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Kumar A. The Complex Genetic Basis and Multilayered Regulatory Control of Yeast Pseudohyphal Growth. Annu Rev Genet 2021; 55:1-21. [PMID: 34280314 DOI: 10.1146/annurev-genet-071719-020249] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Eukaryotic cells are exquisitely responsive to external and internal cues, achieving precise control of seemingly diverse growth processes through a complex interplay of regulatory mechanisms. The budding yeast Saccharomyces cerevisiae provides a fascinating model of cell growth in its stress-responsive transition from planktonic single cells to a filamentous pseudohyphal growth form. During pseudohyphal growth, yeast cells undergo changes in morphology, polarity, and adhesion to form extended and invasive multicellular filaments. This pseudohyphal transition has been studied extensively as a model of conserved signaling pathways regulating cell growth and for its relevance in understanding the pathogenicity of the related opportunistic fungus Candida albicans, wherein filamentous growth is required for virulence. This review highlights the broad gene set enabling yeast pseudohyphal growth, signaling pathways that regulate this process, the role and regulation of proteins conferring cell adhesion, and interesting regulatory mechanisms enabling the pseudohyphal transition. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
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2
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McFarland MR, Keller CD, Childers BM, Adeniyi SA, Corrigall H, Raguin A, Romano MC, Stansfield I. The molecular aetiology of tRNA synthetase depletion: induction of a GCN4 amino acid starvation response despite homeostatic maintenance of charged tRNA levels. Nucleic Acids Res 2020; 48:3071-3088. [PMID: 32016368 PMCID: PMC7102972 DOI: 10.1093/nar/gkaa055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 12/13/2022] Open
Abstract
During protein synthesis, charged tRNAs deliver amino acids to translating ribosomes, and are then re-charged by tRNA synthetases (aaRS). In humans, mutant aaRS cause a diversity of neurological disorders, but their molecular aetiologies are incompletely characterised. To understand system responses to aaRS depletion, the yeast glutamine aaRS gene (GLN4) was transcriptionally regulated using doxycycline by tet-off control. Depletion of Gln4p inhibited growth, and induced a GCN4 amino acid starvation response, indicative of uncharged tRNA accumulation and Gcn2 kinase activation. Using a global model of translation that included aaRS recharging, Gln4p depletion was simulated, confirming slowed translation. Modelling also revealed that Gln4p depletion causes negative feedback that matches translational demand for Gln-tRNAGln to aaRS recharging capacity. This maintains normal charged tRNAGln levels despite Gln4p depletion, confirmed experimentally using tRNA Northern blotting. Model analysis resolves the paradox that Gln4p depletion triggers a GCN4 response, despite maintenance of tRNAGln charging levels, revealing that normally, the aaRS population can sequester free, uncharged tRNAs during aminoacylation. Gln4p depletion reduces this sequestration capacity, allowing uncharged tRNAGln to interact with Gcn2 kinase. The study sheds new light on mutant aaRS disease aetiologies, and explains how aaRS sequestration of uncharged tRNAs can prevent GCN4 activation under non-starvation conditions.
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Affiliation(s)
- Matthew R McFarland
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Corina D Keller
- Institute of Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Brandon M Childers
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Stephen A Adeniyi
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Holly Corrigall
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Adélaïde Raguin
- Institute of Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - M Carmen Romano
- Institute of Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Ian Stansfield
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK
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3
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Impact of Pus1 Pseudouridine Synthase on Specific Decoding Events in Saccharomyces cerevisiae. Biomolecules 2020; 10:biom10050729. [PMID: 32392804 PMCID: PMC7277083 DOI: 10.3390/biom10050729] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 12/19/2022] Open
Abstract
Pus1-dependent pseudouridylation occurs in many tRNAs and at multiple positions, yet the functional impact of this modification is incompletely understood. We analyzed the consequences of PUS1 deletion on the essential decoding of CAG (Gln) codons by tRNAGlnCUG in yeast. Synthetic lethality was observed upon combining the modification defect with destabilized variants of tRNAGlnCUG, pointing to a severe CAG-decoding defect of the hypomodified tRNA. In addition, we demonstrated that misreading of UAG stop codons by a tRNAGlnCUG variant is positively affected by Pus1. Genetic approaches further indicated that mildly elevated temperature decreases the decoding efficiency of CAG and UAG via destabilized tRNAGlnCAG variants. We also determined the misreading of CGC (Arg) codons by tRNAHisGUG, where the CGC decoder tRNAArgICG contains Pus1-dependent pseudouridine, but not the mistranslating tRNAHis. We found that the absence of Pus1 increased CGC misreading by tRNAHis, demonstrating a positive role of the modification in the competition against non-synonymous near-cognate tRNA. Part of the in vivo decoding defects and phenotypes in pus1 mutants and strains carrying destabilized tRNAGlnCAG were suppressible by additional deletion of the rapid tRNA decay (RTD)-relevant MET22, suggesting the involvement of RTD-mediated tRNA destabilization.
