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Jendruchová K, Gaikwad S, Poncová K, Gunišová S, Valášek LS, Hinnebusch AG. Differential effects of 40S ribosome recycling factors on reinitiation at regulatory uORFs in GCN4 mRNA are not dictated by their roles in bulk 40S recycling. Commun Biol 2024; 7:1083. [PMID: 39232119 PMCID: PMC11375166 DOI: 10.1038/s42003-024-06761-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 08/21/2024] [Indexed: 09/06/2024] Open
Abstract
Recycling of 40S ribosomal subunits following translation termination, entailing release of deacylated tRNA and dissociation of the empty 40S from mRNA, involves yeast Tma20/Tma22 heterodimer and Tma64, counterparts of mammalian MCTS1/DENR and eIF2D. MCTS1/DENR enhance reinitiation (REI) at short upstream open reading frames (uORFs) harboring penultimate codons that confer heightened dependence on these factors in bulk 40S recycling. Tma factors, by contrast, inhibited REI at particular uORFs in extracts; however, their roles at regulatory uORFs in vivo were unknown. We examined effects of eliminating Tma proteins on REI at regulatory uORFs mediating translational control of GCN4 optimized for either promoting (uORF1) or preventing (uORF4) REI. We found that the Tma proteins generally impede REI at native uORF4 and its variants equipped with various penultimate codons regardless of their Tma-dependence in bulk recycling. The Tma factors have no effect on REI at native uORF1 and equipping it with Tma-hyperdependent penultimate codons generally did not confer Tma-dependent REI; nor did converting the uORFs to AUG-stop elements. Thus, effects of the Tma proteins vary depending on the REI potential of the uORF and penultimate codon, but unlike in mammals, are not principally dictated by the Tma-dependence of the codon in bulk 40S recycling.
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Affiliation(s)
- Kristína Jendruchová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
- Faculty of Science, Charles University, Albertov 6, 128 00, Prague, Czech Republic
| | - Swati Gaikwad
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kristýna Poncová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Stanislava Gunišová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic.
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
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2
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Jendruchová K, Gaikwad S, Poncová K, Gunišová S, Valášek LS, Hinnebusch AG. Impacts of yeast Tma20/MCTS1, Tma22/DENR and Tma64/eIF2D on translation reinitiation and ribosome recycling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583729. [PMID: 38903097 PMCID: PMC11188067 DOI: 10.1101/2024.03.06.583729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Recycling of 40S ribosomal subunits following translation termination, entailing release of deacylated tRNA and dissociation of the empty 40S subunit from mRNA, involves yeast Tma20/Tma22 heterodimer and Tma64, counterparts of mammalian MCTS1/DENR and eIF2D. MCTS1/DENR enhance reinitiation at short upstream open reading frames (uORFs) harboring penultimate codons that confer dependence on these factors in bulk 40S recycling. Tma factors, by contrast, inhibited reinitiation at particular uORFs in extracts; however, their roles at regulatory uORFs in vivo were unknown. We examined effects of eliminating Tma proteins on reinitiation at regulatory uORFs mediating translational control of GCN4 optimized for either promoting (uORF1) or preventing (uORF4) reinitiation. We found that the Tma proteins generally impede reinitiation at native uORF4 and uORF4 variants equipped with various penultimate codons regardless of their Tma-dependence in bulk recycling. The Tma factors have no effect on reinitiation at native uORF1, and equipping uORF1 with Tma-dependent penultimate codons generally did not confer Tma-dependent reinitiation; nor did converting the uORFs to AUG-stop elements. Thus, effects of the Tma proteins vary depending on the reinitiation potential of the uORF and the penultimate codon, but unlike in mammals, are not principally dictated by the Tma-dependence of the codon in bulk 40S recycling.
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Affiliation(s)
- Kristína Jendruchová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, the Czech Republic
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic
| | - Swati Gaikwad
- Divsion of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kristýna Poncová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, the Czech Republic
| | - Stanislava Gunišová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, the Czech Republic
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, the Czech Republic
| | - Alan G Hinnebusch
- Divsion of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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3
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VanBelzen J, Duan C, Brickner DG, Brickner JH. ChEC-seq2: an improved Chromatin Endogenous Cleavage sequencing method and bioinformatic analysis pipeline for mapping in vivo protein-DNA interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.15.562421. [PMID: 37905156 PMCID: PMC10614805 DOI: 10.1101/2023.10.15.562421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Defining the in vivo DNA binding specificity of transcription factors (TFs) has relied nearly exclusively on chromatin immunoprecipitation (ChIP). While ChIP reveals TF binding patterns, its resolution is low. Higher resolution methods employing nucleases such as ChIP-exo, chromatin endogenous cleavage (ChEC-seq) and CUT&RUN resolve both TF occupancy and binding site protection. ChEC-seq, in which an endogenous TF is fused to micrococcal nuclease, requires neither fixation nor antibodies. However, the specificity of DNA cleavage during ChEC has been suggested to be lower than the specificity of the peaks identified by ChIP or ChIP-exo, perhaps reflecting non-specific binding of transcription factors to DNA. We have simplified the ChEC-seq protocol to minimize nuclease digestion while increasing the yield of cleaved DNA. ChEC-seq2 cleavage patterns were highly reproducible between replicates and with published ChEC-seq data. Combined with DoubleChEC, a new bioinformatic pipeline that removes non-specific cleavage sites, ChEC-seq2 identified high-confidence cleavage sites for three different yeast TFs that are strongly enriched for their known binding sites and adjacent to known target genes.
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Affiliation(s)
- Jake VanBelzen
- Department of Molecular Biosciences, Northwestern University
| | - Chengzhe Duan
- Department of Molecular Biosciences, Northwestern University
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4
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Reprogramming mRNA Expression in Response to Defect in RNA Polymerase III Assembly in the Yeast Saccharomyces cerevisiae. Int J Mol Sci 2021; 22:ijms22147298. [PMID: 34298922 PMCID: PMC8306304 DOI: 10.3390/ijms22147298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/25/2021] [Accepted: 07/03/2021] [Indexed: 12/18/2022] Open
Abstract
The coordinated transcription of the genome is the fundamental mechanism in molecular biology. Transcription in eukaryotes is carried out by three main RNA polymerases: Pol I, II, and III. One basic problem is how a decrease in tRNA levels, by downregulating Pol III efficiency, influences the expression pattern of protein-coding genes. The purpose of this study was to determine the mRNA levels in the yeast mutant rpc128-1007 and its overdose suppressors, RBS1 and PRT1. The rpc128-1007 mutant prevents assembly of the Pol III complex and functionally mimics similar mutations in human Pol III, which cause hypomyelinating leukodystrophies. We applied RNAseq followed by the hierarchical clustering of our complete RNA-seq transcriptome and functional analysis of genes from the clusters. mRNA upregulation in rpc128-1007 cells was generally stronger than downregulation. The observed induction of mRNA expression was mostly indirect and resulted from the derepression of general transcription factor Gcn4, differently modulated by suppressor genes. rpc128-1007 mutation, regardless of the presence of suppressors, also resulted in a weak increase in the expression of ribosome biogenesis genes. mRNA genes that were downregulated by the reduction of Pol III assembly comprise the proteasome complex. In summary, our results provide the regulatory links affected by Pol III assembly that contribute differently to cellular fitness.
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5
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Gaikwad S, Ghobakhlou F, Young DJ, Visweswaraiah J, Zhang H, Hinnebusch AG. Reprogramming of translation in yeast cells impaired for ribosome recycling favors short, efficiently translated mRNAs. eLife 2021; 10:e64283. [PMID: 33764298 PMCID: PMC7993997 DOI: 10.7554/elife.64283] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/04/2021] [Indexed: 12/21/2022] Open
Abstract
In eukaryotes, 43S preinitiation complex (PIC) formation is a rate-determining step of translation. Ribosome recycling following translation termination produces free 40S subunits for re-assembly of 43S PICs. Yeast mutants lacking orthologs of mammalian eIF2D (Tma64), and either MCT-1 (Tma20) or DENR (Tma22), are broadly impaired for 40S recycling; however, it was unknown whether this defect alters the translational efficiencies (TEs) of particular mRNAs. Here, we conducted ribosome profiling of a yeast tma64∆/tma20∆ double mutant and observed a marked reprogramming of translation, wherein the TEs of the most efficiently translated ('strong') mRNAs increase, while those of 'weak' mRNAs generally decline. Remarkably, similar reprogramming was seen on reducing 43S PIC assembly by inducing phosphorylation of eIF2α or by decreasing total 40S subunit levels by depleting Rps26. Our findings suggest that strong mRNAs outcompete weak mRNAs in response to 43S PIC limitation achieved in various ways, in accordance with previous mathematical modeling.
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Affiliation(s)
- Swati Gaikwad
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Fardin Ghobakhlou
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - David J Young
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Jyothsna Visweswaraiah
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Hongen Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
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6
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Global phosphoproteomics pinpoints uncharted Gcn2-mediated mechanisms of translational control. Mol Cell 2021; 81:1879-1889.e6. [PMID: 33743194 DOI: 10.1016/j.molcel.2021.02.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/09/2020] [Accepted: 02/24/2021] [Indexed: 01/04/2023]
Abstract
The conserved Gcn2 protein kinase mediates cellular adaptations to amino acid limitation through translational control of gene expression that is exclusively executed by phosphorylation of the α-subunit of the eukaryotic translation initiation factor 2 (eIF2α). Using quantitative phosphoproteomics, however, we discovered that Gcn2 targets auxiliary effectors to modulate translation. Accordingly, Gcn2 also phosphorylates the β-subunit of the trimeric eIF2 G protein complex to promote its association with eIF5, which prevents spontaneous nucleotide exchange on eIF2 and thereby restricts the recycling of the initiator methionyl-tRNA-bound eIF2-GDP ternary complex in amino-acid-starved cells. This mechanism contributes to the inhibition of translation initiation in parallel to the sequestration of the nucleotide exchange factor eIF2B by phosphorylated eIF2α. Gcn2 further phosphorylates Gcn20 to antagonize, in an inhibitory feedback loop, the formation of the Gcn2-stimulatory Gcn1-Gcn20 complex. Thus, Gcn2 plays a substantially more intricate role in controlling translation initiation than hitherto appreciated.
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7
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Wang J, Wang J, Shin BS, Kim JR, Dever TE, Puglisi JD, Fernández IS. Structural basis for the transition from translation initiation to elongation by an 80S-eIF5B complex. Nat Commun 2020; 11:5003. [PMID: 33024099 PMCID: PMC7538418 DOI: 10.1038/s41467-020-18829-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/16/2020] [Indexed: 11/09/2022] Open
Abstract
Recognition of a start codon by the initiator aminoacyl-tRNA determines the reading frame of messenger RNA (mRNA) translation by the ribosome. In eukaryotes, the GTPase eIF5B collaborates in the correct positioning of the initiator Met-tRNAiMet on the ribosome in the later stages of translation initiation, gating entrance into elongation. Leveraging the long residence time of eIF5B on the ribosome recently identified by single-molecule fluorescence measurements, we determine the cryoEM structure of the naturally long-lived ribosome complex with eIF5B and Met-tRNAiMet immediately before transition into elongation. The structure uncovers an unexpected, eukaryotic specific and dynamic fidelity checkpoint implemented by eIF5B in concert with components of the large ribosomal subunit.
