Chowdhury T, Köhler JR. Ribosomal protein S6 phosphorylation is controlled by TOR and modulated by PKA in Candida albicans. Mol Microbiol 2015; 98:384-402. [PMID: 26173379 DOI: 10.1111/mmi.13130] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2015] [Indexed: 12/25/2022]
Abstract
TOR and PKA signaling pathways control eukaryotic cell growth and proliferation. TOR activity in model fungi, such as Saccharomyces cerevisiae, responds principally to nutrients, e.g., nitrogen and phosphate sources, which are incorporated into the growing cell mass; PKA signaling responds to the availability of the cells' major energy source, glucose. In the fungal commensal and pathogen, Candida albicans, little is known of how these pathways interact. Here, the signal from phosphorylated ribosomal protein S6 (P-S6) was defined as a surrogate marker for TOR-dependent anabolic activity in C. albicans. Nutritional, pharmacologic and genetic modulation of TOR activity elicited corresponding changes in P-S6 levels. The P-S6 signal corresponded to translational activity of a GFP reporter protein. Contributions of four PKA pathway components to anabolic activation were then examined. In high glucose concentrations, only Tpk2 was required to upregulate P-S6 to physiologic levels, whereas all four tested components were required to downregulate P-S6 in low glucose. TOR was epistatic to PKA components with respect to P-S6. In many host niches inhabited by C. albicans, glucose is scarce, with protein being available as a nitrogen source. We speculate that PKA may modulate TOR-dependent cell growth to a rate sustainable by available energy sources, when monomers of anabolic processes, such as amino acids, are abundant.
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Affiliation(s)
- Tahmeena Chowdhury
- Division of Infectious Diseases, Boston Children's Hospital/Harvard Medical School, Boston, MA, 02115, USA
| | - Julia R Köhler
- Division of Infectious Diseases, Boston Children's Hospital/Harvard Medical School, Boston, MA, 02115, USA
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467
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Spatial Regulation of Root Growth: Placing the Plant TOR Pathway in a Developmental Perspective. Int J Mol Sci 2015; 16:19671-97. [PMID: 26295391 PMCID: PMC4581319 DOI: 10.3390/ijms160819671] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 07/11/2015] [Accepted: 08/11/2015] [Indexed: 12/30/2022] Open
Abstract
Plant cells contain specialized structures, such as a cell wall and a large vacuole, which play a major role in cell growth. Roots follow an organized pattern of development, making them the organs of choice for studying the spatio-temporal regulation of cell proliferation and growth in plants. During root growth, cells originate from the initials surrounding the quiescent center, proliferate in the division zone of the meristem, and then increase in length in the elongation zone, reaching their final size and differentiation stage in the mature zone. Phytohormones, especially auxins and cytokinins, control the dynamic balance between cell division and differentiation and therefore organ size. Plant growth is also regulated by metabolites and nutrients, such as the sugars produced by photosynthesis or nitrate assimilated from the soil. Recent literature has shown that the conserved eukaryotic TOR (target of rapamycin) kinase pathway plays an important role in orchestrating plant growth. We will summarize how the regulation of cell proliferation and cell expansion by phytohormones are at the heart of root growth and then discuss recent data indicating that the TOR pathway integrates hormonal and nutritive signals to orchestrate root growth.
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468
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TORC1 activity is partially reduced under nitrogen starvation conditions in sake yeast Kyokai no. 7, Saccharomyces cerevisiae. J Biosci Bioeng 2015; 121:247-52. [PMID: 26272416 DOI: 10.1016/j.jbiosc.2015.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 06/30/2015] [Accepted: 07/07/2015] [Indexed: 11/21/2022]
Abstract
Industrial yeasts are generally unable to sporulate but treatment with the immunosuppressive drug rapamycin restores this ability in a sake yeast strain Kyokai no. 7 (K7), Saccharomyces cerevisiae. This finding suggests that TORC1 is active under sporulation conditions. Here, using a reporter gene assay, Northern and Western blots, we tried to gain insight into how TORC1 function under nitrogen starvation conditions in K7 cells. Similarly to a laboratory strain, RPS26A transcription was repressed and Npr1 was dephosphorylated in K7 cells, indicative of the expected loss of TORC1 function under nitrogen starvation. The expression of nitrogen catabolite repression-sensitive genes, however, was not induced, the level of Cln3 remained constant, and autophagy was more slowly induced than in a laboratory strain, all suggestive of active TORC1. We conclude that TORC1 activity is partially reduced under nitrogen starvation conditions in K7 cells.
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469
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Mohindra N, Agulnik M. Targeted therapy and promising novel agents for the treatment of advanced soft tissue sarcomas. Expert Opin Investig Drugs 2015; 24:1409-18. [PMID: 26289790 DOI: 10.1517/13543784.2015.1076792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Soft tissue sarcomas (STS) are a rare and difficult to treat malignancy. Efforts to utilize targeted therapy have been ongoing for the last decade and have resulted in the approval of pazopanib for treatment of advanced disease. Although several other agents have been investigated, the inability to predict responses remains a limiting factor to the incorporation of these agents into treatment. AREAS COVERED The authors summarize recent clinical findings from studies focused on targeted agents in STS. The authors also discuss the potential approaches and ongoing clinical trials with novel agents. EXPERT OPINION A major challenge in the treatment of advanced STS remains a lack of predictive biomarkers to guide therapy and the heterogeneity of response among different histologies of sarcoma. Incorporation of predictive biomarker analysis into clinical trials is warranted. Additionally, mechanisms of treatment resistance and parallel pathways of tumor growth pose challenges in how we treat these tumors. An active area of research in STS is the use of novel combinations of agents, such as chemotherapy combined with multi-targeted agents. The potential of immune check point inhibitors is being explored in advanced STS and is hoped to further expand our treatment armamentarium.
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Affiliation(s)
- Nisha Mohindra
- a 1 Northwestern University Feinberg School of Medicine, Robert H. Lurie Comprehensive Cancer Center, Division of Hematology/Oncology , Chicago, IL, USA
| | - Mark Agulnik
- b 2 Northwestern University Feinberg School of Medicine, Robert H. Lurie Comprehensive Cancer Center, Division of Hematology/Oncology , 676 North St. Clair Street, Suite 850, Chicago, IL 60611, USA +1 31 2695 1222 ; +1 31 2695 6189 ;
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470
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Castillo-Quan JI, Kinghorn KJ, Bjedov I. Genetics and pharmacology of longevity: the road to therapeutics for healthy aging. ADVANCES IN GENETICS 2015; 90:1-101. [PMID: 26296933 DOI: 10.1016/bs.adgen.2015.06.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Aging can be defined as the progressive decline in tissue and organismal function and the ability to respond to stress that occurs in association with homeostatic failure and the accumulation of molecular damage. Aging is the biggest risk factor for human disease and results in a wide range of aging pathologies. Although we do not completely understand the underlying molecular basis that drives the aging process, we have gained exceptional insights into the plasticity of life span and healthspan from the use of model organisms such as the worm Caenorhabditis elegans and the fruit fly Drosophila melanogaster. Single-gene mutations in key cellular pathways that regulate environmental sensing, and the response to stress, have been identified that prolong life span across evolution from yeast to mammals. These genetic manipulations also correlate with a delay in the onset of tissue and organismal dysfunction. While the molecular genetics of aging will remain a prosperous and attractive area of research in biogerontology, we are moving towards an era defined by the search for therapeutic drugs that promote healthy aging. Translational biogerontology will require incorporation of both therapeutic and pharmacological concepts. The use of model organisms will remain central to the quest for drug discovery, but as we uncover molecular processes regulated by repurposed drugs and polypharmacy, studies of pharmacodynamics and pharmacokinetics, drug-drug interactions, drug toxicity, and therapeutic index will slowly become more prevalent in aging research. As we move from genetics to pharmacology and therapeutics, studies will not only require demonstration of life span extension and an underlying molecular mechanism, but also the translational relevance for human health and disease prevention.