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Destabilization of Eukaryote mRNAs by 5' Proximal Stop Codons Can Occur Independently of the Nonsense-Mediated mRNA Decay Pathway. Cells 2019; 8:cells8080800. [PMID: 31370247 PMCID: PMC6721604 DOI: 10.3390/cells8080800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 11/17/2022] Open
Abstract
In eukaryotes, the binding of poly(A) binding protein (PAB) to the poly(A) tail is central to maintaining mRNA stability. PABP interacts with the translation termination apparatus, and with eIF4G to maintain 3′–5′ mRNA interactions as part of an mRNA closed loop. It is however unclear how ribosome recycling on a closed loop mRNA is influenced by the proximity of the stop codon to the poly(A) tail, and how post-termination ribosome recycling affects mRNA stability. We show that in a yeast disabled for nonsense mediated mRNA decay (NMD), a PGK1 mRNA with an early stop codon at codon 22 of the reading frame is still highly unstable, and that this instability cannot be significantly countered even when 50% stop codon readthrough is triggered. In an NMD-deficient mutant yeast, stable reporter alleles with more 3′ proximal stop codons could not be rendered unstable through Rli1-depletion, inferring defective Rli1 ribosome recycling is insufficient in itself to trigger mRNA instability. Mathematical modelling of a translation system including the effect of ribosome recycling and poly(A) tail shortening supports the hypothesis that impaired ribosome recycling from 5′ proximal stop codons may compromise initiation processes and thus destabilize the mRNA. A model is proposed wherein ribosomes undergo a maturation process during early elongation steps, and acquire competency to re-initiate on the same mRNA as translation elongation progresses beyond the very 5′ proximal regions of the mRNA.
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Collaboration of tRNA modifications and elongation factor eEF1A in decoding and nonsense suppression. Sci Rep 2018; 8:12749. [PMID: 30143741 PMCID: PMC6109124 DOI: 10.1038/s41598-018-31158-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/13/2018] [Indexed: 01/27/2023] Open
Abstract
Transfer RNA (tRNA) from all domains of life contains multiple modified nucleosides, the functions of which remain incompletely understood. Genetic interactions between tRNA modification genes in Saccharomyces cerevisiae suggest that different tRNA modifications collaborate to maintain translational efficiency. Here we characterize such collaborative functions in the ochre suppressor tRNA SUP4. We quantified ochre read-through efficiency in mutants lacking either of the 7 known modifications in the extended anticodon stem loop (G26-C48). Absence of U34, U35, A37, U47 and C48 modifications partially impaired SUP4 function. We systematically combined modification defects and scored additive or synergistic negative effects on SUP4 performance. Our data reveal different degrees of functional redundancy between specific modifications, the strongest of which was demonstrated for those occurring at positions U34 and A37. SUP4 activity in the absence of critical modifications, however, can be rescued in a gene dosage dependent fashion by TEF1 which encodes elongation factor eEF1A required for tRNA delivery to the ribosome. Strikingly, the rescue ability of higher-than-normal eEF1A levels extends to tRNA modification defects in natural non-suppressor tRNAs suggesting that elevated eEF1A abundance can partially compensate for functional defects induced by loss of tRNA modifications.
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6
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Szavits-Nossan J, Ciandrini L, Romano MC. Deciphering mRNA Sequence Determinants of Protein Production Rate. PHYSICAL REVIEW LETTERS 2018; 120:128101. [PMID: 29694095 DOI: 10.1103/physrevlett.120.128101] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 01/18/2018] [Indexed: 06/08/2023]
Abstract
One of the greatest challenges in biophysical models of translation is to identify coding sequence features that affect the rate of translation and therefore the overall protein production in the cell. We propose an analytic method to solve a translation model based on the inhomogeneous totally asymmetric simple exclusion process, which allows us to unveil simple design principles of nucleotide sequences determining protein production rates. Our solution shows an excellent agreement when compared to numerical genome-wide simulations of S. cerevisiae transcript sequences and predicts that the first 10 codons, which is the ribosome footprint length on the mRNA, together with the value of the initiation rate, are the main determinants of protein production rate under physiological conditions. Finally, we interpret the obtained analytic results based on the evolutionary role of the codons' choice for regulating translation rates and ribosome densities.
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Affiliation(s)
- Juraj Szavits-Nossan
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Luca Ciandrini
- L2C, Université de Montpellier, CNRS, Montpellier, France and DIMNP, Université de Montpellier, CNRS, Montpellier, France
| | - M Carmen Romano
- SUPA, Institute for Complex Systems and Mathematical Biology, Department of Physics, Aberdeen AB24 3UE, United Kingdom and Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB24 3FX, United Kingdom
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Stirpe M, Palermo V, Ferrari M, Mroczek S, Kufel J, Falcone C, Mazzoni C. Increased levels of RNA oxidation enhance the reversion frequency in aging pro-apoptotic yeast mutants. Apoptosis 2018; 22:200-206. [PMID: 27803986 PMCID: PMC5306349 DOI: 10.1007/s10495-016-1319-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Despite recent advances in understanding the complexity of RNA processes, regulation of the metabolism of oxidized cellular RNAs and the mechanisms through which oxidized ribonucleotides affect mRNA translation, and consequently cell viability, are not well characterized. We show here that the level of oxidized RNAs is markedly increased in a yeast decapping Kllsm4Δ1 mutant, which accumulates mRNAs, ages much faster that the wild type strain and undergoes regulated-cell-death. We also found that in Kllsm4Δ1 cells the mutation rate increases during chronological life span indicating that the capacity to handle oxidized RNAs in yeast declines with aging. Lowering intracellular ROS levels by antioxidants recovers the wild-type phenotype of mutant cells, including reduced amount of oxidized RNAs and lower mutation rate. Since mRNA oxidation was reported to occur in different neurodegenerative diseases, decapping-deficient cells may represent a useful tool for deciphering molecular mechanisms of cell response to such conditions, providing new insights into RNA modification-based pathogenesis.