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Affiliation(s)
- Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jing Wang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, NY, USA
| | - Byung-Sik Shin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Joo-Ran Kim
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Israel S Fernández
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, NY, USA.
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8
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Ivashov V, Zimmer J, Schwabl S, Kahlhofer J, Weys S, Gstir R, Jakschitz T, Kremser L, Bonn GK, Lindner H, Huber LA, Leon S, Schmidt O, Teis D. Complementary α-arrestin-ubiquitin ligase complexes control nutrient transporter endocytosis in response to amino acids. eLife 2020; 9:e58246. [PMID: 32744498 PMCID: PMC7449699 DOI: 10.7554/elife.58246] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/01/2020] [Indexed: 12/12/2022] Open
Abstract
How cells adjust nutrient transport across their membranes is incompletely understood. Previously, we have shown that S. cerevisiae broadly re-configures the nutrient transporters at the plasma membrane in response to amino acid availability, through endocytosis of sugar- and amino acid transporters (AATs) (Müller et al., 2015). A genome-wide screen now revealed that the selective endocytosis of four AATs during starvation required the α-arrestin family protein Art2/Ecm21, an adaptor for the ubiquitin ligase Rsp5, and its induction through the general amino acid control pathway. Art2 uses a basic patch to recognize C-terminal acidic sorting motifs in AATs and thereby instructs Rsp5 to ubiquitinate proximal lysine residues. When amino acids are in excess, Rsp5 instead uses TORC1-activated Art1 to detect N-terminal acidic sorting motifs within the same AATs, which initiates exclusive substrate-induced endocytosis. Thus, amino acid excess or starvation activate complementary α-arrestin-Rsp5-complexes to control selective endocytosis and adapt nutrient acquisition.
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Affiliation(s)
- Vasyl Ivashov
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - Johannes Zimmer
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - Sinead Schwabl
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - Jennifer Kahlhofer
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - Sabine Weys
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - Ronald Gstir
- ADSI – Austrian Drug Screening Institute GmbHInnsbruckAustria
| | | | - Leopold Kremser
- Division of Clinical Biochemistry, ProteinMicroAnalysis Facility, Medical University of InnsbruckInnsbruckAustria
| | - Günther K Bonn
- ADSI – Austrian Drug Screening Institute GmbHInnsbruckAustria
| | - Herbert Lindner
- Division of Clinical Biochemistry, ProteinMicroAnalysis Facility, Medical University of InnsbruckInnsbruckAustria
| | - Lukas A Huber
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
- ADSI – Austrian Drug Screening Institute GmbHInnsbruckAustria
| | - Sebastien Leon
- Université de Paris, CNRS, Institut Jacques MonodParisFrance
| | - Oliver Schmidt
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
| | - David Teis
- Institute for Cell Biology, Medical University of InnsbruckInnsbruckAustria
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Uluisik İ, Karakaya HC, Koc A. tRNA Wobble Base Modifications and Boric Acid Resistance in Yeast: Boron-Resistant Deletion Mutants Induce the General Amino Acid Control Mechanism and Activate Boron Efflux. Mol Biol 2020. [DOI: 10.1134/s0026893320030188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Maitra N, He C, Blank HM, Tsuchiya M, Schilling B, Kaeberlein M, Aramayo R, Kennedy BK, Polymenis M. Translational control of one-carbon metabolism underpins ribosomal protein phenotypes in cell division and longevity. eLife 2020; 9:53127. [PMID: 32432546 PMCID: PMC7263821 DOI: 10.7554/elife.53127] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
A long-standing problem is how cells that lack one of the highly similar ribosomal proteins (RPs) often display distinct phenotypes. Yeast and other organisms live longer when they lack specific ribosomal proteins, especially of the large 60S subunit of the ribosome. However, longevity is neither associated with the generation time of RP deletion mutants nor with bulk inhibition of protein synthesis. Here, we queried actively dividing RP mutants through the cell cycle. Our data link transcriptional, translational, and metabolic changes to phenotypes associated with the loss of paralogous RPs. We uncovered translational control of transcripts encoding enzymes of methionine and serine metabolism, which are part of one-carbon (1C) pathways. Cells lacking Rpl22Ap, which are long-lived, have lower levels of metabolites associated with 1C metabolism. Loss of 1C enzymes increased the longevity of wild type cells. 1C pathways exist in all organisms and targeting the relevant enzymes could represent longevity interventions.
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Affiliation(s)
- Nairita Maitra
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
| | - Chong He
- Buck Institute for Research on Aging, Novato, United States
| | - Heidi M Blank
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
| | - Mitsuhiro Tsuchiya
- Department of Pathology, University of Washington, Seattle, United States
| | | | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, United States
| | - Rodolfo Aramayo
- Department of Biology, Texas A&M University, College Station, United States
| | - Brian K Kennedy
- Buck Institute for Research on Aging, Novato, United States.,Departments of Biochemistry and Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Centre for Healthy Ageing, National University of Singapore, National University Health System, Singapore, Singapore
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
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11
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Hijazi I, Knupp J, Chang A. Retrograde signaling mediates an adaptive survival response to endoplasmic reticulum stress in Saccharomyces cerevisiae. J Cell Sci 2020; 133:jcs.241539. [PMID: 32005698 DOI: 10.1242/jcs.241539] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/23/2020] [Indexed: 12/11/2022] Open
Abstract
One major cause of endoplasmic reticulum (ER) stress is homeostatic imbalance between biosynthetic protein folding and protein folding capacity. Cells utilize mechanisms such as the unfolded protein response (UPR) to cope with ER stress. Nevertheless, when ER stress is prolonged or severe, cell death may occur, accompanied by production of mitochondrial reactive oxygen species (ROS). Using a yeast model (Saccharomyces cerevisiae), we describe an innate, adaptive response to ER stress to increase select mitochondrial proteins, O2 consumption and cell survival. The mitochondrial response allows cells to resist additional ER stress. The ER stress-induced mitochondrial response is mediated by activation of retrograde (RTG) signaling to enhance anapleurotic reactions of the tricarboxylic acid cycle. Mitochondrial response to ER stress is accompanied by inactivation of the conserved TORC1 pathway, and activation of Snf1/AMPK, the conserved energy sensor and regulator of metabolism. Our results provide new insight into the role of respiration in cell survival in the face of ER stress, and should help in developing therapeutic strategies to limit cell death in disorders linked to ER stress.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Imadeddin Hijazi
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N University, Ann Arbor, MI 48109, USA
| | - Jeffrey Knupp
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N University, Ann Arbor, MI 48109, USA
| | - Amy Chang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N University, Ann Arbor, MI 48109, USA
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12
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Towards a model of GCN2 activation. Biochem Soc Trans 2020; 47:1481-1488. [PMID: 31647517 PMCID: PMC6824675 DOI: 10.1042/bst20190331] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/19/2019] [Accepted: 09/23/2019] [Indexed: 01/06/2023]
Abstract
Cells must be able to sense and adapt to their surroundings to thrive in a dynamic environment. Key to adapting to a low nutrient environment is the Integrated Stress Response (ISR), a short-lived pathway that allows cells to either regain cellular homeostasis or facilitate apoptosis during periods of stress. Central to the ISR is the protein kinase General Control Non-depressible 2 (GCN2), which is responsible for sensing starvation. Upon amino acid deficiency, GCN2 is activated and initiates the ISR by phosphorylating the translation initiation factor eIF2α, stalling protein translation, and activating the transcription factor ATF4, which in turn up-regulates autophagy and biosynthesis pathways. A key outstanding question is how GCN2 is activated from an autoinhibited state. Until recently, a model of activation focussed on the increase of deacylated tRNA associated with amino acid starvation, with deacylated tRNA binding directly to GCN2 and releasing autoinhibition. However, in vivo experiments have pointed towards an alternative, deacylated-tRNA-independent mechanism of activation. Here, we review the various factors that may facilitate GCN2 activation, including recent research showing that the P-stalk complex, a ribosome-associated heteropentameric protein complex, is a potent activator of GCN2.
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13
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Romero AM, Ramos-Alonso L, Alepuz P, Puig S, Martínez-Pastor MT. Global translational repression induced by iron deficiency in yeast depends on the Gcn2/eIF2α pathway. Sci Rep 2020; 10:233. [PMID: 31937829 PMCID: PMC6959253 DOI: 10.1038/s41598-019-57132-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/16/2019] [Indexed: 11/09/2022] Open
Abstract
Iron is an essential element for all eukaryotic organisms because it participates as a redox active cofactor in a wide range of biological processes, including protein synthesis. Translation is probably the most energy consuming process in cells. Therefore, one of the initial responses of eukaryotic cells to stress or nutrient limitation is the arrest of mRNA translation. In first instance, the budding yeast Saccharomyces cerevisiae responds to iron deficiency by activating iron acquisition and remodeling cellular metabolism in order to prioritize essential over non-essential iron-dependent processes. We have determined that, despite a global decrease in transcription, mRNA translation is actively maintained during a short-term exposure to iron scarcity. However, a more severe iron deficiency condition induces a global repression of translation. Our results indicate that the Gcn2-eIF2α pathway limits general translation at its initiation step during iron deficiency. This bulk translational inhibition depends on the uncharged tRNA sensing Gcn1-Gcn20 complex. The involvement of the Gcn2-eIF2α pathway in the response to iron deficiency highlights its central role in the eukaryotic response to stress or nutritional deprivation, which is conserved from yeast to mammals.
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Affiliation(s)
- Antonia María Romero
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
| | - Lucía Ramos-Alonso
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
| | - Paula Alepuz
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Doctor Moliner 50, E-46100, Burjassot, Valencia, Spain.,ERI Biotecmed, Universitat de València, Doctor Moliner 50, E-46100, Burjassot, Valencia, Spain
| | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino 7, E-46980, Paterna, Valencia, Spain.
| | - María Teresa Martínez-Pastor
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Doctor Moliner 50, E-46100, Burjassot, Valencia, Spain.
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Young-Baird SK, Shin BS, Dever TE. MEHMO syndrome mutation EIF2S3-I259M impairs initiator Met-tRNAiMet binding to eukaryotic translation initiation factor eIF2. Nucleic Acids Res 2019; 47:855-867. [PMID: 30517694 PMCID: PMC6344876 DOI: 10.1093/nar/gky1213] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/26/2018] [Indexed: 01/20/2023] Open
Abstract
The heterotrimeric eukaryotic translation initiation factor (eIF) 2 plays critical roles in delivering initiator Met-tRNAiMet to the 40S ribosomal subunit and in selecting the translation initiation site. Genetic analyses of patients with MEHMO syndrome, an X-linked intellectual disability syndrome, have identified several unique mutations in the EIF2S3 gene that encodes the γ subunit of eIF2. To gain insights into the molecular consequences of MEHMO syndrome mutations on eIF2 function, we generated a yeast model of the human eIF2γ-I259M mutant, previously identified in a patient with MEHMO syndrome. The corresponding eIF2γ-I318M mutation impaired yeast cell growth and derepressed GCN4 expression, an indicator of defective eIF2–GTP–Met-tRNAiMet complex formation, and, likewise, overexpression of human eIF2γ-I259M derepressed ATF4 messenger RNA translation in human cells. The yeast eIF2γ-I318M mutation also increased initiation from near-cognate start codons. Biochemical analyses revealed a defect in Met-tRNAiMet binding to the mutant yeast eIF2 complexes in vivo and in vitro. Overexpression of tRNAiMet restored Met-tRNAiMet binding to eIF2 in vivo and rescued the growth defect in the eIF2γ-I318M strain. Based on these findings and the structure of eIF2, we propose that the I259M mutation impairs Met-tRNAiMet binding, causing altered control of protein synthesis that underlies MEHMO syndrome.