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Affiliation(s)
- Jorge Iván Castillo-Quan
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK; Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Kerri J Kinghorn
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK; Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Ivana Bjedov
- Cancer Institute, University College London, London, UK
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471
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Leontieva OV, Paszkiewicz GM, Blagosklonny MV. Fasting levels of hepatic p-S6 are increased in old mice. Cell Cycle 2015; 13:2656-9. [PMID: 25486351 DOI: 10.4161/15384101.2014.949150] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
TOR is involved in aging in a wide range of species from yeast to mammals. Here we show that, after overnight fasting, mTOR activity is higher in the livers of 28 months old female mice compared with middle-aged mice. Taken together with previous reports, our data predict that the life-extending effect of calorie restriction (CR) may be diminished, if CR is started in very old age. In contrast, rapamycin is known to be effective, even when started late in life.
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Affiliation(s)
- Olga V Leontieva
- a Cell Stress Biology; Roswell Park Cancer Institute ; Buffalo , NY USA
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472
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Wang W, He Q, Guo Z, Yang L, Bao L, Bao W, Zheng X, Wang Y, Wang Z. Inhibition of Mammalian Target of Rapamycin Complex 1 (mTORC1) Downregulates ELOVL1 Gene Expression and Fatty Acid Synthesis in Goat Fetal Fibroblasts. Int J Mol Sci 2015. [PMID: 26204830 PMCID: PMC4519958 DOI: 10.3390/ijms160716440] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Elongation of very-long-chain fatty acids 1 (ELOVL1) is a ubiquitously expressed gene that belongs to the ELOVL family and regulates the synthesis of very-long-chain fatty acids (VLCFAs) and sphingolipids, from yeast to mammals. Mammalian target of rapamycin complex 1 (mTORC1) is a central regulator of cell metabolism and is associated with fatty acids synthesis. In this study, we cloned the cDNA that encodes Cashmere goat (Capra hircus) ELOVL1 (GenBank Accession number KF549985) and investigated its expression in 10 tissues. ELOVL1 cDNA was 840 bp, encoding a deduced protein of 279 amino acids, and ELOVL1 mRNA was expressed in a wide range of tissues. Inhibition of mTORC1 by rapamycin decreased ELOVL1 expression and fatty acids synthesis in Cashmere goat fetal fibroblasts. These data show that ELOVL1 expression is regulated by mTORC1 and that mTORC1 has significant function in fatty acids synthesis in Cashmere goat.
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Affiliation(s)
- Weipeng Wang
- College of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
| | - Qiburi He
- College of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
| | - Zhixin Guo
- College of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
| | - Limin Yang
- College of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
| | - Lili Bao
- College of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
- College of Basic Medical Science, Inner Mongolia Medical University, Hohhot 010110, China.
| | - Wenlei Bao
- College of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
| | - Xu Zheng
- College of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
- Hulunbeir Municipal People's Hospital, Hailar 021008, China.
| | - Yanfeng Wang
- College of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
| | - Zhigang Wang
- College of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
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473
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Abstract
Repeated regions are widespread in eukaryotic genomes, and key functional elements such as the ribosomal DNA tend to be formed of high copy repeated sequences organized in tandem arrays. In general, high copy repeats are remarkably stable, but a number of organisms display rapid ribosomal DNA amplification at specific times or under specific conditions. Here we demonstrate that target of rapamycin (TOR) signaling stimulates ribosomal DNA amplification in budding yeast, linking external nutrient availability to ribosomal DNA copy number. We show that ribosomal DNA amplification is regulated by three histone deacetylases: Sir2, Hst3, and Hst4. These enzymes control homologous recombination-dependent and nonhomologous recombination-dependent amplification pathways that act in concert to mediate rapid, directional ribosomal DNA copy number change. Amplification is completely repressed by rapamycin, an inhibitor of the nutrient-responsive TOR pathway; this effect is separable from growth rate and is mediated directly through Sir2, Hst3, and Hst4. Caloric restriction is known to up-regulate expression of nicotinamidase Pnc1, an enzyme that enhances Sir2, Hst3, and Hst4 activity. In contrast, normal glucose concentrations stretch the ribosome synthesis capacity of cells with low ribosomal DNA copy number, and we find that these cells show a previously unrecognized transcriptional response to caloric excess by reducing PNC1 expression. PNC1 down-regulation forms a key element in the control of ribosomal DNA amplification as overexpression of PNC1 substantially reduces ribosomal DNA amplification rate. Our results reveal how a signaling pathway can orchestrate specific genome changes and demonstrate that the copy number of repetitive DNA can be altered to suit environmental conditions.
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474
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Calap-Quintana P, Soriano S, Llorens JV, Al-Ramahi I, Botas J, Moltó MD, Martínez-Sebastián MJ. TORC1 Inhibition by Rapamycin Promotes Antioxidant Defences in a Drosophila Model of Friedreich's Ataxia. PLoS One 2015; 10:e0132376. [PMID: 26158631 PMCID: PMC4497667 DOI: 10.1371/journal.pone.0132376] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/14/2015] [Indexed: 12/22/2022] Open
Abstract
Friedreich's ataxia (FRDA), the most common inherited ataxia in the Caucasian population, is a multisystemic disease caused by a significant decrease in the frataxin level. To identify genes capable of modifying the severity of the symptoms of frataxin depletion, we performed a candidate genetic screen in a Drosophila RNAi-based model of FRDA. We found that genetic reduction in TOR Complex 1 (TORC1) signalling improves the impaired motor performance phenotype of FRDA model flies. Pharmacologic inhibition of TORC1 signalling by rapamycin also restored this phenotype and increased the lifespan and ATP levels. Furthermore, rapamycin reduced the altered levels of malondialdehyde + 4-hydroxyalkenals and total glutathione of the model flies. The rapamycin-mediated protection against oxidative stress is due in part to an increase in the transcription of antioxidant genes mediated by cap-n-collar (Drosophila ortholog of Nrf2). Our results suggest that autophagy is indeed necessary for the protective effect of rapamycin in hyperoxia. Rapamycin increased the survival and aconitase activity of model flies subjected to high oxidative insult, and this improvement was abolished by the autophagy inhibitor 3-methyladenine. These results point to the TORC1 pathway as a new potential therapeutic target for FRDA and as a guide to finding new promising molecules for disease treatment.