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Affiliation(s)
- Mariarita Stirpe
- Department of Biology and Biotechnology "Charles Darwin", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, University "Sapienza" of Rome, Piazzale Aldo Moro 5, Rome, Italy
| | - Vanessa Palermo
- Department of Biology and Biotechnology "Charles Darwin", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, University "Sapienza" of Rome, Piazzale Aldo Moro 5, Rome, Italy
| | - Matteo Ferrari
- Department of Biology and Biotechnology "Charles Darwin", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, University "Sapienza" of Rome, Piazzale Aldo Moro 5, Rome, Italy
| | - Seweryn Mroczek
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Joanna Kufel
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Claudio Falcone
- Department of Biology and Biotechnology "Charles Darwin", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, University "Sapienza" of Rome, Piazzale Aldo Moro 5, Rome, Italy
| | - Cristina Mazzoni
- Department of Biology and Biotechnology "Charles Darwin", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, University "Sapienza" of Rome, Piazzale Aldo Moro 5, Rome, Italy.
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8
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Fernandes LD, Moura APSD, Ciandrini L. Gene length as a regulator for ribosome recruitment and protein synthesis: theoretical insights. Sci Rep 2017; 7:17409. [PMID: 29234048 PMCID: PMC5727216 DOI: 10.1038/s41598-017-17618-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/28/2017] [Indexed: 01/14/2023] Open
Abstract
Protein synthesis rates are determined, at the translational level, by properties of the transcript’s sequence. The efficiency of an mRNA can be tuned by varying the ribosome binding sites controlling the recruitment of the ribosomes, or the codon usage establishing the speed of protein elongation. In this work we propose transcript length as a further key determinant of translation efficiency. Based on a physical model that considers the kinetics of ribosomes advancing on the mRNA and diffusing in its surrounding, as well as mRNA circularisation and ribosome drop-off, we explain how the transcript length may play a central role in establishing ribosome recruitment and the overall translation rate of an mRNA. According to our results, the proximity of the 3′ end to the ribosomal recruitment site of the mRNA could induce a feedback in the translation process that would favour the recycling of ribosomes. We also demonstrate how this process may be involved in shaping the experimental ribosome density-gene length dependence. Finally, we argue that cells could exploit this mechanism to adjust and balance the usage of its ribosomal resources.
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Affiliation(s)
- Lucas D Fernandes
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura Luiz de Queiroz - Universidade de São Paulo (USP), 13418-900, Piracicaba/SP, Brazil.,Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Alessandro P S de Moura
- Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Luca Ciandrini
- DIMNP UMR 5235, Université de Montpellier and CNRS, F-34095, Montpellier, France. .,Laboratoire Charles Coulomb UMR5221, Université de Montpellier and CNRS, F-34095, Montpellier, France.
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9
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Generation of an arginine-tRNA-adapted Saccharomyces cerevisiae strain for effective heterologous protein expression. Curr Genet 2017; 64:589-598. [PMID: 29098364 DOI: 10.1007/s00294-017-0774-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/30/2017] [Accepted: 10/27/2017] [Indexed: 10/18/2022]
Abstract
The tRNA population reflects the codon bias of the organism and affects the translation of heterologous target mRNA molecules. In this study, Saccharomyces cerevisiae strains with modified levels of rare tRNA were engineered, that allowed efficient generation of recombinant proteins with unfavorable codon usage. We established a novel synthetic tRNA expression cassette and verified functional nonsense suppressor tRNAGlnSCUA generation in a stop codon read-through assay with a modified β-galactosidase reporter gene. Correlation between altered tRNA and protein level was shown by survival of copper sensitive S. cerevisiae cells in the presence of copper ions by an increased transcription of tRNAArgCCG molecules, recognizing rare codons in a modified CUP1 gene. Genome integration of tRNA expression cassette led to the generation of arginine-tRNA-adapted S. cerevisiae strains, which showed elevated tRNA levels (tRNAArgCCG, tRNAArgGCG and tRNAArgUCG) pairing to rare codons. The modified strain MNY3 revealed a considerably improved monitoring of protein-protein interaction from Aspergillus fumigatus bait and prey sequences in yeast two-hybrid experiments. In future, this principle to overcome limited recombinant protein expression by tRNA adaption of expression strains instead of codon adaption might provide new designer yeast cells for an efficient protein production and for improved genome-wide protein-protein interaction analyses.