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Affiliation(s)
- Sara K Young-Baird
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.,National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Byung-Sik Shin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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15
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Iacovella MG, Bremang M, Basha O, Giacò L, Carotenuto W, Golfieri C, Szakal B, Dal Maschio M, Infantino V, Beznoussenko GV, Joseph CR, Visintin C, Mironov AA, Visintin R, Branzei D, Ferreira-Cerca S, Yeger-Lotem E, De Wulf P. Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae. Nucleic Acids Res 2019; 46:7586-7611. [PMID: 30011030 PMCID: PMC6125641 DOI: 10.1093/nar/gky618] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/28/2018] [Indexed: 12/14/2022] Open
Abstract
The Saccharomyces cerevisiae kinase/adenosine triphosphatase Rio1 regulates rDNA transcription and segregation, pre-rRNA processing and small ribosomal subunit maturation. Other roles are unknown. When overexpressed, human ortholog RIOK1 drives tumor growth and metastasis. Likewise, RIOK1 promotes 40S ribosomal subunit biogenesis and has not been characterized globally. We show that Rio1 manages directly and via a series of regulators, an essential signaling network at the protein, chromatin and RNA levels. Rio1 orchestrates growth and division depending on resource availability, in parallel to the nutrient-activated Tor1 kinase. To define the Rio1 network, we identified its physical interactors, profiled its target genes/transcripts, mapped its chromatin-binding sites and integrated our data with yeast’s protein–protein and protein–DNA interaction catalogs using network computation. We experimentally confirmed network components and localized Rio1 also to mitochondria and vacuoles. Via its network, Rio1 commands protein synthesis (ribosomal gene expression, assembly and activity) and turnover (26S proteasome expression), and impinges on metabolic, energy-production and cell-cycle programs. We find that Rio1 activity is conserved to humans and propose that pathological RIOK1 may fuel promiscuous transcription, ribosome production, chromosomal instability, unrestrained metabolism and proliferation; established contributors to cancer. Our study will advance the understanding of numerous processes, here revealed to depend on Rio1 activity.
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Affiliation(s)
- Maria G Iacovella
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Michael Bremang
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.,Current address: Proteome Sciences Plc, Hamilton House, Mabledon Place, London, United Kingdom
| | - Omer Basha
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, POB 653, Beer-Sheva 84105, Israel
| | - Luciano Giacò
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Walter Carotenuto
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Cristina Golfieri
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Barnabas Szakal
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Marianna Dal Maschio
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Valentina Infantino
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Galina V Beznoussenko
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Chinnu R Joseph
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Clara Visintin
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Alexander A Mironov
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Rosella Visintin
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Dana Branzei
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy.,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Sébastien Ferreira-Cerca
- Lehrstuhl für Biochemie III, Universität Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Esti Yeger-Lotem
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, POB 653, Beer-Sheva 84105, Israel
| | - Peter De Wulf
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.,Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
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16
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Antony A C, Ram AK, Dutta K, Alone PV. Ribosomal mutation in helix 32 of 18S rRNA alters fidelity of eukaryotic translation start site selection. FEBS Lett 2019; 593:852-867. [PMID: 30900251 DOI: 10.1002/1873-3468.13369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 11/09/2022]
Abstract
The 40S ribosome plays a critical role in start codon selection. To gain insights into the role of its 18S rRNA in start codon selection, a suppressor screen was performed that suppressed the preferential UUG start codon recognition (Suppressor of initiation codon: Sui- phenotype) associated with the eIF5G31R mutant. The C1209U mutation in helix h32 of 18S rRNA was found to suppress the Sui- and Gcn- (failure to derepress GCN4 expression) phenotype of the eIF5G31R mutant. The C1209U mutation suppressed Sui- and Gcd- (constitutive derepression of GCN4 expression) phenotype of eIF2βS264Y , eIF1K60E , and eIF1A-ΔC mutation. We propose that the C1209U mutation in 40S ribosomal may perturb the premature head rotation in 'Closed/PIN ' state and enhance the stringency of translation start site selection.
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Affiliation(s)
- Charles Antony A
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Anup Kumar Ram
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Kalloly Dutta
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Pankaj V Alone
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
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17
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Gregory LC, Ferreira CB, Young-Baird SK, Williams HJ, Harakalova M, van Haaften G, Rahman SA, Gaston-Massuet C, Kelberman D, GOSgene, Qasim W, Camper SA, Dever TE, Shah P, Robinson ICAF, Dattani MT. Impaired EIF2S3 function associated with a novel phenotype of X-linked hypopituitarism with glucose dysregulation. EBioMedicine 2019; 42:470-480. [PMID: 30878599 PMCID: PMC6492072 DOI: 10.1016/j.ebiom.2019.03.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 11/25/2022] Open
Abstract
Background The heterotrimeric GTP-binding protein eIF2 forms a ternary complex with initiator methionyl-tRNA and recruits it to the 40S ribosomal subunit for start codon selection and thereby initiates protein synthesis. Mutations in EIF2S3, encoding the eIF2γ subunit, are associated with severe intellectual disability and microcephaly, usually as part of MEHMO syndrome. Methods Exome sequencing of the X chromosome was performed on three related males with normal head circumferences and mild learning difficulties, hypopituitarism (GH and TSH deficiencies), and an unusual form of glucose dysregulation. In situ hybridisation on human embryonic tissue, EIF2S3-knockdown studies in a human pancreatic cell line, and yeast assays on the mutated corresponding eIF2γ protein, were performed in this study. Findings We report a novel hemizygous EIF2S3 variant, p.Pro432Ser, in the three boys (heterozygous in their mothers). EIF2S3 expression was detectable in the developing pituitary gland and pancreatic islets of Langerhans. Cells lacking EIF2S3 had increased caspase activity/cell death. Impaired protein synthesis and relaxed start codon selection stringency was observed in mutated yeast. Interpretation Our data suggest that the p.Pro432Ser mutation impairs eIF2γ function leading to a relatively mild novel phenotype compared with previous EIF2S3 mutations. Our studies support a critical role for EIF2S3 in human hypothalamo-pituitary development and function, and glucose regulation, expanding the range of phenotypes associated with EIF2S3 mutations beyond classical MEHMO syndrome. Untreated hypoglycaemia in previous cases may have contributed to their more severe neurological impairment and seizures in association with impaired EIF2S3. Fund GOSH, MRF, BRC, MRC/Wellcome Trust and NIGMS funded this study.
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Affiliation(s)
- Louise C Gregory
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, United Kingdom
| | - Carolina B Ferreira
- Infection, Immunology Inflammation & Physiological Medicine, UCL Great Ormond Street Institute of Child Health, WC1N 1EH London, United Kingdom
| | - Sara K Young-Baird
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, United States; National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MA 20892, United States
| | - Hywel J Williams
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, United Kingdom
| | - Magdalena Harakalova
- Department of Genetics, University Medical Center Utrecht, 3584, the Netherlands
| | - Gijs van Haaften
- Department of Genetics, University Medical Center Utrecht, 3584, the Netherlands
| | - Sofia A Rahman
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, United Kingdom
| | - Carles Gaston-Massuet
- Centre for Endocrinology, William Harvey Research Institute, Barts & The London Medical School, Queen Mary University of London, EC1M 6BQ, United Kingdom
| | - Daniel Kelberman
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, United Kingdom
| | - GOSgene
- NIHR Biomedical Research Centre at Great Ormond Street Hospital, Children NHS Foundation Trust and UCL, London WC1N 1EH, United Kingdom
| | - Waseem Qasim
- Infection, Immunology Inflammation & Physiological Medicine, UCL Great Ormond Street Institute of Child Health, WC1N 1EH London, United Kingdom
| | - Sally A Camper
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, United States
| | - Pratik Shah
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, United Kingdom
| | | | - Mehul T Dattani
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, United Kingdom.
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18
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Zeidan Q, He F, Zhang F, Zhang H, Jacobson A, Hinnebusch AG. Conserved mRNA-granule component Scd6 targets Dhh1 to repress translation initiation and activates Dcp2-mediated mRNA decay in vivo. PLoS Genet 2018; 14:e1007806. [PMID: 30532217 PMCID: PMC6307823 DOI: 10.1371/journal.pgen.1007806] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 12/27/2018] [Accepted: 11/02/2018] [Indexed: 12/21/2022] Open
Abstract
Scd6 protein family members are evolutionarily conserved components of translationally silent mRNA granules. Yeast Scd6 interacts with Dcp2 and Dhh1, respectively a subunit and a regulator of the mRNA decapping enzyme, and also associates with translation initiation factor eIF4G to inhibit translation in cell extracts. However, the role of Scd6 in mRNA turnover and translational repression in vivo is unclear. We demonstrate that tethering Scd6 to a GFP reporter mRNA reduces mRNA abundance via Dcp2 and suppresses reporter mRNA translation via Dhh1. Thus, in a dcp2Δ mutant, tethered Scd6 reduces GFP protein expression with little effect on mRNA abundance, whereas tethered Scd6 has no impact on GFP protein or mRNA expression in a dcp2Δ dhh1Δ double mutant. The conserved LSm domain of Scd6 is required for translational repression and mRNA turnover by tethered Scd6. Both functions are enhanced in a ccr4Δ mutant, suggesting that the deadenylase function of Ccr4-Not complex interferes with a more efficient repression pathway enlisted by Scd6. Ribosome profiling and RNA-Seq analysis of scd6Δ and dhh1Δ mutants suggests that Scd6 cooperates with Dhh1 in translational repression and turnover of particular native mRNAs, with both processes dependent on Dcp2. Our results suggest that Scd6 can (i) recruit Dhh1 to confer translational repression and (ii) activate mRNA decapping by Dcp2 with attendant degradation of specific mRNAs in vivo, in a manner dependent on the Scd6 LSm domain and modulated by Ccr4.