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Affiliation(s)
| | - Sirena Soriano
- Department of Genetics, University of Valencia, Burjassot, Valencia, Spain
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | | | - Ismael Al-Ramahi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Juan Botas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - María Dolores Moltó
- Department of Genetics, University of Valencia, Burjassot, Valencia, Spain
- CIBERSAM, INCLIVA, Valencia, Spain
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475
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Dibble CC, Cantley LC. Regulation of mTORC1 by PI3K signaling. Trends Cell Biol 2015; 25:545-55. [PMID: 26159692 DOI: 10.1016/j.tcb.2015.06.002] [Citation(s) in RCA: 559] [Impact Index Per Article: 62.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 06/08/2015] [Accepted: 06/08/2015] [Indexed: 11/29/2022]
Abstract
The class I phosphoinositide 3-kinase (PI3K)-mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) signaling network directs cellular metabolism and growth. Activation of mTORC1 [composed of mTOR, regulatory-associated protein of mTOR (Raptor), mammalian lethal with SEC13 protein 8(mLST8), 40-kDa proline-rich Akt substrate (PRAS40), and DEP domain-containing mTOR-interacting protein (DEPTOR)] depends on the Ras-related GTPases (Rags) and Ras homolog enriched in brain (Rheb) GTPase and requires signals from amino acids, glucose, oxygen, energy (ATP), and growth factors (including cytokines and hormones such as insulin). Here we discuss the signal transduction mechanisms through which growth factor-responsive PI3K signaling activates mTORC1. We focus on how PI3K-dependent activation of Akt and spatial regulation of the tuberous sclerosis complex (TSC) complex (TSC complex) [composed of TSC1, TSC2, and Tre2-Bub2-Cdc16-1 domain family member 7 (TBC1D7)] switches on Rheb at the lysosome, where mTORC1 is activated. Integration of PI3K- and amino acid-dependent signals upstream of mTORC1 at the lysosome is detailed in a working model. A coherent understanding of the PI3K-mTORC1 network is imperative as its dysregulation has been implicated in diverse pathologies including cancer, diabetes, autism, and aging.
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Affiliation(s)
- Christian C Dibble
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA.
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476
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Peng B, Williams TC, Henry M, Nielsen LK, Vickers CE. Controlling heterologous gene expression in yeast cell factories on different carbon substrates and across the diauxic shift: a comparison of yeast promoter activities. Microb Cell Fact 2015; 14:91. [PMID: 26112740 PMCID: PMC4480987 DOI: 10.1186/s12934-015-0278-5] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 06/01/2015] [Indexed: 11/10/2022] Open
Abstract
Background Predictable control of gene expression is necessary for the rational design and optimization of cell factories. In the yeast Saccharomyces cerevisiae, the promoter is one of the most important tools available for controlling gene expression. However, the complex expression patterns of yeast promoters have not been fully characterised and compared on different carbon sources (glucose, sucrose, galactose and ethanol) and across the diauxic shift in glucose batch cultivation. These conditions are of importance to yeast cell factory design because they are commonly used and encountered in industrial processes. Here, the activities of a series of “constitutive” and inducible promoters were characterised in single cells throughout the fermentation using green fluorescent protein (GFP) as a reporter. Results The “constitutive” promoters, including glycolytic promoters, transcription elongation factor promoters and ribosomal promoters, differed in their response patterns to different carbon sources; however, in glucose batch cultivation, expression driven by these promoters decreased sharply as glucose was depleted and cells moved towards the diauxic shift. Promoters induced at low-glucose levels (PHXT7, PSSA1 and PADH2) varied in induction strength on non-glucose carbon sources (sucrose, galactose and ethanol); in contrast to the “constitutive” promoters, GFP expression increased as glucose decreased and cells moved towards the diauxic shift. While lower than several “constitutive” promoters during the exponential phase, expression from the SSA1 promoter was higher in the post-diauxic phase than the commonly-used TEF1 promoter. The galactose-inducible GAL1 promoter provided the highest GFP expression on galactose, and the copper-inducible CUP1 promoter provided the highest induced GFP expression following the diauxic shift. Conclusions The data provides a foundation for predictable and optimised control of gene expression levels on different carbon sources and throughout batch fermentation, including during and after the diauxic shift. This information can be applied for designing expression approaches to improve yields, rates and titres in yeast cell factories. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0278-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bingyin Peng
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Thomas C Williams
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Matthew Henry
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
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477
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Abstract
The ubiquitin family member Sumo has important functions in many cellular processes including DNA repair, transcription and cell division. Numerous studies have shown that Sumo is essential for maintaining cell homeostasis when the cell encounters endogenous or environmental stress, such as osmotic stress, hypoxia, heat shock, genotoxic stress, and nutrient stress. Regulation of transcription is a key component of the Sumo stress response, and multiple mechanisms have been described by which Sumo can regulate transcription. Although many individual substrates have been described that are sumoylated during the Sumo stress response, an emerging concept is modification of entire complexes or pathways by Sumo. This review focuses on the function and regulation of Sumo during the stress response.
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Affiliation(s)
- Jorrit M Enserink
- Institute for Microbiology, Oslo University Hospital, Sognsvannsveien 20N-0027, Oslo, Norway
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478
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Jevtov I, Zacharogianni M, van Oorschot MM, van Zadelhoff G, Aguilera-Gomez A, Vuillez I, Braakman I, Hafen E, Stocker H, Rabouille C. TORC2 mediates the heat stress response in Drosophila by promoting the formation of stress granules. J Cell Sci 2015; 128:2497-508. [PMID: 26054799 PMCID: PMC4510851 DOI: 10.1242/jcs.168724] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 06/03/2015] [Indexed: 12/29/2022] Open
Abstract
The kinase TOR is found in two complexes, TORC1, which is involved in growth control, and TORC2, whose roles are less well defined. Here, we asked whether TORC2 has a role in sustaining cellular stress. We show that TORC2 inhibition in Drosophila melanogaster leads to a reduced tolerance to heat stress, whereas sensitivity to other stresses is not affected. Accordingly, we show that upon heat stress, both in the animal and Drosophila cultured S2 cells, TORC2 is activated and is required for maintaining the level of its known target, Akt1 (also known as PKB). We show that the phosphorylation of the stress-activated protein kinases is not modulated by TORC2 nor is the heat-induced upregulation of heat-shock proteins. Instead, we show, both in vivo and in cultured cells, that TORC2 is required for the assembly of heat-induced cytoprotective ribonucleoprotein particles, the pro-survival stress granules. These granules are formed in response to protein translation inhibition imposed by heat stress that appears to be less efficient in the absence of TORC2 function. We propose that TORC2 mediates heat resistance in Drosophila by promoting the cell autonomous formation of stress granules.
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Affiliation(s)
- Irena Jevtov
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | | | - Marinke M van Oorschot
- Hubrecht Institute of the KNAW and UMC Utrecht, Uppsalalaan 8, Utrecht 3584 CT, Netherlands
| | - Guus van Zadelhoff
- Cellular Protein Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | | | - Igor Vuillez
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Ineke Braakman
- Cellular Protein Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Ernst Hafen
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Hugo Stocker
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Catherine Rabouille
- Hubrecht Institute of the KNAW and UMC Utrecht, Uppsalalaan 8, Utrecht 3584 CT, Netherlands Department of Cell Biology, UMC Utrecht, Heidelberglaan 100, Utrecht 3584 CX, The Netherlands
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479
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Ikeda A, Muneoka T, Murakami S, Hirota A, Yabuki Y, Karashima T, Nakazono K, Tsuruno M, Pichler H, Shirahige K, Kodama Y, Shimamoto T, Mizuta K, Funato K. Sphingolipids regulate telomere clustering by affecting the transcription of genes involved in telomere homeostasis. J Cell Sci 2015; 128:2454-67. [PMID: 26045446 DOI: 10.1242/jcs.164160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 05/20/2015] [Indexed: 12/14/2022] Open
Abstract
In eukaryotic organisms, including mammals, nematodes and yeasts, the ends of chromosomes, telomeres are clustered at the nuclear periphery. Telomere clustering is assumed to be functionally important because proper organization of chromosomes is necessary for proper genome function and stability. However, the mechanisms and physiological roles of telomere clustering remain poorly understood. In this study, we demonstrate a role for sphingolipids in telomere clustering in the budding yeast Saccharomyces cerevisiae. Because abnormal sphingolipid metabolism causes downregulation of expression levels of genes involved in telomere organization, sphingolipids appear to control telomere clustering at the transcriptional level. In addition, the data presented here provide evidence that telomere clustering is required to protect chromosome ends from DNA-damage checkpoint signaling. As sphingolipids are found in all eukaryotes, we speculate that sphingolipid-based regulation of telomere clustering and the protective role of telomere clusters in maintaining genome stability might be conserved in eukaryotes.