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10
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Klassen R, Schaffrath R. Role of Pseudouridine Formation by Deg1 for Functionality of Two Glutamine Isoacceptor tRNAs. Biomolecules 2017; 7:biom7010008. [PMID: 28134782 PMCID: PMC5372720 DOI: 10.3390/biom7010008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/20/2017] [Accepted: 01/20/2017] [Indexed: 12/22/2022] Open
Abstract
Loss of Deg1/Pus3 and concomitant elimination of pseudouridine in tRNA at positions 38 and 39 (ψ38/39) was shown to specifically impair the function of tRNAGlnUUG under conditions of temperature-induced down-regulation of wobble uridine thiolation in budding yeast and is linked to intellectual disability in humans. To further characterize the differential importance of the frequent ψ38/39 modification for tRNAs in yeast, we analyzed the in vivo function of non-sense suppressor tRNAs SUP4 and sup70-65 in the absence of the modifier. In the tRNATyrGψA variant SUP4, UAA read-through is enabled due to an anticodon mutation (UψA), whereas sup70-65 is a mutant form of tRNAGlnCUG (SUP70) that mediates UAG decoding due to a mutation of the anticodon-loop closing base pair (G31:C39 to A31:C39). While SUP4 function is unaltered in deg1/pus3 mutants, the ability of sup70-65 to mediate non-sense suppression and to complement a genomic deletion of the essential SUP70 gene is severely compromised. These results and the differential suppression of growth defects in deg1 mutants by multi-copy SUP70 or tQ(UUG) are consistent with the interpretation that ψ38 is most important for tRNAGlnUUG function under heat stress but becomes crucial for tRNAGlnCUG as well when the anticodon loop is destabilized by the sup70-65 mutation. Thus, ψ38/39 may protect the anticodon loop configuration from disturbances by loss of other modifications or base changes.
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Affiliation(s)
- Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, D-34132 Kassel, Germany.
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, D-34132 Kassel, Germany.
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General Amino Acid Control and 14-3-3 Proteins Bmh1/2 Are Required for Nitrogen Catabolite Repression-Sensitive Regulation of Gln3 and Gat1 Localization. Genetics 2016; 205:633-655. [PMID: 28007891 DOI: 10.1534/genetics.116.195800] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 12/21/2016] [Indexed: 01/08/2023] Open
Abstract
Nitrogen catabolite repression (NCR), the ability of Saccharomyces cerevisiae to use good nitrogen sources in preference to poor ones, derives from nitrogen-responsive regulation of the GATA family transcription activators Gln3 and Gat1 In nitrogen-replete conditions, the GATA factors are cytoplasmic and NCR-sensitive transcription minimal. When only poor nitrogen sources are available, Gln3 is nuclear, dramatically increasing GATA factor-mediated transcription. This regulation was originally attributed to mechanistic Tor protein kinase complex 1 (mTorC1)-mediated control of Gln3 However, we recently showed that two regulatory systems act cumulatively to maintain cytoplasmic Gln3 sequestration, only one of which is mTorC1. Present experiments demonstrate that the other previously elusive component is uncharged transfer RNA-activated, Gcn2 protein kinase-mediated general amino acid control (GAAC). Gcn2 and Gcn4 are required for NCR-sensitive nuclear Gln3-Myc13 localization, and from epistasis experiments Gcn2 appears to function upstream of Ure2 Bmh1/2 are also required for nuclear Gln3-Myc13 localization and appear to function downstream of Ure2 Overall, Gln3 phosphorylation levels decrease upon loss of Gcn2, Gcn4, or Bmh1/2 Our results add a new dimension to nitrogen-responsive GATA-factor regulation and demonstrate the cumulative participation of the mTorC1 and GAAC pathways, which respond oppositely to nitrogen availability, in the nitrogen-responsive control of catabolic gene expression in yeast.
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Klassen R, Ciftci A, Funk J, Bruch A, Butter F, Schaffrath R. tRNA anticodon loop modifications ensure protein homeostasis and cell morphogenesis in yeast. Nucleic Acids Res 2016; 44:10946-10959. [PMID: 27496282 PMCID: PMC5159529 DOI: 10.1093/nar/gkw705] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 07/29/2016] [Indexed: 11/17/2022] Open
Abstract
Using budding yeast, we investigated a negative interaction network among genes for tRNA modifications previously implicated in anticodon-codon interaction: 5-methoxy-carbonyl-methyl-2-thio-uridine (mcm5s2U34: ELP3, URM1), pseudouridine (Ψ38/39: DEG1) and cyclic N6-threonyl-carbamoyl-adenosine (ct6A37: TCD1). In line with functional cross talk between these modifications, we find that combined removal of either ct6A37 or Ψ38/39 and mcm5U34 or s2U34 results in morphologically altered cells with synthetic growth defects. Phenotypic suppression by tRNA overexpression suggests that these defects are caused by malfunction of tRNALysUUU or tRNAGlnUUG, respectively. Indeed, mRNA translation and synthesis of the Gln-rich prion Rnq1 are severely impaired in the absence of Ψ38/39 and mcm5U34 or s2U34, and this defect can be rescued by overexpression of tRNAGlnUUG. Surprisingly, we find that combined modification defects in the anticodon loops of different tRNAs induce similar cell polarity- and nuclear segregation defects that are accompanied by increased aggregation of cellular proteins. Since conditional expression of an artificial aggregation-prone protein triggered similar cytological aberrancies, protein aggregation is likely responsible for loss of morphogenesis and cytokinesis control in mutants with inappropriate tRNA anticodon loop modifications.