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Affiliation(s)
- Quira Zeidan
- Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, MD, United States of America
| | - Feng He
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Fan Zhang
- Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, MD, United States of America
| | - Hongen Zhang
- Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, MD, United States of America
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Alan G. Hinnebusch
- Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, MD, United States of America
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19
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Singh A, Chowdhury D, Gupta A, Meena RC, Chakrabarti A. TORC1-signalling is down-regulated in Saccharomyces cerevisiae hsp30Δ cells by SNF1-dependent mechanisms. Yeast 2018; 35:653-667. [PMID: 30335186 DOI: 10.1002/yea.3360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 10/05/2018] [Accepted: 10/10/2018] [Indexed: 01/23/2023] Open
Abstract
Hsp30 is a plasma membrane localized heat shock protein in Saccharomyces cerevisiae whose expression is induced by numerous environmental stressors. Elucidation of its mechanism of action has remained elusive primarily because hsp30Δ cells do not show a strong phenotype. To identify cellular functions associated with Hsp30, we thus compared the transcriptome of BY4741hsp30Δ with that of its wild type counterpart. Our studies indicate down-regulation of the target of rapamycin complex 1 (TORC1)-dependent gene-expression programme in hsp30Δ cells. We further show that TORC1-signalling through its effectors (Sch9 and Tap42) was down-regulated in the deletion strain. Specifically, (a) phosphorylation levels of Sch9 were lower and nuclear exclusion of Rim15 (Sch9-downstream function) was overridden in hsp30Δ cells, (b) membrane association of Tor1 and Tap42 was lower in hsp30Δ cells, and (c) Tap42-downstream functions were abrogated in the deletion strain. Furthermore, transcription factors Rtg1, Rtg3, Gat1, and Gln3 were localized in the nucleus of the hsp30Δ as observed upon inactivation of TORC1. Studies aimed at determining how TORC1-signalling is down-regulated in hsp30Δ cells indicated that total reducing sugar levels were lower and ADP:ATP ratio was higher in hsp30Δ cells -conditions known to activate the Snf1 kinase and consequently to the inactivation of TORC1. We thus determined if TORC1-signalling could be restored in hsp30Δ cells upon the deletion of SNF1. Sch9 phosphorylation levels (TORC1-signalling) was restored to wild type levels in hsp30Δsnf1Δ cells. TORC1-signalling is thus down-regulated in hsp30Δ cells by SNF1-dependent mechanisms. A probable role for Hsp30 is discussed.
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Affiliation(s)
- Ajeet Singh
- Department of Molecular Biology, Defence Institute of Physiology and Allied Sciences, Delhi, India
| | - Daipayan Chowdhury
- Department of Molecular Biology, Defence Institute of Physiology and Allied Sciences, Delhi, India
| | - Avinash Gupta
- Department of Molecular Biology, Defence Institute of Physiology and Allied Sciences, Delhi, India
| | - Ramesh Chand Meena
- Department of Molecular Biology, Defence Institute of Physiology and Allied Sciences, Delhi, India
| | - Amitabha Chakrabarti
- Department of Molecular Biology, Defence Institute of Physiology and Allied Sciences, Delhi, India
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20
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Uppala JK, Ghosh C, Sathe L, Dey M. Phosphorylation of translation initiation factor eIF2α at Ser51 depends on site- and context-specific information. FEBS Lett 2018; 592:3116-3125. [PMID: 30070006 DOI: 10.1002/1873-3468.13214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 07/09/2018] [Accepted: 07/27/2018] [Indexed: 01/29/2023]
Abstract
Protein kinases phosphorylate specific amino acid residues of substrate proteins and regulate many cellular processes. Specificity for phosphorylation depends on the accessibility of these residues, and more importantly, kinases have preferences for certain residues flanking the phospho-acceptor site. Translation initiation factor 2α [eukaryotic translation initiation factor 2α (eIF2α)] kinase phosphorylates serine51 (Ser51) of eIF2α and downregulates cellular protein synthesis. Structural information on eIF2α reveals that Ser51 is located within a flexible loop, referred to as the Ser51 loop. Recently, we have shown that conformational change of the Ser51 loop increases the accessibility of Ser51 to the kinase active site for phosphorylation. Here, we show that the specificity of Ser51 phosphorylation depends largely on its relative position in the Ser51 loop and minimally on the flanking residues.
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Affiliation(s)
| | - Chandrima Ghosh
- Department of Biological Sciences, University of Wisconsin-Milwaukee, WI, USA
| | - Leena Sathe
- Department of Biological Sciences, University of Wisconsin-Milwaukee, WI, USA
| | - Madhusudan Dey
- Department of Biological Sciences, University of Wisconsin-Milwaukee, WI, USA
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21
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Fidelity of HIS4 start codon selection influences 3-amino-1,2,4-triazole sensitivity in GTPase activating protein function defective eIF5. J Genet 2018. [DOI: 10.1007/s12041-018-0989-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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22
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Charles Antony A, Alone PV. Fidelity of HIS4 start codon selection influences 3-amino-1,2,4-triazole sensitivity in GTPase activating protein function defective eIF5. J Genet 2018; 97:953-964. [PMID: 30262708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The eIF5 protein plays an important role in the fidelity of AUG start codon selection. However, the hyper GTPase eIF5G31R mutation in yeast causes preferential utilization of UUG as initiation codon and is termed as suppressor of initiation codon (Sui-) phenotype. The eIF5G31R mutant recognizes upUUG initiation codon from the 5' regulatory leader region of GCN4 transcript and dominantly represses GCN4 expression thereby conferring sensitivity to 3-amino-1,2,4-triazole (3AT)-induced starvation. The 3AT sensitivity was rescued by supplementing HIS4UUG allele. The eIF5G31R mutant has a better efficiency of UUG codon recognition from the HIS4UUG allele under starvation conditions. Moreover, the expression of HIS4UUG allele was significantly lower than the critical level causing additional derepression of GCN4 expression in eIF5G31R mutant to rescue its 3AT sensitivity. The overexpression of eIF1 improved expression of HIS4AUG allele and GCN4 transcript causing 3AT resistance, whereas overexpression of eIF1 resulted in diminished UUG codon recognition of HIS4UUG allele causing 3AT sensitivity, despite having higher GCN4 expression. This paper reports the critical role of HIS4 expression necessary in response to 3AT-induced starvation in the eIF5G31R mutant which is ostensibly not a direct target of 3AT inhibition.
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Affiliation(s)
- A Charles Antony
- School of Biological Sciences, National Institute of Science Education and Research, P.O. Jatni, Bhubaneswar, Khurda 752 050, India.
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23
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Hu Z, Xia B, Postnikoff SD, Shen ZJ, Tomoiaga AS, Harkness TA, Seol JH, Li W, Chen K, Tyler JK. Ssd1 and Gcn2 suppress global translation efficiency in replicatively aged yeast while their activation extends lifespan. eLife 2018; 7:35551. [PMID: 30117416 PMCID: PMC6097839 DOI: 10.7554/elife.35551] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/03/2018] [Indexed: 12/21/2022] Open
Abstract
Translational efficiency correlates with longevity, yet its role in lifespan determination remains unclear. Using ribosome profiling, translation efficiency is globally reduced during replicative aging in budding yeast by at least two mechanisms: Firstly, Ssd1 is induced during aging, sequestering mRNAs to P-bodies. Furthermore, Ssd1 overexpression in young cells reduced translation and extended lifespan, while loss of Ssd1 reduced the translational deficit of old cells and shortened lifespan. Secondly, phosphorylation of eIF2α, mediated by the stress kinase Gcn2, was elevated in old cells, contributing to the global reduction in translation without detectable induction of the downstream Gcn4 transcriptional activator. tRNA overexpression activated Gcn2 in young cells and extended lifespan in a manner dependent on Gcn4. Moreover, overexpression of Gcn4 sufficed to extend lifespan in an autophagy-dependent manner in the absence of changes in global translation, indicating that Gcn4-mediated autophagy induction is the ultimate downstream target of activated Gcn2, to extend lifespan.
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Affiliation(s)
- Zheng Hu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, United States
| | - Bo Xia
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, United States.,Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, United States
| | - Spike Dl Postnikoff
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, United States
| | - Zih-Jie Shen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, United States
| | - Alin S Tomoiaga
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, United States.,Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, United States.,Manhattan College, Bronx, United States
| | - Troy A Harkness
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, Canada
| | - Ja Hwan Seol
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, United States
| | - Wei Li
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, United States
| | - Kaifu Chen
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, United States.,Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, United States
| | - Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, United States
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24
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Regulation of Sensing, Transportation, and Catabolism of Nitrogen Sources in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 2018; 82:82/1/e00040-17. [PMID: 29436478 DOI: 10.1128/mmbr.00040-17] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Nitrogen is one of the most important essential nutrient sources for biogenic activities. Regulation of nitrogen metabolism in microorganisms is complicated and elaborate. For this review, the yeast Saccharomyces cerevisiae was chosen to demonstrate the regulatory mechanism of nitrogen metabolism because of its relative clear genetic background. Current opinions on the regulation processes of nitrogen metabolism in S. cerevisiae, including nitrogen sensing, transport, and catabolism, are systematically reviewed. Two major upstream signaling pathways, the Ssy1-Ptr3-Ssy5 sensor system and the target of rapamycin pathway, which are responsible for sensing extracellular and intracellular nitrogen, respectively, are discussed. The ubiquitination of nitrogen transporters, which is the most general and efficient means for controlling nitrogen transport, is also summarized. The following metabolic step, nitrogen catabolism, is demonstrated at two levels: the transcriptional regulation process related to GATA transcriptional factors and the translational regulation process related to the general amino acid control pathway. The interplay between nitrogen regulation and carbon regulation is also discussed. As a model system, understanding the meticulous process by which nitrogen metabolism is regulated in S. cerevisiae not only could facilitate research on global regulation mechanisms and yeast metabolic engineering but also could provide important insights and inspiration for future studies of other common microorganisms and higher eukaryotic cells.
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25
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Martin-Marcos P, Zhou F, Karunasiri C, Zhang F, Dong J, Nanda J, Kulkarni SD, Sen ND, Tamame M, Zeschnigk M, Lorsch JR, Hinnebusch AG. eIF1A residues implicated in cancer stabilize translation preinitiation complexes and favor suboptimal initiation sites in yeast. eLife 2017; 6:31250. [PMID: 29206102 PMCID: PMC5756025 DOI: 10.7554/elife.31250] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/04/2017] [Indexed: 11/13/2022] Open
Abstract
The translation pre-initiation complex (PIC) scans the mRNA for an AUG codon in favorable context, and AUG recognition stabilizes a closed PIC conformation. The unstructured N-terminal tail (NTT) of yeast eIF1A deploys five basic residues to contact tRNAi, mRNA, or 18S rRNA exclusively in the closed state. Interestingly, EIF1AX mutations altering the human eIF1A NTT are associated with uveal melanoma (UM). We found that substituting all five basic residues, and seven UM-associated substitutions, in yeast eIF1A suppresses initiation at near-cognate UUG codons and AUGs in poor context. Ribosome profiling of NTT substitution R13P reveals heightened discrimination against unfavorable AUG context genome-wide. Both R13P and K16D substitutions destabilize the closed complex at UUG codons in reconstituted PICs. Thus, electrostatic interactions involving the eIF1A NTT stabilize the closed conformation and promote utilization of suboptimal start codons. We predict UM-associated mutations alter human gene expression by increasing discrimination against poor initiation sites.