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Affiliation(s)
- Atsuko Ikeda
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Tetsuya Muneoka
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Suguru Murakami
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Ayaka Hirota
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Yukari Yabuki
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Takefumi Karashima
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Kota Nakazono
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Masahiro Tsuruno
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Harald Pichler
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14/2, Graz 8010, Austria
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Institute of Molecular and Cellular Biosciences, the University of Tokyo, Tokyo 113-0032, Japan
| | | | - Toshi Shimamoto
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Keiko Mizuta
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Kouichi Funato
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
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480
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Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis. Cell 2015; 161:1413-24. [DOI: 10.1016/j.cell.2015.04.051] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 02/05/2015] [Accepted: 04/09/2015] [Indexed: 02/06/2023]
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481
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Experimental and computational analysis of a large protein network that controls fat storage reveals the design principles of a signaling network. PLoS Comput Biol 2015; 11:e1004264. [PMID: 26020510 PMCID: PMC4447291 DOI: 10.1371/journal.pcbi.1004264] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 04/02/2015] [Indexed: 01/26/2023] Open
Abstract
An approach combining genetic, proteomic, computational, and physiological analysis was used to define a protein network that regulates fat storage in budding yeast (Saccharomyces cerevisiae). A computational analysis of this network shows that it is not scale-free, and is best approximated by the Watts-Strogatz model, which generates “small-world” networks with high clustering and short path lengths. The network is also modular, containing energy level sensing proteins that connect to four output processes: autophagy, fatty acid synthesis, mRNA processing, and MAP kinase signaling. The importance of each protein to network function is dependent on its Katz centrality score, which is related both to the protein’s position within a module and to the module’s relationship to the network as a whole. The network is also divisible into subnetworks that span modular boundaries and regulate different aspects of fat metabolism. We used a combination of genetics and pharmacology to simultaneously block output from multiple network nodes. The phenotypic results of this blockage define patterns of communication among distant network nodes, and these patterns are consistent with the Watts-Strogatz model. We discovered a large protein network that regulates fat storage in budding yeast. This network contains 94 proteins, almost all of which bind to other proteins in the network. To understand the functions of large protein collections such as these, it will be necessary to move away from one-by-one analysis of individual proteins and create computational models of entire networks. This will allow classification of networks into categories and permit researchers to identify key network proteins on theoretical grounds. We show here that the fat regulation network fits a Watts-Strogatz small-world model. This model was devised to explain the clustering phenomena often observed in real networks, but has not been previously applied to signaling networks within cells. The short path length and high clustering coefficients characteristic of the Watts-Strogatz topology allow for rapid communication between distant nodes and for division of the network into modules that perform different functions. The fat regulation network has modules, and it is divisible into subnetworks that span modular boundaries and regulate different aspects of fat metabolism. We experimentally examined communication between nodes within the network using a combination of genetics and pharmacology, and showed that the communication patterns are consistent with the Watts-Strogatz topology.
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482
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Gaubitz C, Oliveira TM, Prouteau M, Leitner A, Karuppasamy M, Konstantinidou G, Rispal D, Eltschinger S, Robinson GC, Thore S, Aebersold R, Schaffitzel C, Loewith R. Molecular Basis of the Rapamycin Insensitivity of Target Of Rapamycin Complex 2. Mol Cell 2015; 58:977-88. [PMID: 26028537 DOI: 10.1016/j.molcel.2015.04.031] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 03/31/2015] [Accepted: 04/22/2015] [Indexed: 10/23/2022]
Abstract
Target of Rapamycin (TOR) plays central roles in the regulation of eukaryote growth as the hub of two essential multiprotein complexes: TORC1, which is rapamycin-sensitive, and the lesser characterized TORC2, which is not. TORC2 is a key regulator of lipid biosynthesis and Akt-mediated survival signaling. In spite of its importance, its structure and the molecular basis of its rapamycin insensitivity are unknown. Using crosslinking-mass spectrometry and electron microscopy, we determined the architecture of TORC2. TORC2 displays a rhomboid shape with pseudo-2-fold symmetry and a prominent central cavity. Our data indicate that the C-terminal part of Avo3, a subunit unique to TORC2, is close to the FKBP12-rapamycin-binding domain of Tor2. Removal of this sequence generated a FKBP12-rapamycin-sensitive TORC2 variant, which provides a powerful tool for deciphering TORC2 function in vivo. Using this variant, we demonstrate a role for TORC2 in G2/M cell-cycle progression.
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Affiliation(s)
- Christl Gaubitz
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Taiana M Oliveira
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France; Fondation ARC, 9 rue Guy Môquet, BP 90003, 04803 Villejuif Cedex, France
| | - Manoel Prouteau
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Manikandan Karuppasamy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Georgia Konstantinidou
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Delphine Rispal
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Sandra Eltschinger
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Graham C Robinson
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Stéphane Thore
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland; University of Bordeaux, European Institute for Chemistry and Biology, ARNA Laboratory, F-33607 Pessac, France; Institut National de la Santé Et de la Recherche Médicale, INSERM-U869, ARNA Laboratory, F-33000, Bordeaux, France
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland; Faculty of Science, University of Zürich, 8057 Zürich, Switzerland
| | - Christiane Schaffitzel
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France; School of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom.
| | - Robbie Loewith
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland; National Centre of Competence in Research "Chemical Biology," University of Geneva, Geneva CH-1211, Switzerland.
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483
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Baldin C, Valiante V, Krüger T, Schafferer L, Haas H, Kniemeyer O, Brakhage AA. Comparative proteomics of a tor inducible Aspergillus fumigatus mutant reveals involvement of the Tor kinase in iron regulation. Proteomics 2015; 15:2230-43. [PMID: 25728394 DOI: 10.1002/pmic.201400584] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/27/2015] [Accepted: 02/24/2015] [Indexed: 01/20/2023]
Abstract
The Tor (target of rapamycin) kinase is one of the major regulatory nodes in eukaryotes. Here, we analyzed the Tor kinase in Aspergillus fumigatus, which is the most important airborne fungal pathogen of humans. Because deletion of the single tor gene was apparently lethal, we generated a conditional lethal tor mutant by replacing the endogenous tor gene by the inducible xylp-tor gene cassette. By both 2DE and gel-free LC-MS/MS, we found that Tor controls a variety of proteins involved in nutrient sensing, stress response, cell cycle progression, protein biosynthesis and degradation, but also processes in mitochondria, such as respiration and ornithine metabolism, which is required for siderophore formation. qRT-PCR analyses indicated that mRNA levels of ornithine biosynthesis genes were increased under iron limitation. When tor was repressed, iron regulation was lost. In a deletion mutant of the iron regulator HapX also carrying the xylp-tor cassette, the regulation upon iron deprivation was similar to that of the single tor inducible mutant strain. In line, hapX expression was significantly reduced when tor was repressed. Thus, Tor acts either upstream of HapX or independently of HapX as a repressor of the ornithine biosynthesis genes and thereby regulates the production of siderophores.