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Affiliation(s)
- Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, D-34132 Kassel, Germany
| | - Akif Ciftci
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, D-34132 Kassel, Germany
| | - Johanna Funk
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, D-34132 Kassel, Germany
| | - Alexander Bruch
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, D-34132 Kassel, Germany
| | - Falk Butter
- Institut für Molekulare Biologie, Ackermannweg 4, D-55128 Mainz, Germany
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, D-34132 Kassel, Germany
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13
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Gorgoni B, Ciandrini L, McFarland MR, Romano MC, Stansfield I. Identification of the mRNA targets of tRNA-specific regulation using genome-wide simulation of translation. Nucleic Acids Res 2016; 44:9231-9244. [PMID: 27407108 PMCID: PMC5100601 DOI: 10.1093/nar/gkw630] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/02/2016] [Indexed: 01/11/2023] Open
Abstract
tRNA gene copy number is a primary determinant of tRNA abundance and therefore the rate at which each tRNA delivers amino acids to the ribosome during translation. Low-abundance tRNAs decode rare codons slowly, but it is unclear which genes might be subject to tRNA-mediated regulation of expression. Here, those mRNA targets were identified via global simulation of translation. In-silico mRNA translation rates were compared for each mRNA in both wild-type and a \documentclass[12pt]{minimal}
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}{}${\rm{tRNA}}_{{\rm{CUG}}}^{{\rm{Gln}}}$\end{document}sup70-65 mutant, which exhibits a pseudohyphal growth phenotype and a 75% slower CAG codon translation rate. Of 4900 CAG-containing mRNAs, 300 showed significantly reduced in silico translation rates in a simulated tRNA mutant. Quantitative immunoassay confirmed that the reduced translation rates of sensitive mRNAs were \documentclass[12pt]{minimal}
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}{}${\rm{tRNA}}_{{\rm{CUG}}}^{{\rm{Gln}}}$\end{document} concentration-dependent. Translation simulations showed that reduced \documentclass[12pt]{minimal}
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}{}${\rm{tRNA}}_{{\rm{CUG}}}^{{\rm{Gln}}}$\end{document} concentrations triggered ribosome queues, which dissipated at reduced translation initiation rates. To validate this prediction experimentally, constitutive gcn2 kinase mutants were used to reduce in vivo translation initiation rates. This repaired the relative translational rate defect of target mRNAs in the sup70-65 background, and ameliorated sup70-65 pseudohyphal growth phenotypes. We thus validate global simulation of translation as a new tool to identify mRNA targets of tRNA-specific gene regulation.
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Affiliation(s)
- Barbara Gorgoni
- University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Luca Ciandrini
- DIMNP - UMR 5235 & CNRS, Université de Montpellier, 34095 Montpellier, France.,Laboratoire Charles Coulomb UMR5221 & CNRS, Université de Montpellier, 34095 Montpellier, France
| | - Matthew R McFarland
- University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - M Carmen Romano
- University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK.,University of Aberdeen, Institute for Complex Systems and Mathematical Biology, King's College, Aberdeen AB24 3UE, UK
| | - Ian Stansfield
- University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
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Petrova A, Kiktev D, Askinazi O, Chabelskaya S, Moskalenko S, Zemlyanko O, Zhouravleva G. The translation termination factor eRF1 (Sup45p) of Saccharomyces cerevisiae is required for pseudohyphal growth and invasion. FEMS Yeast Res 2015; 15:fov033. [PMID: 26054854 DOI: 10.1093/femsyr/fov033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 01/16/2023] Open
Abstract
Mutations in the essential genes SUP45 and SUP35, encoding yeast translation termination factors eRF1 and eRF3, respectively, lead to a wide range of phenotypes and affect various cell processes. In this work, we show that nonsense and missense mutations in the SUP45, but not the SUP35, gene abolish diploid pseudohyphal and haploid invasive growth. Missense mutations that change phosphorylation sites of Sup45 protein do not affect the ability of yeast strains to form pseudohyphae. Deletion of the C-terminal part of eRF1 did not lead to impairment of filamentation. We show a correlation between the filamentation defect and the budding pattern in sup45 strains. Inhibition of translation with specific antibiotics causes a significant reduction in pseudohyphal growth in the wild-type strain, suggesting a strong correlation between translation and the ability for filamentous growth. Partial restoration of pseudohyphal growth by addition of exogenous cAMP assumes that sup45 mutants are defective in the cAMP-dependent pathway that control filament formation.
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Affiliation(s)
- Alexandra Petrova
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Denis Kiktev
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Olga Askinazi
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Svetlana Chabelskaya
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Svetlana Moskalenko
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Olga Zemlyanko
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Galina Zhouravleva
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
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15
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Klassen R, Grunewald P, Thüring KL, Eichler C, Helm M, Schaffrath R. Loss of anticodon wobble uridine modifications affects tRNA(Lys) function and protein levels in Saccharomyces cerevisiae. PLoS One 2015; 10:e0119261. [PMID: 25747122 PMCID: PMC4352028 DOI: 10.1371/journal.pone.0119261] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 01/22/2015] [Indexed: 11/22/2022] Open
Abstract
In eukaryotes, wobble uridines in the anticodons of tRNALysUUU, tRNAGluUUC and tRNAGlnUUG are modified to 5-methoxy-carbonyl-methyl-2-thio-uridine (mcm5s2U). While mutations in subunits of the Elongator complex (Elp1-Elp6), which disable mcm5 side chain formation, or removal of components of the thiolation pathway (Ncs2/Ncs6, Urm1, Uba4) are individually tolerated, the combination of both modification defects has been reported to have lethal effects on Saccharomyces cerevisiae. Contrary to such absolute requirement of mcm5s2U for viability, we demonstrate here that in the S. cerevisiae S288C-derived background, both pathways can be simultaneously inactivated, resulting in combined loss of tRNA anticodon modifications (mcm5U and s2U) without a lethal effect. However, an elp3 disruption strain displays synthetic sick interaction and synergistic temperature sensitivity when combined with either uba4 or urm1 mutations, suggesting major translational defects in the absence of mcm5s2U modifications. Consistent with this notion, we find cellular protein levels drastically decreased in an elp3uba4 double mutant and show that this effect as well as growth phenotypes can be partially rescued by excess of tRNALysUUU. These results may indicate a global translational or protein homeostasis defect in cells simultaneously lacking mcm5 and s2 wobble uridine modification that could account for growth impairment and mainly originates from tRNALysUUU hypomodification and malfunction.