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Affiliation(s)
- Pilar Martin-Marcos
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States.,Instituto de Biología Funcional y Genómica, IBFG-CSIC, Universidad de Salamanca, Salamanca, Spain
| | - Fujun Zhou
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
| | - Charm Karunasiri
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
| | - Fan Zhang
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
| | - Jinsheng Dong
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
| | - Jagpreet Nanda
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
| | - Shardul D Kulkarni
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
| | - Neelam Dabas Sen
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
| | - Mercedes Tamame
- Instituto de Biología Funcional y Genómica, IBFG-CSIC, Universidad de Salamanca, Salamanca, Spain
| | - Michael Zeschnigk
- Institute of Human Genetics, University Duisburg-Essen, Essen, Germany.,Eye Cancer Research Group, Faculty of Medicine, University Duisburg-Essen, Essen, Germany
| | - Jon R Lorsch
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
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26
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Antony A C, Alone PV. Defect in the GTPase activating protein (GAP) function of eIF5 causes repression of GCN4 translation. Biochem Biophys Res Commun 2017; 486:1110-1115. [PMID: 28385532 DOI: 10.1016/j.bbrc.2017.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 04/01/2017] [Indexed: 10/19/2022]
Abstract
In eukaryotes, the eIF5 protein plays an important role in translation start site selection by providing the GAP (GTPase activating protein) function. However, in yeast translation initiation fidelity defective eIF5G31R mutant causes preferential utilization of UUG as initiation codon and is termed as Suppressor of initiation codon (Sui-) phenotype due to its hyper GTPase activity. The eIF5G31R mutant dominantly represses GCN4 expression and confers sensitivity to 3-Amino-1,2,4-Trizole (3AT) induced starvation. The down-regulation of the GCN4 expression (Gcn- phenotype) in the eIF5G31R mutant was not because of leaky scanning defects; rather was due to the utilization of upUUG initiation codons at the 5' regulatory region present between uORF1 and the main GCN4 ORF.
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Affiliation(s)
- Charles Antony A
- School of Biological Sciences, National Institute of Science Education and Research Bhubaneswar, Constituent Institutes of Homi Bhabha National Institute (HBNI), P.O Jatni, Khurda 752050 India
| | - Pankaj V Alone
- School of Biological Sciences, National Institute of Science Education and Research Bhubaneswar, Constituent Institutes of Homi Bhabha National Institute (HBNI), P.O Jatni, Khurda 752050 India.
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27
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Lord CL, Ospovat O, Wente SR. Nup100 regulates Saccharomyces cerevisiae replicative life span by mediating the nuclear export of specific tRNAs. RNA (NEW YORK, N.Y.) 2017; 23:365-377. [PMID: 27932586 PMCID: PMC5311497 DOI: 10.1261/rna.057612.116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 11/29/2016] [Indexed: 06/06/2023]
Abstract
Nuclear pore complexes (NPCs), which are composed of nucleoporins (Nups) and regulate transport between the nucleus and cytoplasm, significantly impact the replicative life span (RLS) of Saccharomyces cerevisiae We previously reported that deletion of the nonessential gene NUP100 increases RLS, although the molecular basis for this effect was unknown. In this study, we find that nuclear tRNA accumulation contributes to increased longevity in nup100Δ cells. Fluorescence in situ hybridization (FISH) experiments demonstrate that several specific tRNAs accumulate in the nuclei of nup100Δ mutants. Protein levels of the transcription factor Gcn4 are increased when NUP100 is deleted, and GCN4 is required for the elevated life spans of nup100Δ mutants, similar to other previously described tRNA export and ribosomal mutants. Northern blots indicate that tRNA splicing and aminoacylation are not significantly affected in nup100Δ cells, suggesting that Nup100 is largely required for nuclear export of mature, processed tRNAs. Distinct tRNAs accumulate in the nuclei of nup100Δ and msn5Δ mutants, while Los1-GFP nucleocytoplasmic shuttling is unaffected by Nup100. Thus, we conclude that Nup100 regulates tRNA export in a manner distinct from Los1 or Msn5. Together, these experiments reveal a novel Nup100 role in the tRNA life cycle that impacts the S. cerevisiae life span.
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Affiliation(s)
- Christopher L Lord
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37240, USA
| | - Ophir Ospovat
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37240, USA
| | - Susan R Wente
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37240, USA
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28
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Visweswaraiah J, Hinnebusch AG. Interface between 40S exit channel protein uS7/Rps5 and eIF2α modulates start codon recognition in vivo. eLife 2017; 6. [PMID: 28169832 PMCID: PMC5323038 DOI: 10.7554/elife.22572] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/06/2017] [Indexed: 12/26/2022] Open
Abstract
The eukaryotic pre-initiation complex (PIC) bearing the eIF2·GTP·Met-tRNAiMet ternary complex (TC) scans the mRNA for an AUG codon in favorable context. AUG recognition evokes rearrangement of the PIC from an open, scanning to a closed, arrested conformation. Cryo-EM reconstructions of yeast PICs suggest remodeling of the interface between 40S protein Rps5/uS7 and eIF2α between open and closed states; however, its importance was unknown. uS7 substitutions disrupting eIF2α contacts favored in the open complex increase initiation at suboptimal sites, and uS7-S223D stabilizes TC binding to PICs reconstituted with a UUG start codon, indicating inappropriate rearrangement to the closed state. Conversely, uS7-D215 substitutions, perturbing uS7-eIF2α interaction in the closed state, confer the opposite phenotypes of hyperaccuracy and (for D215L) accelerated TC dissociation from reconstituted PICs. Thus, remodeling of the uS7/eIF2α interface appears to stabilize first the open, and then the closed state of the PIC to promote accurate AUG selection in vivo. DOI:http://dx.doi.org/10.7554/eLife.22572.001
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Affiliation(s)
- Jyothsna Visweswaraiah
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
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29
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Skopkova M, Hennig F, Shin BS, Turner CE, Stanikova D, Brennerova K, Stanik J, Fischer U, Henden L, Müller U, Steinberger D, Leshinsky-Silver E, Bottani A, Kurdiova T, Ukropec J, Nyitrayova O, Kolnikova M, Klimes I, Borck G, Bahlo M, Haas SA, Kim JR, Lotspeich-Cole LE, Gasperikova D, Dever TE, Kalscheuer VM. EIF2S3 Mutations Associated with Severe X-Linked Intellectual Disability Syndrome MEHMO. Hum Mutat 2017; 38:409-425. [PMID: 28055140 DOI: 10.1002/humu.23170] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/19/2016] [Accepted: 01/02/2017] [Indexed: 12/15/2022]
Abstract
Impairment of translation initiation and its regulation within the integrated stress response (ISR) and related unfolded-protein response has been identified as a cause of several multisystemic syndromes. Here, we link MEHMO syndrome, whose genetic etiology was unknown, to this group of disorders. MEHMO is a rare X-linked syndrome characterized by profound intellectual disability, epilepsy, hypogonadism and hypogenitalism, microcephaly, and obesity. We have identified a C-terminal frameshift mutation (Ile465Serfs) in the EIF2S3 gene in three families with MEHMO syndrome and a novel maternally inherited missense EIF2S3 variant (c.324T>A; p.Ser108Arg) in another male patient with less severe clinical symptoms. The EIF2S3 gene encodes the γ subunit of eukaryotic translation initiation factor 2 (eIF2), crucial for initiation of protein synthesis and regulation of the ISR. Studies in patient fibroblasts confirm increased ISR activation due to the Ile465Serfs mutation and functional assays in yeast demonstrate that the Ile465Serfs mutation impairs eIF2γ function to a greater extent than tested missense mutations, consistent with the more severe clinical phenotype of the Ile465Serfs male mutation carriers. Thus, we propose that more severe EIF2S3 mutations cause the full MEHMO phenotype, while less deleterious mutations cause a milder form of the syndrome with only a subset of the symptoms.
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Affiliation(s)
- Martina Skopkova
- DIABGENE & Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Friederike Hennig
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Byung-Sik Shin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Clesson E Turner
- Department of Genetics, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Daniela Stanikova
- DIABGENE & Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia.,First Department of Pediatrics, Medical Faculty of Comenius University, Bratislava, Slovakia
| | - Katarina Brennerova
- First Department of Pediatrics, Medical Faculty of Comenius University, Bratislava, Slovakia
| | - Juraj Stanik
- DIABGENE & Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia.,First Department of Pediatrics, Medical Faculty of Comenius University, Bratislava, Slovakia.,Center for Pediatric Research Leipzig, Hospital for Children & Adolescents, University of Leipzig, Germany
| | - Ute Fischer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lyndal Henden
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Ulrich Müller
- Institut für Humangenetik, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Daniela Steinberger
- Institut für Humangenetik, Justus-Liebig-Universität Giessen, Giessen, Germany.,bio.logis Center for Human Genetics, Frankfurt a. M., Germany
| | - Esther Leshinsky-Silver
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel.,Metabolic-Neurogenetic Clinic, Wolfson Medical Center, Holon, Israel.,Molecular Genetics Laboratory, Wolfson Medical Center, Holon, Israel
| | - Armand Bottani
- Service of Genetic Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Timea Kurdiova
- DIABGENE & Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jozef Ukropec
- DIABGENE & Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Miriam Kolnikova
- Department of Pediatric Neurology, Medical Faculty of Comenius University, Bratislava, Slovakia
| | - Iwar Klimes
- DIABGENE & Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Guntram Borck
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Joo-Ran Kim
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Leda E Lotspeich-Cole
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Daniela Gasperikova
- DIABGENE & Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
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30
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Vlahakis A, Lopez Muniozguren N, Powers T. Calcium channel regulator Mid1 links TORC2-mediated changes in mitochondrial respiration to autophagy. J Cell Biol 2016; 215:779-788. [PMID: 27899413 PMCID: PMC5166500 DOI: 10.1083/jcb.201605030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 09/02/2016] [Accepted: 11/08/2016] [Indexed: 01/03/2023] Open
Abstract
Rapamycin-insensitive TORC2 signaling promotes amino acid starvation–induced autophagy through inhibition of the calcium-dependent phosphatase calcineurin. Vlahakis et al. show that this regulation requires the ER calcium channel regulatory protein Mid1, which couples mitochondrial ROS accumulation in TORC2 mutants to calcineurin activation and autophagy repression. Autophagy is a catabolic process that recycles cytoplasmic contents and is crucial for cell survival during stress. The target of rapamycin (TOR) kinase regulates autophagy as part of two distinct protein complexes, TORC1 and TORC2. TORC1 negatively regulates autophagy according to nitrogen availability. In contrast, TORC2 functions as a positive regulator of autophagy during amino acid starvation, via its target kinase Ypk1, by repressing the activity of the calcium-dependent phosphatase calcineurin and promoting the general amino acid control (GAAC) response. Precisely how TORC2-Ypk1 signaling regulates calcineurin within this pathway remains unknown. Here we demonstrate that activation of calcineurin requires Mid1, an endoplasmic reticulum–localized calcium channel regulatory protein implicated in the oxidative stress response. We find that normal mitochondrial respiration is perturbed in TORC2-Ypk1–deficient cells, which results in the accumulation of mitochondrial-derived reactive oxygen species that signal to Mid1 to activate calcineurin, thereby inhibiting the GAAC response and autophagy. These findings describe a novel pathway involving TORC2, mitochondrial oxidative stress, and calcium homeostasis for autophagy regulation.