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Affiliation(s)
- Clara Baldin
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany.,Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Vito Valiante
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany
| | - Thomas Krüger
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany
| | - Lukas Schafferer
- Division of Molecular Biology, Biocenter, Innsbruck Medical University, Austria
| | - Hubertus Haas
- Division of Molecular Biology, Biocenter, Innsbruck Medical University, Austria
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI), Jena, Germany.,Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany
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484
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Sundaram V, Petkova MI, Pujol-Carrion N, Boada J, de la Torre-Ruiz MA. Tor1, Sch9 and PKA downregulation in quiescence rely on Mtl1 to preserve mitochondrial integrity and cell survival. Mol Microbiol 2015; 97:93-109. [DOI: 10.1111/mmi.13013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Venkatraghavan Sundaram
- Department of Basic Medical Sciences; IRB-Lleida; University of Lleida; Av. Alcalde Rovira Roure n° 80 25198 Lleida Spain
| | - Mima I. Petkova
- Department of Basic Medical Sciences; IRB-Lleida; University of Lleida; Av. Alcalde Rovira Roure n° 80 25198 Lleida Spain
| | - Nuria Pujol-Carrion
- Department of Basic Medical Sciences; IRB-Lleida; University of Lleida; Av. Alcalde Rovira Roure n° 80 25198 Lleida Spain
| | - Jordi Boada
- Department of Experimental Medicine; IRB-Lleida; University of Lleida; Av. Alcalde Rovira Roure n° 80 25198 Lleida Spain
| | - Maria Angeles de la Torre-Ruiz
- Department of Basic Medical Sciences; IRB-Lleida; University of Lleida; Av. Alcalde Rovira Roure n° 80 25198 Lleida Spain
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485
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Millson SH, Piper PW. Insights from yeast into whether the inhibition of heat shock transcription factor (Hsf1) by rapamycin can prevent the Hsf1 activation that results from treatment with an Hsp90 inhibitor. Oncotarget 2015; 5:5054-64. [PMID: 24970820 PMCID: PMC4148121 DOI: 10.18632/oncotarget.2077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In human cells TORC1 mTOR (target of rapamycin) protein kinase complex renders heat shock transcription factor 1 (Hsf1) competent for stress activation. In such cells, as well as in yeast, the selective TORC1 inhibitor rapamycin blocks this activation in contrast to Hsp90 inhibitors which potently activate Hsf1. Potentially therefore rapamycin could prevent the Hsf1 activation that frequently compromises the efficiency of Hsp90 inhibitor cancer drugs. Little synergy was found between the effects of rapamycin and the Hsp90 inhibitor radicicol on yeast growth. However certain rapamycin resistance mutations sensitised yeast to Hsp90 inhibitor treatment and an Hsp90 mutation that overactivates Hsf1 sensitised cells to rapamycin. Rapamycin inhibition of the yeast Hsf1 was abolished by this Hsp90 mutation, as well as with the loss of Ppt1, the Hsp90-interacting protein phosphatase that is the ortholog of mammalian PP5. Unexpectedly Hsf1 activation was found to have a requirement for the rapamycin binding immunophilin FKBP12 even in the absence of rapamycin, while TORC1 “bypass” strains revealed that the rapamycin inhibition of yeast Hsf1 is not exerted through two of the major downstream targets of TORC1, the protein phosphatase regulator Tap42 and the protein kinase Sch9 – the latter the ortholog of human S6 protein kinase 1. Significance: A problem with most of the Hsp90 inhibitor drugs now in cancer clinic trials is that they potently activate Hsf1. This leads to an induction of heat shock proteins, many of which have a “pro-survival” role in that they help to protect cells from apopotosis. As the activation of Hsf1 requires TORC1, inhibitors of mTOR kinase could potentially block this activation of Hsf1 and be of value when used in combination drug therapies with Hsp90 inhibitors. However many of the mechanistic details of the TORC1 regulation of Hsf1, as well as the interplay between cellular resistances to rapamycin and to Hsp90 inhibitors, still remain to be resolved.
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Affiliation(s)
- Stefan H Millson
- Dept. of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Peter W Piper
- Dept. of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, United Kingdom
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486
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Maegawa K, Takii R, Ushimaru T, Kozaki A. Evolutionary conservation of TORC1 components, TOR, Raptor, and LST8, between rice and yeast. Mol Genet Genomics 2015; 290:2019-30. [PMID: 25956502 DOI: 10.1007/s00438-015-1056-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 04/21/2015] [Indexed: 01/08/2023]
Abstract
Target of rapamycin (TOR) is a conserved eukaryotic serine/threonine kinase that functions as a central controller of cell growth. TOR protein is structurally defined by the presence several conserved domains such as the HEAT repeat, focal adhesion target (FAT), FKBP12/rapamycin binding (FRB), kinase, and FATC domains starting from the N-terminus. In most eukaryotes, TOR forms two distinct physical and functional complexes, which are termed as TOR complex 1 (TORC1) and TORC2. However, plants contain only TORC1 components, i.e., TOR, Raptor, and LST8. In this study, we analyzed the gene structure and functions of TORC components in rice to understand the properties of the TOR complex in plants. Comparison of the locations of introns in these genes among rice and other eukaryotes showed that they were well conserved among plants except for Chlamydomonas. Moreover, the intron positions in the coding sequence of human Raptor and LST8 were closer to those of plants than of fly or nematode. Complementation tests of rice TOR (OsTOR) components in yeast showed that although OsTOR did not complement yeast tor mutants, chimeric TOR, which consisted of the HEAT repeat and FAT domain from yeast and other regions from rice, rescued the tor mutants, indicating that the HEAT repeat and FAT domains are important for species-specific signaling. OsRaptor perfectly complemented a kog1 (yeast Raptor homolog) mutant, and OsLST8 partially complemented an lst8 mutant. Together, these data suggest the importance of the N-terminal region of the TOR, HEAT, and FAT domains for functional diversification of the TOR complex.
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Affiliation(s)
- Kentaro Maegawa
- Department of Biology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka, 422-8529, Japan
| | - Rumi Takii
- Department of Biology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka, 422-8529, Japan
| | - Takashi Ushimaru
- Department of Biology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka, 422-8529, Japan
| | - Akiko Kozaki
- Department of Biology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka, 422-8529, Japan.
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487
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Dokudovskaya S, Rout MP. SEA you later alli-GATOR--a dynamic regulator of the TORC1 stress response pathway. J Cell Sci 2015; 128:2219-28. [PMID: 25934700 DOI: 10.1242/jcs.168922] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cells constantly adapt to various environmental changes and stresses. The way in which nutrient and stress levels in a cell feed back to control metabolism and growth are, unsurprisingly, extremely complex, as responding with great sensitivity and speed to the 'feast or famine, slack or stress' status of its environment is a central goal for any organism. The highly conserved target of rapamycin complex 1 (TORC1) controls eukaryotic cell growth and response to a variety of signals, including nutrients, hormones and stresses, and plays the key role in the regulation of autophagy. A lot of attention has been paid recently to the factors in this pathway functioning upstream of TORC1. In this Commentary, we focus on a major, newly discovered upstream regulator of TORC1--the multiprotein SEA complex, also known as GATOR. We describe the structural and functional features of the yeast complex and its mammalian homolog, and their involvement in the regulation of the TORC1 pathway and TORC1-independent processes. We will also provide an overview of the consequences of GATOR deregulation in cancer and other diseases.