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Affiliation(s)
- Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
- * E-mail: (RK); (RS)
| | - Pia Grunewald
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Kathrin L. Thüring
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Christian Eichler
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Mark Helm
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
- * E-mail: (RK); (RS)
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16
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Fraser CS. Quantitative studies of mRNA recruitment to the eukaryotic ribosome. Biochimie 2015; 114:58-71. [PMID: 25742741 DOI: 10.1016/j.biochi.2015.02.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/20/2015] [Indexed: 12/20/2022]
Abstract
The process of peptide bond synthesis by ribosomes is conserved between species, but the initiation step differs greatly between the three kingdoms of life. This is illustrated by the evolution of roughly an order of magnitude more initiation factor mass found in humans compared with bacteria. Eukaryotic initiation of translation is comprised of a number of sub-steps: (i) recruitment of an mRNA and initiator methionyl-tRNA to the 40S ribosomal subunit; (ii) migration of the 40S subunit along the 5' UTR to locate the initiation codon; and (iii) recruitment of the 60S subunit to form the 80S initiation complex. Although the mechanism and regulation of initiation has been studied for decades, many aspects of the pathway remain unclear. In this review, I will focus discussion on what is known about the mechanism of mRNA selection and its recruitment to the 40S subunit. I will summarize how the 43S preinitiation complex (PIC) is formed and stabilized by interactions between its components. I will discuss what is known about the mechanism of mRNA selection by the eukaryotic initiation factor 4F (eIF4F) complex and how the selected mRNA is recruited to the 43S PIC. The regulation of this process by secondary structure located in the 5' UTR of an mRNA will also be discussed. Finally, I present a possible kinetic model with which to explain the process of mRNA selection and recruitment to the eukaryotic ribosome.
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Affiliation(s)
- Christopher S Fraser
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA.
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17
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Marshall E, Stansfield I, Romano MC. Ribosome recycling induces optimal translation rate at low ribosomal availability. J R Soc Interface 2015; 11:20140589. [PMID: 25008084 PMCID: PMC4233708 DOI: 10.1098/rsif.2014.0589] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During eukaryotic cellular protein synthesis, ribosomal translation is made more efficient through interaction between the two ends of the messenger RNA (mRNA). Ribosomes reaching the 3′ end of the mRNA can thus recycle and begin translation again on the same mRNA, the so-called ‘closed-loop’ model. Using a driven diffusion lattice model of translation, we study the effects of ribosome recycling on the dynamics of ribosome flow and density on the mRNA. We show that ribosome recycling induces a substantial increase in ribosome current. Furthermore, for sufficiently large values of the recycling rate, the lattice does not transition directly from low to high ribosome density, as seen in lattice models without recycling. Instead, a maximal current phase becomes accessible for much lower values of the initiation rate, and multiple phase transitions occur over a wide region of the phase plane. Crucially, we show that in the presence of ribosome recycling, mRNAs can exhibit a peak in protein production at low values of the initiation rate, beyond which translation rate decreases. This has important implications for translation of certain mRNAs, suggesting that there is an optimal concentration of ribosomes at which protein synthesis is maximal, and beyond which translational efficiency is impaired.
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Affiliation(s)
- E Marshall
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK SUPA, Institute for Complex Systems and Mathematical Biology, King's College, University of Aberdeen, Aberdeen AB24 3UE, UK
| | - I Stansfield
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - M C Romano
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK SUPA, Institute for Complex Systems and Mathematical Biology, King's College, University of Aberdeen, Aberdeen AB24 3UE, UK
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18
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Han L, Kon Y, Phizicky EM. Functional importance of Ψ38 and Ψ39 in distinct tRNAs, amplified for tRNAGln(UUG) by unexpected temperature sensitivity of the s2U modification in yeast. RNA (NEW YORK, N.Y.) 2015; 21:188-201. [PMID: 25505024 PMCID: PMC4338347 DOI: 10.1261/rna.048173.114] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The numerous modifications of tRNA play central roles in controlling tRNA structure and translation. Modifications in and around the anticodon loop often have critical roles in decoding mRNA and in maintaining its reading frame. Residues U38 and U39 in the anticodon stem-loop are frequently modified to pseudouridine (Ψ) by members of the widely conserved TruA/Pus3 family of pseudouridylases. We investigate here the cause of the temperature sensitivity of pus3Δ mutants of the yeast Saccharomyces cerevisiae and find that, although Ψ38 or Ψ39 is found on at least 19 characterized cytoplasmic tRNA species, the temperature sensitivity is primarily due to poor function of tRNA(Gln(UUG)), which normally has Ψ38. Further investigation reveals that at elevated temperatures there are substantially reduced levels of the s(2)U moiety of mcm(5)s(2)U34 of tRNA(Gln(UUG)) and the other two cytoplasmic species with mcm(5)s(2)U34, that the reduced s(2)U levels occur in the parent strain BY4741 and in the widely used strain W303, and that reduced levels of the s(2)U moiety are detectable in BY4741 at temperatures as low as 33°C. Additional examination of the role of Ψ38,39 provides evidence that Ψ38 is important for function of tRNA(Gln(UUG)) at permissive temperature, and indicates that Ψ39 is important for the function of tRNA(Trp(CCA)) in trm10Δ pus3Δ mutants and of tRNA(Leu(CAA)) as a UAG nonsense suppressor. These results provide evidence for important roles of both Ψ38 and Ψ39 in specific tRNAs, and establish that modification of the wobble position is subject to change under relatively mild growth conditions.