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Affiliation(s)
- Ariadne Vlahakis
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, CA 95616
| | - Nerea Lopez Muniozguren
- 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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31
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He C, Tsuchiyama SK, Nguyen QT, Plyusnina EN, Terrill SR, Sahibzada S, Patel B, Faulkner AR, Shaposhnikov MV, Tian R, Tsuchiya M, Kaeberlein M, Moskalev AA, Kennedy BK, Polymenis M. Enhanced longevity by ibuprofen, conserved in multiple species, occurs in yeast through inhibition of tryptophan import. PLoS Genet 2014; 10:e1004860. [PMID: 25521617 PMCID: PMC4270464 DOI: 10.1371/journal.pgen.1004860] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 10/29/2014] [Indexed: 11/29/2022] Open
Abstract
The common non-steroidal anti-inflammatory drug ibuprofen has been associated with a reduced risk of some age-related pathologies. However, a general pro-longevity role for ibuprofen and its mechanistic basis remains unclear. Here we show that ibuprofen increased the lifespan of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster, indicative of conserved eukaryotic longevity effects. Studies in yeast indicate that ibuprofen destabilizes the Tat2p permease and inhibits tryptophan uptake. Loss of Tat2p increased replicative lifespan (RLS), but ibuprofen did not increase RLS when Tat2p was stabilized or in an already long-lived strain background impaired for aromatic amino acid uptake. Concomitant with lifespan extension, ibuprofen moderately reduced cell size at birth, leading to a delay in the G1 phase of the cell cycle. Similar changes in cell cycle progression were evident in a large dataset of replicatively long-lived yeast deletion strains. These results point to fundamental cell cycle signatures linked with longevity, implicate aromatic amino acid import in aging and identify a largely safe drug that extends lifespan across different kingdoms of life. Aging is the greatest risk factor for many diseases, which together account for the majority of global deaths and healthcare costs. Here we show that the common drug ibuprofen increases the lifespan of yeast, worms and flies, indicative of conserved longevity effects. In budding yeast, an excellent model of cellular longevity mechanisms, ibuprofen's pro-longevity action is independent of its known anti-inflammatory role. We show that the critical function of ibuprofen in longevity is to inhibit the uptake of aromatic amino acids, by destabilizing the high-affinity tryptophan permease. We further show that ibuprofen alters cell cycle progression. Mirroring the effects of ibuprofen, we found that most yeast long-lived mutants were also similarly affected in cell cycle progression. These findings identify a safe drug that extends the lifespan of divergent organisms and reveal fundamental cellular properties associated with longevity.
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Affiliation(s)
- Chong He
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Scott K. Tsuchiyama
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Quynh T. Nguyen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Ekaterina N. Plyusnina
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia
- Syktyvkar State University, Syktyvkar, Russia
| | - Samuel R. Terrill
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Sarah Sahibzada
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Bhumil Patel
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Alena R. Faulkner
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Mikhail V. Shaposhnikov
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia
- Syktyvkar State University, Syktyvkar, Russia
| | - Ruilin Tian
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Mitsuhiro Tsuchiya
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Alexey A. Moskalev
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia
- Syktyvkar State University, Syktyvkar, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | - Brian K. Kennedy
- Buck Institute for Research on Aging, Novato, California, United States of America
- * E-mail: (BKK); (MP)
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
- * E-mail: (BKK); (MP)
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32
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Rawal Y, Qiu H, Hinnebusch AG. Accumulation of a threonine biosynthetic intermediate attenuates general amino acid control by accelerating degradation of Gcn4 via Pho85 and Cdk8. PLoS Genet 2014; 10:e1004534. [PMID: 25079372 PMCID: PMC4117449 DOI: 10.1371/journal.pgen.1004534] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 06/11/2014] [Indexed: 11/19/2022] Open
Abstract
Gcn4 is a master transcriptional regulator of amino acid and vitamin biosynthetic enzymes subject to the general amino acid control (GAAC), whose expression is upregulated in response to amino acid starvation in Saccharomyces cerevisiae. We found that accumulation of the threonine pathway intermediate β-aspartate semialdehyde (ASA), substrate of homoserine dehydrogenase (Hom6), attenuates the GAAC transcriptional response by accelerating degradation of Gcn4, already an exceedingly unstable protein, in cells starved for isoleucine and valine. The reduction in Gcn4 abundance on ASA accumulation requires Cdk8/Srb10 and Pho85, cyclin-dependent kinases (CDKs) known to mediate rapid turnover of Gcn4 by the proteasome via phosphorylation of the Gcn4 activation domain under nonstarvation conditions. Interestingly, rescue of Gcn4 abundance in hom6 cells by elimination of SRB10 is not accompanied by recovery of transcriptional activation, while equivalent rescue of UAS-bound Gcn4 in hom6 pho85 cells restores greater than wild-type activation of Gcn4 target genes. These and other findings suggest that the two CDKs target different populations of Gcn4 on ASA accumulation, with Srb10 clearing mostly inactive Gcn4 molecules at the promoter that are enriched for sumoylation of the activation domain, and Pho85 clearing molecules unbound to the UAS that include both fully functional and inactive Gcn4 species. Transcriptional activator Gcn4 maintains amino acid homeostasis in budding yeast by inducing multiple amino acid biosynthetic pathways in response to starvation for any amino acid—the general amino acid control. Gcn4 abundance is tightly regulated by the interplay between an intricate translational control mechanism, which induces Gcn4 synthesis in starved cells, and a pathway of phosphorylation and ubiquitylation that mediates its rapid degradation by the proteasome. Here, we discovered that accumulation of a threonine biosynthetic pathway intermediate, β-aspartate semialdehyde (ASA), in hom6Δ mutant cells impairs general amino acid control in cells starved for isoleucine and valine by accelerating the already rapid degradation of Gcn4, in a manner requiring its phosphorylation by cyclin-dependent kinases Cdk8/Srb10 and Pho85. Interestingly, our results unveil a division of labor between these two kinases wherein Srb10 primarily targets inactive Gcn4 molecules—presumably damaged under conditions of ASA excess—while Pho85 clears a greater proportion of functional Gcn4 species from the cell. The ability of ASA to inhibit transcriptional induction of threonine pathway enzymes by Gcn4, dampening ASA accumulation and its toxic effects on cell physiology, should be adaptive in the wild when yeast encounters natural antibiotics that target Hom6 enzymatic activity.
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Affiliation(s)
- Yashpal Rawal
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hongfang Qiu
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alan G. Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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33
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Martin-Marcos P, Nanda JS, Luna RE, Zhang F, Saini AK, Cherkasova VA, Wagner G, Lorsch JR, Hinnebusch AG. Enhanced eIF1 binding to the 40S ribosome impedes conformational rearrangements of the preinitiation complex and elevates initiation accuracy. RNA (NEW YORK, N.Y.) 2014; 20:150-67. [PMID: 24335188 PMCID: PMC3895268 DOI: 10.1261/rna.042069.113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 10/17/2013] [Indexed: 05/20/2023]
Abstract
In the current model of translation initiation by the scanning mechanism, eIF1 promotes an open conformation of the 40S subunit competent for rapidly loading the eIF2·GTP·Met-tRNAi ternary complex (TC) in a metastable conformation (POUT) capable of sampling triplets entering the P site while blocking accommodation of Met-tRNAi in the PIN state and preventing completion of GTP hydrolysis (Pi release) by the TC. All of these functions should be reversed by eIF1 dissociation from the preinitiation complex (PIC) on AUG recognition. We tested this model by selecting eIF1 Ssu(-) mutations that suppress the elevated UUG initiation and reduced rate of TC loading in vivo conferred by an eIF1 (Sui(-)) substitution that eliminates a direct contact of eIF1 with the 40S subunit. Importantly, several Ssu(-) substitutions increase eIF1 affinity for 40S subunits in vitro, and the strongest-binding variant (D61G), predicted to eliminate ionic repulsion with 18S rRNA, both reduces the rate of eIF1 dissociation and destabilizes the PIN state of TC binding in reconstituted PICs harboring Sui(-) variants of eIF5 or eIF2. These findings establish that eIF1 dissociation from the 40S subunit is required for the PIN mode of TC binding and AUG recognition and that increasing eIF1 affinity for the 40S subunit increases initiation accuracy in vivo. Our results further demonstrate that the GTPase-activating protein eIF5 and β-subunit of eIF2 promote accuracy by controlling eIF1 dissociation and the stability of TC binding to the PIC, beyond their roles in regulating GTP hydrolysis by eIF2.
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Affiliation(s)
- Pilar Martin-Marcos
- Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jagpreet S. Nanda
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Rafael E. Luna
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Fan Zhang
- Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Adesh K. Saini
- Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
- Department of Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh-173212, India
| | - Vera A. Cherkasova
- Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jon R. Lorsch
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Corresponding authorsE-mail E-mail
| | - Alan G. Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
- Corresponding authorsE-mail E-mail
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34
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Abstract
The purpose of this assay is to measure the incorporation of radiolabeled [(35)S]-methionine into newly synthesized proteins in exponentially growing yeast cells. This allows for a quantitative in vivo measurement of total protein synthesis.
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35
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Xu X, Hu J, McGrath BC, Cavener DR. GCN2 regulates the CCAAT enhancer binding protein beta and hepatic gluconeogenesis. Am J Physiol Endocrinol Metab 2013; 305:E1007-17. [PMID: 23900421 PMCID: PMC3798698 DOI: 10.1152/ajpendo.00063.2013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mice deficient for general control nondepressible-2 (Gcn2) either globally or specifically in the liver display reduced capacity to maintain glucose homeostasis during fasting, suggesting the hypothesis that GCN2 may regulate gluconeogenesis (GNG), which normally plays a key role maintaining peripheral glucose homeostasis. Gcn2-deficient mice exhibit normal insulin sensitivity and plasma insulin but show reduced GNG when administered pyruvate, a gluconeogenic substrate. The basal expression of phosphoenolpyruvate carboxykinase, a rate-limiting enzyme in GNG, is abnormally elevated in Gcn2 knockout (KO) mice in the fed state but fails to be further induced during fasting. The level of tricarboxylic acid cycle intermediates, including malate and oxaloacetate, and the NADH-to-NAD(+) ratio are perturbed in the liver of Gcn2 KO mice either in the fed or fasted state, which may directly impinge upon GNG. Additionally, the expression of the CCAAT enhancer-binding protein-β (C/EBPβ) in the liver fails to be induced in Gcn2 KO mice after 24 h fasting, and the liver-specific Cebpβ KO mice show reduced fasting GNG similar to that seen in Gcn2-deficient mice. Our study demonstrates that GCN2 is important in maintaining GNG in the liver, which is likely to be mediated through regulation of C/EBPβ.