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Affiliation(s)
- Svetlana Dokudovskaya
- CNRS UMR 8126, Université Paris-Sud 11, Institut Gustave Roussy, 114, rue Edouard Vaillant, 94805, Villejuif, France
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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488
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489
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Oliveira AP, Ludwig C, Zampieri M, Weisser H, Aebersold R, Sauer U. Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis. Sci Signal 2015; 8:rs4. [PMID: 25921291 DOI: 10.1126/scisignal.2005768] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Phosphoproteomics studies have unraveled the extent of protein phosphorylation as a key cellular regulation mechanism, but assigning functionality to specific phosphorylation events remains a major challenge. TORC1 (target of rapamycin complex 1) is a kinase-containing protein complex that transduces changes in nutrient availability into phosphorylation signaling events that alter cell growth and proliferation. To resolve the temporal sequence of phosphorylation responses to nutritionally and chemically induced changes in TORC1 signaling and to identify previously unknown kinase-substrate relationships in Saccharomyces cerevisiae, we performed quantitative mass spectrometry-based phosphoproteomic analyses after shifts in nitrogen sources and rapamycin treatment. From early phosphorylation events that were consistent over at least two experimental perturbations, we identified 51 candidate and 10 known proximal targets of TORC1 that were direct substrates of TORC1 or of one of its kinase or phosphatase substrates. By correlating these phosphoproteomics data with dynamic metabolomics data, we inferred the functional role of phosphorylation on the metabolic activity of 12 enzymes, including three candidate TORC1-proximal targets: Amd1, which is involved in nucleotide metabolism; Hom3, which is involved in amino acid metabolism; and Tsl1, which mediates carbohydrate storage. Finally, we identified the TORC1 substrates Sch9 and Atg1 as candidate kinases that phosphorylate Amd1 and Hom3, respectively.
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Affiliation(s)
- Ana Paula Oliveira
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
| | - Christina Ludwig
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Mattia Zampieri
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Hendrik Weisser
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland. Faculty of Science, University of Zurich, 8057 Zurich, Switzerland
| | - Uwe Sauer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
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490
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Marroquin-Guzman M, Wilson RA. GATA-Dependent Glutaminolysis Drives Appressorium Formation in Magnaporthe oryzae by Suppressing TOR Inhibition of cAMP/PKA Signaling. PLoS Pathog 2015; 11:e1004851. [PMID: 25901357 PMCID: PMC4406744 DOI: 10.1371/journal.ppat.1004851] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 04/03/2015] [Indexed: 01/14/2023] Open
Abstract
Fungal plant pathogens are persistent and global food security threats. To invade their hosts they often form highly specialized infection structures, known as appressoria. The cAMP/ PKA- and MAP kinase-signaling cascades have been functionally delineated as positive-acting pathways required for appressorium development. Negative-acting regulatory pathways that block appressorial development are not known. Here, we present the first detailed evidence that the conserved Target of Rapamycin (TOR) signaling pathway is a powerful inhibitor of appressorium formation by the rice blast fungus Magnaporthe oryzae. We determined TOR signaling was activated in an M. oryzae mutant strain lacking a functional copy of the GATA transcription factor-encoding gene ASD4. Δasd4 mutant strains could not form appressoria and expressed GLN1, a glutamine synthetase-encoding orthologue silenced in wild type. Inappropriate expression of GLN1 increased the intracellular steady-state levels of glutamine in Δasd4 mutant strains during axenic growth when compared to wild type. Deleting GLN1 lowered glutamine levels and promoted appressorium formation by Δasd4 strains. Furthermore, glutamine is an agonist of TOR. Treating Δasd4 mutant strains with the specific TOR kinase inhibitor rapamycin restored appressorium development. Rapamycin was also shown to induce appressorium formation by wild type and Δcpka mutant strains on non-inductive hydrophilic surfaces but had no effect on the MAP kinase mutant Δpmk1. When taken together, we implicate Asd4 in regulating intracellular glutamine levels in order to modulate TOR inhibition of appressorium formation downstream of cPKA. This study thus provides novel insight into the metabolic mechanisms that underpin the highly regulated process of appressorium development. Many fungal pathogens destroy important crops by first gaining entrance to the host using specialized appressorial cells. Understanding the molecular mechanisms that control appressorium formation could provide new routes for managing severe plant diseases. Here, we describe a previously unknown regulatory pathway that suppresses appressorium formation by the rice pathogen Magnaporthe oryzae. We provide evidence that a mutant M. oryzae strain, unable to form appressoria, accumulates intracellular glutamine that, in turn, inappropriately activates a conserved signaling pathway called TOR. Reducing intracellular glutamine levels, or inactivating TOR, restored appressorium formation to the mutant strain. TOR activation is thus a powerful inhibitor of appressorium formation and could be leveraged to develop sustainable mitigation practices against recalcitrant fungal pathogens.
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Affiliation(s)
- Margarita Marroquin-Guzman
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Richard A. Wilson
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- * E-mail:
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491
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Müller M, Schmidt O, Angelova M, Faserl K, Weys S, Kremser L, Pfaffenwimmer T, Dalik T, Kraft C, Trajanoski Z, Lindner H, Teis D. The coordinated action of the MVB pathway and autophagy ensures cell survival during starvation. eLife 2015; 4:e07736. [PMID: 25902403 PMCID: PMC4424281 DOI: 10.7554/elife.07736] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 04/19/2015] [Indexed: 01/19/2023] Open
Abstract
The degradation and recycling of cellular components is essential for cell growth and survival. Here we show how selective and non-selective lysosomal protein degradation pathways cooperate to ensure cell survival upon nutrient limitation. A quantitative analysis of starvation-induced proteome remodeling in yeast reveals comprehensive changes already in the first three hours. In this period, many different integral plasma membrane proteins undergo endocytosis and degradation in vacuoles via the multivesicular body (MVB) pathway. Their degradation becomes essential to maintain critical amino acids levels that uphold protein synthesis early during starvation. This promotes cellular adaptation, including the de novo synthesis of vacuolar hydrolases to boost the vacuolar catabolic activity. This order of events primes vacuoles for the efficient degradation of bulk cytoplasm via autophagy. Hence, a catabolic cascade including the coordinated action of the MVB pathway and autophagy is essential to enter quiescence to survive extended periods of nutrient limitation.