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Affiliation(s)
- Lu Han
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Yoshiko Kon
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Eric M Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
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19
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Nitrogen starvation and TorC1 inhibition differentially affect nuclear localization of the Gln3 and Gat1 transcription factors through the rare glutamine tRNACUG in Saccharomyces cerevisiae. Genetics 2014; 199:455-74. [PMID: 25527290 DOI: 10.1534/genetics.114.173831] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A leucine, leucyl-tRNA synthetase-dependent pathway activates TorC1 kinase and its downstream stimulation of protein synthesis, a major nitrogen consumer. We previously demonstrated, however, that control of Gln3, a transcription activator of catabolic genes whose products generate the nitrogenous precursors for protein synthesis, is not subject to leucine-dependent TorC1 activation. This led us to conclude that excess nitrogen-dependent down-regulation of Gln3 occurs via a second mechanism that is independent of leucine-dependent TorC1 activation. A major site of Gln3 and Gat1 (another GATA-binding transcription activator) control occurs at their access to the nucleus. In excess nitrogen, Gln3 and Gat1 are sequestered in the cytoplasm in a Ure2-dependent manner. They become nuclear and activate transcription when nitrogen becomes limiting. Long-term nitrogen starvation and treatment of cells with the glutamine synthetase inhibitor methionine sulfoximine (Msx) also elicit nuclear Gln3 localization. The sensitivity of Gln3 localization to glutamine and inhibition of glutamine synthesis prompted us to investigate the effects of a glutamine tRNA mutation (sup70-65) on nitrogen-responsive control of Gln3 and Gat1. We found that nuclear Gln3 localization elicited by short- and long-term nitrogen starvation; growth in a poor, derepressive medium; Msx or rapamycin treatment; or ure2Δ mutation is abolished in a sup70-65 mutant. However, nuclear Gat1 localization, which also exhibits a glutamine tRNACUG requirement for its response to short-term nitrogen starvation or growth in proline medium or a ure2Δ mutation, does not require tRNACUG for its response to rapamycin. Also, in contrast with Gln3, Gat1 localization does not respond to long-term nitrogen starvation. These observations demonstrate the existence of a specific nitrogen-responsive component participating in the control of Gln3 and Gat1 localization and their downstream production of nitrogenous precursors. This component is highly sensitive to the function of the rare glutamine tRNACUG, which cannot be replaced by the predominant glutamine tRNACAA. Our observations also demonstrate distinct mechanistic differences between the responses of Gln3 and Gat1 to rapamycin inhibition of TorC1 and nitrogen starvation.
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20
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Mean of the typical decoding rates: a new translation efficiency index based on the analysis of ribosome profiling data. G3-GENES GENOMES GENETICS 2014; 5:73-80. [PMID: 25452418 PMCID: PMC4291471 DOI: 10.1534/g3.114.015099] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Gene translation modeling and prediction is a fundamental problem that has numerous biomedical implementations. In this work we present a novel, user-friendly tool/index for calculating the mean of the typical decoding rates that enables predicting translation elongation efficiency of protein coding genes for different tissue types, developmental stages, and experimental conditions. The suggested translation efficiency index is based on the analysis of the organism’s ribosome profiling data. This index could be used for example to predict changes in translation elongation efficiency of lowly expressed genes that usually have relatively low and/or biased ribosomal densities and protein levels measurements, or can be used for example for predicting translation efficiency of new genetically engineered genes. We demonstrate the usability of this index via the analysis of six organisms in different tissues and developmental stages. Distributable cross platform application and guideline are available for download at: http://www.cs.tau.ac.il/~tamirtul/MTDR/MTDR_Install.html
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21
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Tarrant D, von der Haar T. Synonymous codons, ribosome speed, and eukaryotic gene expression regulation. Cell Mol Life Sci 2014; 71:4195-206. [PMID: 25038778 PMCID: PMC11113527 DOI: 10.1007/s00018-014-1684-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 06/26/2014] [Accepted: 07/14/2014] [Indexed: 12/27/2022]
Abstract
Quantitative control of gene expression occurs at multiple levels, including the level of translation. Within the overall process of translation, most identified regulatory processes impinge on the initiation phase. However, recent studies have revealed that the elongation phase can also regulate translation if elongation and initiation occur with specific, not mutually compatible rate parameters. Translation elongation then limits the overall amount of protein that can be made from an mRNA. Several recently discovered control mechanisms of biological pathways are based on such elongation control. Here, we review the molecular mechanisms that determine ribosome speed in eukaryotic organisms, and discuss under which conditions ribosome speed can become the controlling parameter of gene expression levels.