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Affiliation(s)
- Xu Xu
- Department of Biology, Center for Cellular Dynamics, Pennsylvania State University, University Park, Pennsylvania
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36
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Thorburn RR, Gonzalez C, Brar GA, Christen S, Carlile TM, Ingolia NT, Sauer U, Weissman JS, Amon A. Aneuploid yeast strains exhibit defects in cell growth and passage through START. Mol Biol Cell 2013; 24:1274-89. [PMID: 23468524 PMCID: PMC3639041 DOI: 10.1091/mbc.e12-07-0520] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Aneuploidy causes cell proliferation defects in budding yeast, with many aneuploid strains exhibiting a G1 delay. This study shows that the G1 delay in aneuploid budding yeast is caused by a growth defect and delayed passage through START due to delayed G1 cyclin accumulation. Aneuploidy, a chromosome content that is not a multiple of the haploid karyotype, is associated with reduced fitness in all organisms analyzed to date. In budding yeast aneuploidy causes cell proliferation defects, with many different aneuploid strains exhibiting a delay in G1, a cell cycle stage governed by extracellular cues, growth rate, and cell cycle events. Here we characterize this G1 delay. We show that 10 of 14 aneuploid yeast strains exhibit a growth defect during G1. Furthermore, 10 of 14 aneuploid strains display a cell cycle entry delay that correlates with the size of the additional chromosome. This cell cycle entry delay is due to a delayed accumulation of G1 cyclins that can be suppressed by supplying cells with high levels of a G1 cyclin. Our results indicate that aneuploidy frequently interferes with the ability of cells to grow and, as with many other cellular stresses, entry into the cell cycle.
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Affiliation(s)
- Rebecca R Thorburn
- David H. Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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37
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Borck G, Shin BS, Stiller B, Mimouni-Bloch A, Thiele H, Kim JR, Thakur M, Skinner C, Aschenbach L, Smirin-Yosef P, Har-Zahav A, Nürnberg G, Altmüller J, Frommolt P, Hofmann K, Konen O, Nürnberg P, Munnich A, Schwartz CE, Gothelf D, Colleaux L, Dever TE, Kubisch C, Basel-Vanagaite L. eIF2γ mutation that disrupts eIF2 complex integrity links intellectual disability to impaired translation initiation. Mol Cell 2012; 48:641-6. [PMID: 23063529 DOI: 10.1016/j.molcel.2012.09.005] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 07/24/2012] [Accepted: 09/06/2012] [Indexed: 12/26/2022]
Abstract
Together with GTP and initiator methionyl-tRNA, translation initiation factor eIF2 forms a ternary complex that binds the 40S ribosome and then scans an mRNA to select the AUG start codon for protein synthesis. Here, we show that a human X-chromosomal neurological disorder characterized by intellectual disability and microcephaly is caused by a missense mutation in eIF2γ (encoded by EIF2S3), the core subunit of the heterotrimeric eIF2 complex. Biochemical studies of human cells overexpressing the eIF2γ mutant and of yeast eIF2γ with the analogous mutation revealed a defect in binding the eIF2β subunit to eIF2γ. Consistent with this loss of eIF2 integrity, the yeast eIF2γ mutation impaired translation start codon selection and eIF2 function in vivo in a manner that was suppressed by overexpressing eIF2β. These findings directly link intellectual disability to impaired translation initiation, and provide a mechanistic basis for the human disease due to partial loss of eIF2 function.
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Affiliation(s)
- Guntram Borck
- Institute of Human Genetics, University of Ulm, Ulm, Germany.
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38
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Initiation factor eIF2γ promotes eIF2-GTP-Met-tRNAi(Met) ternary complex binding to the 40S ribosome. Nat Struct Mol Biol 2011; 18:1227-34. [PMID: 22002225 PMCID: PMC3210414 DOI: 10.1038/nsmb.2133] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Accepted: 08/09/2011] [Indexed: 11/24/2022]
Abstract
In contrast to elongation factor EF-Tu, which delivers aminoacyl-tRNAs to the ribosomal A-site, eukaryotic initiation factor eIF2 binds initiator Met-tRNAiMet to the P-site of the 40S ribosomal subunit. We used directed hydroxyl radical probing experiments to map the binding of Saccharomyces cerevisiae eIF2 on the ribosome and on Met-tRNAiMet. Our results identify a key binding-interface between domain III of eIF2γ and 18S rRNA helix h44 on the 40S subunit. Moreover, we showed that eIF2γ primarily contacts the acceptor stem of Met-tRNAiMet. Whereas the analogous domain III of EF-Tu contacts the T-stem of tRNAs, biochemical analyses demonstrated that eIF2γ domain III is important for ribosome, but not Met-tRNAiMet, binding. Thus despite their structural similarity, eIF2 and EF-Tu bind tRNAs in substantially different manners, and we propose that the tRNA-binding domain III of EF-Tu has acquired a new ribosome-binding function in eIF2γ.
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39
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Shin BS, Acker MG, Kim JR, Maher KN, Arefin SM, Lorsch JR, Dever TE. Structural integrity of {alpha}-helix H12 in translation initiation factor eIF5B is critical for 80S complex stability. RNA (NEW YORK, N.Y.) 2011; 17:687-696. [PMID: 21335519 PMCID: PMC3062179 DOI: 10.1261/rna.2412511] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 12/21/2010] [Indexed: 05/30/2023]
Abstract
Translation initiation factor eIF5B promotes GTP-dependent ribosomal subunit joining in the final step of the translation initiation pathway. The protein resembles a chalice with the α-helix H12 forming the stem connecting the GTP-binding domain cup to the domain IV base. Helix H12 has been proposed to function as a rigid lever arm governing domain IV movements in response to nucleotide binding and as a molecular ruler fixing the distance between domain IV and the G domain of the factor. To investigate its function, helix H12 was lengthened or shortened by one or two turns. In addition, six consecutive residues in the helix were substituted by Gly to alter the helical rigidity. Whereas the mutations had minimal impacts on the factor's binding to the ribosome and its GTP binding and hydrolysis activities, shortening the helix by six residues impaired the rate of subunit joining in vitro and both this mutation and the Gly substitution mutation lowered the yield of Met-tRNA(i)(Met) bound to 80S complexes formed in the presence of nonhydrolyzable GTP. Thus, these two mutations, which impair yeast cell growth and enhance ribosome leaky scanning in vivo, impair the rate of formation and stability of the 80S product of subunit joining. These data support the notion that helix H12 functions as a ruler connecting the GTPase center of the ribosome to the P site where Met-tRNA(i)(Met) is bound and that helix H12 rigidity is required to stabilize Met-tRNA(i)(Met) binding.
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Affiliation(s)
- Byung-Sik Shin
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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40
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Zhang F, Hinnebusch AG. An upstream ORF with non-AUG start codon is translated in vivo but dispensable for translational control of GCN4 mRNA. Nucleic Acids Res 2011; 39:3128-40. [PMID: 21227927 PMCID: PMC3082883 DOI: 10.1093/nar/gkq1251] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Genome-wide analysis of ribosome locations in mRNAs of Saccharomyces cerevisiae has revealed the translation of upstream open reading frames that initiate with near-cognate start codons in many transcripts. Two such non-translation initiation codon (AUG)-initiated upstream open reading frames (uORFs) (nAuORFs 1 and 2) occur in GCN4 mRNA upstream of the four AUG-initiated uORFs (uORFs 1–4) that regulate GCN4 translation. We verified that nAuORF2 is translated in vivo by demonstrating β-galactosidase production from lacZ coding sequences fused to nAuORF2, in a manner abolished by replacing its non-AUG initiation codon (AUA) start codon with the non-cognate triplet AAA, whereas translation of nAuORF1 was not detected. Importantly, replacing the near-cognate start codons of both nAuORFs with non-cognate triplets had little or no effect on the repression of GCN4 translation in non-starved cells, nor on its derepression in response to histidine limitation, nutritional shift-down or treatment with rapamycin, hydrogen peroxide or methyl methanesulfonate. Additionally, we found no evidence that initiation from the AUA codon of nAuORF2 is substantially elevated, or dependent on Gcn2, the sole eIF2α kinase of yeast, in histidine-deprived cells. Thus, although nAuORF2 is translated in vivo, it appears that this event is not stimulated by eIF2α phosphorylation nor significantly influences GCN4 translational induction under various starvation or stress conditions.
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Affiliation(s)
- Fan Zhang
- Laboratory of Gene Regulation and Development, Eunice K Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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41
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Hernández H, Aranda C, Riego L, González A. Gln3-Gcn4 hybrid transcriptional activator determines catabolic and biosynthetic gene expression in the yeast Saccharomyces cerevisiae. Biochem Biophys Res Commun 2010; 404:859-64. [PMID: 21184740 DOI: 10.1016/j.bbrc.2010.12.075] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 12/15/2010] [Indexed: 10/18/2022]
Abstract
The yeast Saccharomyces cerevisiae is able to sense the availability and quality of nitrogen sources and the intrinsic variation of amino acid disponibility for protein synthesis. When this yeast is provided with secondary nitrogen sources, transcription of genes encoding enzymes involved in their catabolism is elicited through the action of Gln3, which constitutes the main activator of the Nitrogen Catabolite Repression network (NCR). Activation of genes encoding enzymes involved in the amino acid biosynthetic pathways is achieved through the action of the GCN4-encoded transcriptional modulator whose transcriptional activation is induced at the translational level by limitation for any amino acid. Thus the role of each one of these activators had been secluded to either catabolic or biosynthetic pathways. However, some observations have suggested that under peculiar physiological conditions, Gln3 and Gcn4 could act simultaneously in order to contemporaneously increase expression of both sets of genes. This paper addresses the question of whether Gln3 and Gcn4 cooperatively determine expression of their target genes. Results presented herein show that induced expression of catabolic and biosynthetic genes when cells are grown under nitrogen derepressive conditions and amino acid deprivation is dependent on the concurrent action of Gln3 and Gcn4, which form part of a unique transcriptional complex. We propose that the combination of Gln3 and Gcn4 results in the constitution of a hybrid modulator which elicits a novel transcriptional response, not evoked when these modulators act in a non-combinatorial fashion.
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Affiliation(s)
- Hugo Hernández
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, 04510 Mexico City, Mexico
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42
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Metabolic control of antifungal drug resistance. Fungal Genet Biol 2010; 47:81-93. [DOI: 10.1016/j.fgb.2009.07.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Revised: 07/01/2009] [Accepted: 07/06/2009] [Indexed: 11/16/2022]
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43
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Alvers AL, Fishwick LK, Wood MS, Hu D, Chung HS, Dunn WA, Aris JP. Autophagy and amino acid homeostasis are required for chronological longevity in Saccharomyces cerevisiae. Aging Cell 2009; 8:353-69. [PMID: 19302372 DOI: 10.1111/j.1474-9726.2009.00469.x] [Citation(s) in RCA: 190] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Following cessation of growth, yeast cells remain viable in a nondividing state for a period of time known as the chronological lifespan (CLS). Autophagy is a degradative process responsible for amino acid recycling in response to nitrogen starvation and amino acid limitation. We have investigated the role of autophagy during chronological aging of yeast grown in glucose minimal media containing different supplemental essential and nonessential amino acids. Deletion of ATG1 or ATG7, both of which are required for autophagy, reduced CLS, whereas deletion of ATG11, which is required for selective targeting of cellular components to the vacuole for degradation, did not reduce CLS. The nonessential amino acids isoleucine and valine, and the essential amino acid leucine, extended CLS in autophagy-deficient as well as autophagy-competent yeast. This extension was suppressed by constitutive expression of GCN4, which encodes a transcriptional regulator of general amino acid control (GAAC). Consistent with this, GCN4 expression was reduced by isoleucine and valine. Furthermore, elimination of the leucine requirement extended CLS and prevented the effects of constitutive expression of GCN4. Interestingly, deletion of LEU3, a GAAC target gene encoding a transcriptional regulator of branched side chain amino acid synthesis, dramatically increased CLS in the absence of amino acid supplements. In general, this indicates that activation of GAAC reduces CLS whereas suppression of GAAC extends CLS in minimal medium. These findings demonstrate important roles for autophagy and amino acid homeostasis in determining CLS in yeast.