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Affiliation(s)
- Martin Müller
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Oliver Schmidt
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Mihaela Angelova
- Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Klaus Faserl
- Division of Clinical Biochemistry, ProteinMicroAnalysis Facility, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Sabine Weys
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, ProteinMicroAnalysis Facility, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Thomas Dalik
- Department of Chemistry, University of Natural Resources and Applied Biosciences, Vienna, Austria
| | - Claudine Kraft
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Zlatko Trajanoski
- Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, ProteinMicroAnalysis Facility, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - David Teis
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
- Austrian Drug Screening Institute, Innsbruck, Austria
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492
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Andrukov BG, Somova LM, Timchenko NF. STRATEGY OF PROGRAMMED CELL DEATH IN PROKARYOTES. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2015. [DOI: 10.15789/2220-7619-2015-1-15-26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Programmed cell death (PCD) was first studied in eukaryotic organisms. This system also operates in the development life cycle of prokaryotes. The system PCD in microorganisms is activated a wide range of signals in response to the stresses associated with adverse environmental conditions or exposure to antibacterial agents. The results of numerous studies in the past decade allow considering the system PCD in prokaryotes as an evolutionary conservation of the species. These results significantly expanded understanding of the role of PCD in microorganisms and opened a number of important areas of research of the morphological and molecular genetic approaches to the study of death strategies for the survival in bacterial populations. The purpose of the review is to summarize the morphological and molecular genetic characteristics of PCD in prokaryotes which are real manifestations of the mechanisms of this phenomenon.
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493
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Oliveira AP, Dimopoulos S, Busetto AG, Christen S, Dechant R, Falter L, Haghir Chehreghani M, Jozefczuk S, Ludwig C, Rudroff F, Schulz JC, González A, Soulard A, Stracka D, Aebersold R, Buhmann JM, Hall MN, Peter M, Sauer U, Stelling J. Inferring causal metabolic signals that regulate the dynamic TORC1-dependent transcriptome. Mol Syst Biol 2015; 11:802. [PMID: 25888284 PMCID: PMC4422559 DOI: 10.15252/msb.20145475] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cells react to nutritional cues in changing environments via the integrated action of signaling, transcriptional, and metabolic networks. Mechanistic insight into signaling processes is often complicated because ubiquitous feedback loops obscure causal relationships. Consequently, the endogenous inputs of many nutrient signaling pathways remain unknown. Recent advances for system-wide experimental data generation have facilitated the quantification of signaling systems, but the integration of multi-level dynamic data remains challenging. Here, we co-designed dynamic experiments and a probabilistic, model-based method to infer causal relationships between metabolism, signaling, and gene regulation. We analyzed the dynamic regulation of nitrogen metabolism by the target of rapamycin complex 1 (TORC1) pathway in budding yeast. Dynamic transcriptomic, proteomic, and metabolomic measurements along shifts in nitrogen quality yielded a consistent dataset that demonstrated extensive re-wiring of cellular networks during adaptation. Our inference method identified putative downstream targets of TORC1 and putative metabolic inputs of TORC1, including the hypothesized glutamine signal. The work provides a basis for further mechanistic studies of nitrogen metabolism and a general computational framework to study cellular processes.
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Affiliation(s)
- Ana Paula Oliveira
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Sotiris Dimopoulos
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | | | - Stefan Christen
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Reinhard Dechant
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Laura Falter
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | - Szymon Jozefczuk
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Christina Ludwig
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Florian Rudroff
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Juliane Caroline Schulz
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | - Alexandre Soulard
- Biozentrum, University of Basel, Basel, Switzerland UMR5240 MAP, Université Lyon 1, Villeurbanne, France
| | | | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland Faculty of Science, University of Zurich, Zurich, Switzerland
| | | | | | - Matthias Peter
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Uwe Sauer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jörg Stelling
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
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494
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Rispal D, Eltschinger S, Stahl M, Vaga S, Bodenmiller B, Abraham Y, Filipuzzi I, Movva NR, Aebersold R, Helliwell SB, Loewith R. Target of Rapamycin Complex 2 Regulates Actin Polarization and Endocytosis via Multiple Pathways. J Biol Chem 2015; 290:14963-78. [PMID: 25882841 DOI: 10.1074/jbc.m114.627794] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Indexed: 11/06/2022] Open
Abstract
Target of rapamycin is a Ser/Thr kinase that operates in two conserved multiprotein complexes, TORC1 and TORC2. Unlike TORC1, TORC2 is insensitive to rapamycin, and its functional characterization is less advanced. Previous genetic studies demonstrated that TORC2 depletion leads to loss of actin polarization and loss of endocytosis. To determine how TORC2 regulates these readouts, we engineered a yeast strain in which TORC2 can be specifically and acutely inhibited by the imidazoquinoline NVP-BHS345. Kinetic analyses following inhibition of TORC2, supported with quantitative phosphoproteomics, revealed that TORC2 regulates these readouts via distinct pathways as follows: rapidly through direct protein phosphorylation cascades and slowly through indirect changes in the tensile properties of the plasma membrane. The rapid signaling events are mediated in large part through the phospholipid flippase kinases Fpk1 and Fpk2, whereas the slow signaling pathway involves increased plasma membrane tension resulting from a gradual depletion of sphingolipids. Additional hits in our phosphoproteomic screens highlight the intricate control TORC2 exerts over diverse aspects of eukaryote cell physiology.
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Affiliation(s)
- Delphine Rispal
- From the Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 1211 Geneva
| | - Sandra Eltschinger
- From the Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 1211 Geneva
| | - Michael Stahl
- From the Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 1211 Geneva
| | - Stefania Vaga
- the Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich
| | - Bernd Bodenmiller
- the Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich
| | - Yann Abraham
- the Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel
| | - Ireos Filipuzzi
- the Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel
| | - N Rao Movva
- the Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel
| | - Ruedi Aebersold
- the Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, the Faculty of Science, University of Zürich, 8057 Zürich, and
| | - Stephen B Helliwell
- the Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel,
| | - Robbie Loewith
- From the Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 1211 Geneva, the National Centre for Competence in Research Chemical Biology, 1211 Geneva, Switzerland
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495
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The role of TORC1 in muscle development in Drosophila. Sci Rep 2015; 5:9676. [PMID: 25866192 PMCID: PMC4394354 DOI: 10.1038/srep09676] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 03/16/2015] [Indexed: 01/15/2023] Open
Abstract
Myogenesis is an important process during both development and muscle repair. Previous studies suggest that mTORC1 plays a role in the formation of mature muscle from immature muscle precursor cells. Here we show that gene expression for several myogenic transcription factors including Myf5, Myog and Mef2c but not MyoD and myosin heavy chain isoforms decrease when C2C12 cells are treated with rapamycin, supporting a role for mTORC1 pathway during muscle development. To investigate the possibility that mTORC1 can regulate muscle in vivo we ablated the essential dTORC1 subunit Raptor in Drosophila melanogaster and found that muscle-specific knockdown of Raptor causes flies to be too weak to emerge from their pupal cases during eclosion. Using a series of GAL4 drivers we also show that muscle-specific Raptor knockdown also causes shortened lifespan, even when eclosure is unaffected. Together these results highlight an important role for TORC1 in muscle development, integrity and function in both Drosophila and mammalian cells.
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496
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Chymkowitch P, Nguéa AP, Aanes H, Koehler CJ, Thiede B, Lorenz S, Meza-Zepeda LA, Klungland A, Enserink JM. Sumoylation of Rap1 mediates the recruitment of TFIID to promote transcription of ribosomal protein genes. Genome Res 2015; 25:897-906. [PMID: 25800674 PMCID: PMC4448685 DOI: 10.1101/gr.185793.114] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 03/17/2015] [Indexed: 01/20/2023]
Abstract
Transcription factors are abundant Sumo targets, yet the global distribution of Sumo along the chromatin and its physiological relevance in transcription are poorly understood. Using Saccharomyces cerevisiae, we determined the genome-wide localization of Sumo along the chromatin. We discovered that Sumo-enriched genes are almost exclusively involved in translation, such as tRNA genes and ribosomal protein genes (RPGs). Genome-wide expression analysis showed that Sumo positively regulates their transcription. We also discovered that the Sumo consensus motif at RPG promoters is identical to the DNA binding motif of the transcription factor Rap1. We demonstrate that Rap1 is a molecular target of Sumo and that sumoylation of Rap1 is important for cell viability. Furthermore, Rap1 sumoylation promotes recruitment of the basal transcription machinery, and sumoylation of Rap1 cooperates with the target of rapamycin kinase complex 1 (TORC1) pathway to promote RPG transcription. Strikingly, our data reveal that sumoylation of Rap1 functions in a homeostatic feedback loop that sustains RPG transcription during translational stress. Taken together, Sumo regulates the cellular translational capacity by promoting transcription of tRNA genes and RPGs.