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Affiliation(s)
- Daniel Tarrant
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Tobias von der Haar
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
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22
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Abstract
Translational control is central to the gene expression pathway and was the focus of the 2013 annual Translation UK meeting held at the University of Kent. The meeting brought together scientists at all career stages to present and discuss research in the mRNA translation field, with an emphasis on the presentations on the research of early career scientists. The diverse nature of this field was represented by the broad range of papers presented at the meeting. The complexity of mRNA translation and its control is emphasized by the interdisciplinary research approaches required to address this area with speakers highlighting emerging systems biology techniques and their application to understanding mRNA translation and the network of pathways controlling it.
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23
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Hersch SJ, Elgamal S, Katz A, Ibba M, Navarre WW. Translation initiation rate determines the impact of ribosome stalling on bacterial protein synthesis. J Biol Chem 2014; 289:28160-71. [PMID: 25148683 DOI: 10.1074/jbc.m114.593277] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Ribosome stalling during translation can be caused by a number of characterized mechanisms. However, the impact of elongation stalls on protein levels is variable, and the reasons for this are often unclear. To investigate this relationship, we examined the bacterial translation elongation factor P (EF-P), which plays a critical role in rescuing ribosomes stalled at specific amino acid sequences including polyproline motifs. In previous proteomic analyses of both Salmonella and Escherichia coli efp mutants, it was evident that not all proteins containing a polyproline motif were dependent on EF-P for efficient expression in vivo. The α- and β-subunits of ATP synthase, AtpA and AtpD, are translated from the same mRNA transcript, and both contain a PPG motif; however, proteomic analysis revealed that AtpD levels are strongly dependent on EF-P, whereas AtpA levels are independent of EF-P. Using these model proteins, we systematically determined that EF-P dependence is strongly influenced by elements in the 5'-untranslated region of the mRNA. By mutating either the Shine-Dalgarno sequence or the start codon, we find that EF-P dependence correlates directly with the rate of translation initiation where strongly expressed proteins show the greatest dependence on EF-P. Our findings demonstrate that polyproline-induced stalls exert a net effect on protein levels only if they limit translation significantly more than initiation. This model can be generalized to explain why sequences that induce pauses in translation elongation to, for example, facilitate folding do not necessarily exact a penalty on the overall production of the protein.
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Affiliation(s)
- Steven J Hersch
- From the Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada and
| | - Sara Elgamal
- the Department of Microbiology, Ohio State University, Columbus, Ohio 43210
| | - Assaf Katz
- the Department of Microbiology, Ohio State University, Columbus, Ohio 43210
| | - Michael Ibba
- the Department of Microbiology, Ohio State University, Columbus, Ohio 43210
| | - William Wiley Navarre
- From the Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada and
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24
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Controlling translation elongation efficiency: tRNA regulation of ribosome flux on the mRNA. Biochem Soc Trans 2014; 42:160-5. [DOI: 10.1042/bst20130132] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Gene expression can be regulated by a wide variety of mechanisms. One example concerns the growing body of evidence that the protein-production rate can be regulated at the level of translation elongation by controlling ribosome flux across the mRNA. Variations in the abundance of tRNA molecules cause different rates of translation of their counterpart codons. This, in turn, produces a variable landscape of translational rate across each and every mRNA, with the dynamic formation and deformation of ribosomal queues being regulated by both tRNA availability and the rates of translation initiation and termination. In the present article, a range of examples of tRNA control of gene expression are reviewed, and the use of mathematical modelling to develop a predictive understanding of the consequences of that regulation is discussed and explained. These findings encourage a view that predicting the protein-synthesis rate of each mRNA requires a holistic understanding of how each stage of translation, including elongation, contributes to the overall protein-production rate.
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25
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Chu D, Kazana E, Bellanger N, Singh T, Tuite MF, von der Haar T. Translation elongation can control translation initiation on eukaryotic mRNAs. EMBO J 2013; 33:21-34. [PMID: 24357599 DOI: 10.1002/embj.201385651] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Synonymous codons encode the same amino acid, but differ in other biophysical properties. The evolutionary selection of codons whose properties are optimal for a cell generates the phenomenon of codon bias. Although recent studies have shown strong effects of codon usage changes on protein expression levels and cellular physiology, no translational control mechanism is known that links codon usage to protein expression levels. Here, we demonstrate a novel translational control mechanism that responds to the speed of ribosome movement immediately after the start codon. High initiation rates are only possible if start codons are liberated sufficiently fast, thus accounting for the observation that fast codons are overrepresented in highly expressed proteins. In contrast, slow codons lead to slow liberation of the start codon by initiating ribosomes, thereby interfering with efficient translation initiation. Codon usage thus evolved as a means to optimise translation on individual mRNAs, as well as global optimisation of ribosome availability.
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Affiliation(s)
- Dominique Chu
- School of Computing, University of Kent, Canterbury, UK
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26
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Transient dual-luciferase assay combined with a glucocorticoid-inducible system for rice protoplasts. Biosci Biotechnol Biochem 2013; 77:2480-2. [PMID: 24317047 DOI: 10.1271/bbb.130480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We describe a transient dual-luciferase assay combined with a glucocorticoid-inducible system for rice protoplasts. Luciferase genes were efficiently induced by adding 0.1 µM of dexamethasone to the protoplast suspension, the activity of the luciferases reaching a maximum 6 h after induction. This assay system is applicable to studying the translation efficiency of rice by using the luciferase gene harboring tandem copies of an interesting codon at the 5' end.
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