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Affiliation(s)
- Ashley L Alvers
- Department of Anatomy and Cell Biology, Health Science Center, University of Florida, Gainesville, 32610-0235, USA
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44
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Smets B, De Snijder P, Engelen K, Joossens E, Ghillebert R, Thevissen K, Marchal K, Winderickx J. Genome-wide expression analysis reveals TORC1-dependent and -independent functions of Sch9. FEMS Yeast Res 2008; 8:1276-88. [DOI: 10.1111/j.1567-1364.2008.00432.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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45
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de Almeida RA, Burgess D, Shema R, Motlekar N, Napper AD, Diamond SL, Pavitt GD. A Saccharomyces cerevisiae cell-based quantitative beta-galactosidase assay compatible with robotic handling and high-throughput screening. Yeast 2008; 25:71-6. [PMID: 17957822 DOI: 10.1002/yea.1570] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Reporter-gene assays that employ the Escherichia coli lacZ gene are ubiquitously employed in biological research. However, we were not able to readily identify a quantitative method that worked reliably with yeast (Saccharomyces cerevisiae) cells and that was compatible with high-throughput screening and robotic liquid handling tools. We have therefore adapted a commercially available assay employing a 6-O-beta-galactopyranosyl-luciferin substrate to provide the required sensitivity with minimal sample handling times. Our assay uses only one-tenth of the reagents suggested by the reagent manufacturer (Promega) for equivalent assays with mammalian cell cultures and produces rapid, sensitive and reproducible analysis with as little as 1 microl yeast cell culture and with < 100 cells. We demonstrate that the assay is compatible with yeast strains generated by the systematic yeast deletion project and functions equally well with genomically integrated or plasmid-encoded lacZ reporters and with cells grown in complex or defined media. The high-sensitivity, miniaturized format reduced sample handling required will make this assay useful for a wide range of applications.
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46
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Ishida C, Aranda C, Valenzuela L, Riego L, Deluna A, Recillas-Targa F, Filetici P, López-Revilla R, González A. The UGA3-GLT1 intergenic region constitutes a promoter whose bidirectional nature is determined by chromatin organization in Saccharomyces cerevisiae. Mol Microbiol 2006; 59:1790-806. [PMID: 16553884 DOI: 10.1111/j.1365-2958.2006.05055.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transcription of an important number of divergent genes of Saccharomyces cerevisiae is controlled by intergenic regions, which constitute factual bidirectional promoters. However, few of such promoters have been characterized in detail. The analysis of the UGA3-GLT1 intergenic region has provided an interesting model to study the joint action of two global transcriptional activators that had been considered to act independently. Our results show that Gln3p and Gcn4p exert their effect upon cis-acting elements, which are shared in a bidirectional promoter. Accordingly, when yeast is grown on a low-quality nitrogen source, or under amino acid deprivation, the expression of both UGA3 and GLT1 is induced through the action of both these global transcriptional modulators that bind to a region of the bidirectional promoter. In addition, we demonstrate that chromatin organization plays a major role in the bidirectional properties of the UGA3-GLT1 promoter, through the action of an upstream Abf1p-binding consensus sequence and a polydAdT(tract). Mutations in these cis-elements differentially affect transcription of UGA3 and GLT1, and thus alter the overall relative expression. This is the first example of an intergenic region constituting a promoter whose bidirectional character is determined by chromatin organization.
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Affiliation(s)
- Cecilia Ishida
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México
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47
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Todeschini AL, Condon C, Bénard L. Sodium-induced GCN4 expression controls the accumulation of the 5' to 3' RNA degradation inhibitor, 3'-phosphoadenosine 5'-phosphate. J Biol Chem 2006; 281:3276-82. [PMID: 16352596 DOI: 10.1074/jbc.m511688200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most cytoplasmic mRNAs are decapped and digested by the 5'-3'-exonuclease Xrn1p in Saccharomyces cerevisiae. The activity of Xrn1p is naturally inhibited in the presence of 3'-phosphoadenosine 5'-phosphate (pAp), a metabolite produced during sulfate assimilation that is quickly metabolized to AMP by the enzymatic activity of Hal2p. However, pAp accumulates and 5'-3' degradation decreases in the presence of ions known to inhibit Hal2p activity, such as sodium or lithium. We have shown that yeast cells can better adapt to the presence of sodium than lithium because of their ability to reduce pAp accumulation by activating HAL2 expression in a Gcn4p-dependent response, a regulatory loop that is likely to be conserved in different yeast species. We have thus identified a new role for the transcriptional activity of Gcn4p in maintaining an active mRNA degradation pathway under conditions of sodium stress. Since deregulation of proteins involved in different metabolic pathways is observed in xrn1Delta mutants, the maintenance of mRNA degradation capacity is likely to be important for the accurate and rapid adaptation of gene expression to salt stress.
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48
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Abstract
Cells reprogram gene expression in response to environmental changes by mobilizing transcriptional activators. The activator protein Gcn4 of the yeast Saccharomyces cerevisiae is regulated by an intricate translational control mechanism, which is the primary focus of this review, and also by the modulation of its stability in response to nutrient availability. Translation of GCN4 mRNA is derepressed in amino acid-deprived cells, leading to transcriptional induction of nearly all genes encoding amino acid biosynthetic enzymes. The trans-acting proteins that control GCN4 translation have general functions in the initiation of protein synthesis, or regulate the activities of initiation factors, so that the molecular events that induce GCN4 translation also reduce the rate of general protein synthesis. This dual regulatory response enables cells to limit their consumption of amino acids while diverting resources into amino acid biosynthesis in nutrient-poor environments. Remarkably, mammalian cells use the same strategy to downregulate protein synthesis while inducing transcriptional activators of stress-response genes under various stressful conditions, including amino acid starvation.
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Affiliation(s)
- Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, Bethesda, Maryland 20892, USA.
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49
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Fekete CA, Applefield DJ, Blakely SA, Shirokikh N, Pestova T, Lorsch JR, Hinnebusch AG. The eIF1A C-terminal domain promotes initiation complex assembly, scanning and AUG selection in vivo. EMBO J 2005; 24:3588-601. [PMID: 16193068 PMCID: PMC1276705 DOI: 10.1038/sj.emboj.7600821] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2005] [Accepted: 08/26/2005] [Indexed: 11/09/2022] Open
Abstract
Translation initiation factor 1A stimulates 40S-binding of the eukaryotic initiation factor 2 (eIF2)/GTP/Met-tRNA(iMet) ternary complex (TC) and promotes scanning in vitro. eIF1A contains an OB-fold present in bacterial IF1 plus N- and C-terminal extensions. Truncating the C-terminus (deltaC) or mutating OB-fold residues (66-70) of eIF1A reduced general translation in vivo but increased GCN4 translation (Gcd- phenotype) in a manner suppressed by overexpressing TC. Consistent with this, both mutations diminished 40S-bound TC, eIF5 and eIF3 in vivo, and deltaC impaired TC recruitment in vitro. The assembly defects of the OB-fold mutation can be attributed to reduced 40S-binding of eIF1A, whereas deltaC impairs eIF1A function on the ribosome. A substitution in the C-terminal helix (98-101) also reduced 43S assembly in vivo. Rather than producing a Gcd- phenotype, however, 98-101 impairs GCN4 derepression in a manner consistent with defective scanning by reinitiating ribosomes. Indeed, 98-101 allows formation of aberrant 48S complexes in vitro and increases utilization of non-AUG codons in vivo. Thus, the OB-fold is crucial for ribosome-binding and the C-terminal domain of eIF1A has eukaryotic-specific functions in TC recruitment and scanning.
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Affiliation(s)
- Christie A Fekete
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Drew J Applefield
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephen A Blakely
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Nikolay Shirokikh
- Department of Microbiology and Immunology, State University of New York Health Science Center at Brooklyn, Brooklyn, NY, USA
| | - Tatyana Pestova
- Department of Microbiology and Immunology, State University of New York Health Science Center at Brooklyn, Brooklyn, NY, USA
| | - Jon R Lorsch
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, NIH, Building 6A/Room B1A-13, Bethesda, MD 20892, USA. Tel.: +1 301 496 4480; Fax: +1 301 496 6828; E-mail:
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50
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Palmer LK, Shoemaker JL, Baptiste BA, Wolfe D, Keil RL. Inhibition of translation initiation by volatile anesthetics involves nutrient-sensitive GCN-independent and -dependent processes in yeast. Mol Biol Cell 2005; 16:3727-39. [PMID: 15930127 PMCID: PMC1182311 DOI: 10.1091/mbc.e05-02-0127] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2005] [Revised: 05/20/2005] [Accepted: 05/24/2005] [Indexed: 11/11/2022] Open
Abstract
Volatile anesthetics including isoflurane affect all cells examined, but their mechanisms of action remain unknown. To investigate the cellular basis of anesthetic action, we are studying Saccharomyces cerevisiae mutants altered in their response to anesthetics. The zzz3-1 mutation renders yeast isoflurane resistant and is an allele of GCN3. Gcn3p functions in the evolutionarily conserved general amino acid control (GCN) pathway that regulates protein synthesis and gene expression in response to nutrient availability through phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF2alpha). Hyperphosphorylation of eIF2alpha inhibits translation initiation during amino acid starvation. Isoflurane rapidly (in <15 min) inhibits yeast cell division and amino acid uptake. Unexpectedly, phosphorylation of eIF2alpha decreased dramatically upon initial exposure although hyperphosphorylation occurred later. Translation initiation was inhibited by isoflurane even when eIF2alpha phosphorylation decreased and this inhibition was GCN-independent. Maintenance of inhibition required GCN-dependent hyperphosphorylation of eIF2alpha. Thus, two nutrient-sensitive stages displaying unique features promote isoflurane-induced inhibition of translation initiation. The rapid phase is GCN-independent and apparently has not been recognized previously. The maintenance phase is GCN-dependent and requires inhibition of general translation imparted by enhanced eIF2alpha phosphorylation. Surprisingly, as shown here, the transcription activator Gcn4p does not affect anesthetic response.
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Affiliation(s)
- Laura K Palmer
- Department of Biochemistry and Molecular Biology, The Milton S. Hershey Medical Center, The Pennsylvania State University, Hershey, PA 17033-2390, USA
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