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Affiliation(s)
- Pierre Chymkowitch
- Institute of Microbiology, Clinic for Diagnostics and Intervention, Oslo University Hospital, N-0027 Oslo, Norway; University of Oslo, 0316 Oslo, Norway
| | - Aurélie P Nguéa
- Institute of Microbiology, Clinic for Diagnostics and Intervention, Oslo University Hospital, N-0027 Oslo, Norway; University of Oslo, 0316 Oslo, Norway
| | - Håvard Aanes
- Institute of Microbiology, Clinic for Diagnostics and Intervention, Oslo University Hospital, N-0027 Oslo, Norway; University of Oslo, 0316 Oslo, Norway
| | | | - Bernd Thiede
- The Biotechnology Centre of Oslo, University of Oslo, 0349 Oslo, Norway
| | - Susanne Lorenz
- Department of Tumor Biology, The Norwegian Radium Hospital, and Genomics Core Facility, Oslo University Hospital, NO-0310 Oslo, Norway
| | - Leonardo A Meza-Zepeda
- Department of Tumor Biology, The Norwegian Radium Hospital, and Genomics Core Facility, Oslo University Hospital, NO-0310 Oslo, Norway
| | - Arne Klungland
- Institute of Microbiology, Clinic for Diagnostics and Intervention, Oslo University Hospital, N-0027 Oslo, Norway; University of Oslo, 0316 Oslo, Norway
| | - Jorrit M Enserink
- Institute of Microbiology, Clinic for Diagnostics and Intervention, Oslo University Hospital, N-0027 Oslo, Norway; University of Oslo, 0316 Oslo, Norway
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497
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Systematic identification of signal integration by protein kinase A. Proc Natl Acad Sci U S A 2015; 112:4501-6. [PMID: 25831502 DOI: 10.1073/pnas.1409938112] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cellular processes and homeostasis control in eukaryotic cells is achieved by the action of regulatory proteins such as protein kinase A (PKA). Although the outbound signals from PKA directed to processes such as metabolism, growth, and aging have been well charted, what regulates this conserved regulator remains to be systematically identified to understand how it coordinates biological processes. Using a yeast PKA reporter assay, we identified genes that influence PKA activity by measuring protein-protein interactions between the regulatory and the two catalytic subunits of the PKA complex in 3,726 yeast genetic-deletion backgrounds grown on two carbon sources. Overall, nearly 500 genes were found to be connected directly or indirectly to PKA regulation, including 80 core regulators, denoting a wide diversity of signals regulating PKA, within and beyond the described upstream linear pathways. PKA regulators span multiple processes, including the antagonistic autophagy and methionine biosynthesis pathways. Our results converge toward mechanisms of PKA posttranslational regulation by lysine acetylation, which is conserved between yeast and humans and that, we show, regulates protein complex formation in mammals and carbohydrate storage and aging in yeast. Taken together, these results show that the extent of PKA input matches with its output, because this kinase receives information from upstream and downstream processes, and highlight how biological processes are interconnected and coordinated by PKA.
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498
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Polymenis M, Aramayo R. Translate to divide: сontrol of the cell cycle by protein synthesis. MICROBIAL CELL 2015; 2:94-104. [PMID: 28357283 PMCID: PMC5348972 DOI: 10.15698/mic2015.04.198] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein synthesis underpins much of cell growth and, consequently, cell multiplication. Understanding how proliferating cells commit and progress into the cell cycle requires knowing not only which proteins need to be synthesized, but also what determines their rate of synthesis during cell division.
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Affiliation(s)
- Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Rodolfo Aramayo
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
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499
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González A, Shimobayashi M, Eisenberg T, Merle DA, Pendl T, Hall MN, Moustafa T. TORC1 promotes phosphorylation of ribosomal protein S6 via the AGC kinase Ypk3 in Saccharomyces cerevisiae. PLoS One 2015; 10:e0120250. [PMID: 25767889 PMCID: PMC4359079 DOI: 10.1371/journal.pone.0120250] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/21/2015] [Indexed: 11/21/2022] Open
Abstract
The target of rapamycin complex 1 (TORC1) is an evolutionarily conserved sensor of nutrient availability. Genetic and pharmacological studies in the yeast Saccharomyces cerevisiae have provided mechanistic insights on the regulation of TORC1 signaling in response to nutrients. Using a highly specific antibody that recognizes phosphorylation of the bona fide TORC1 target ribosomal protein S6 (Rps6) in yeast, we found that nutrients rapidly induce Rps6 phosphorylation in a TORC1-dependent manner. Moreover, we demonstrate that Ypk3, an AGC kinase which exhibits high homology to human S6 kinase (S6K), is required for the phosphorylation of Rps6 in vivo. Rps6 phosphorylation is completely abolished in cells lacking Ypk3 (ypk3Δ), whereas Sch9, previously reported to be the yeast ortholog of S6K, is dispensable for Rps6 phosphorylation. Phosphorylation-deficient mutations in regulatory motifs of Ypk3 abrogate Rps6 phosphorylation, and complementation of ypk3Δ cells with human S6 kinase restores Rps6 phosphorylation in a rapamycin-sensitive manner. Our findings demonstrate that Ypk3 is a critical component of the TORC1 pathway and that the use of a phospho-S6 specific antibody offers a valuable tool to identify new nutrient-dependent and rapamycin-sensitive targets in vivo.
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Affiliation(s)
| | | | - Tobias Eisenberg
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Tobias Pendl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Tarek Moustafa
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- * E-mail:
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500
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Kleessen S, Irgang S, Klie S, Giavalisco P, Nikoloski Z. Integration of transcriptomics and metabolomics data specifies the metabolic response of Chlamydomonas to rapamycin treatment. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:822-35. [PMID: 25600836 DOI: 10.1111/tpj.12763] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/19/2014] [Indexed: 05/19/2023]
Abstract
Flux phenotypes predicted by constraint-based methods can be refined by the inclusion of heterogeneous data. While recent advances facilitate the integration of transcriptomics and proteomics data, purely stoichiometry-based approaches for the prediction of flux phenotypes by considering metabolomics data are lacking. Here we propose a constraint-based method, termed TREM-Flux, for integrating time-resolved metabolomics and transcriptomics data. We demonstrate the applicability of TREM-Flux in the dissection of the metabolic response of Chlamydomonas reinhardtii to rapamycin treatment by integrating the expression levels of 982 genes and the content of 45 metabolites obtained from two growth conditions. The findings pinpoint cysteine and methionine metabolism to be most affected by the rapamycin treatment. Our study shows that the integration of time-resolved unlabeled metabolomics data in addition to transcriptomics data can specify the metabolic pathways involved in the system's response to a studied treatment.
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