101
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García P, Encinar Del Dedo J, Ayté J, Hidalgo E. Genome-wide Screening of Regulators of Catalase Expression: ROLE OF A TRANSCRIPTION COMPLEX AND HISTONE AND tRNA MODIFICATION COMPLEXES ON ADAPTATION TO STRESS. J Biol Chem 2016; 291:790-9. [PMID: 26567340 DOI: 10.1074/jbc.m115.696658] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Indexed: 12/22/2022] Open
Abstract
In response to environmental cues, the mitogen-activated protein kinase Sty1-driven signaling cascade activates hundreds of genes to induce a robust anti-stress cellular response in fission yeast. Thus, upon stress imposition Sty1 transiently accumulates in the nucleus where it up-regulates transcription through the Atf1 transcription factor. Several regulators of transcription and translation have been identified as important to mount an integral response to oxidative stress, such as the Spt-Ada-Gcn5-acetyl transferase or Elongator complexes, respectively. With the aim of identifying new regulators of this massive gene expression program, we have used a GFP-based protein reporter and screened a fission yeast deletion collection using flow cytometry. We find that the levels of catalase fused to GFP, both before and after a threat of peroxides, are altered in hundreds of strains lacking components of chromatin modifiers, transcription complexes, and modulators of translation. Thus, the transcription elongation complex Paf1, the histone methylase Set1-COMPASS, and the translation-related Trm112 dimers are all involved in full expression of Ctt1-GFP and in wild-type tolerance to peroxides.
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Affiliation(s)
- Patricia García
- From the Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/ Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Javier Encinar Del Dedo
- From the Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/ Dr. Aiguader 88, 08003 Barcelona, Spain
| | - José Ayté
- From the Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/ Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Elena Hidalgo
- From the Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/ Dr. Aiguader 88, 08003 Barcelona, Spain
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102
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Thiaville PC, Legendre R, Rojas-Benítez D, Baudin-Baillieu A, Hatin I, Chalancon G, Glavic A, Namy O, de Crécy-Lagard V. Global translational impacts of the loss of the tRNA modification t 6A in yeast. MICROBIAL CELL 2016; 3:29-45. [PMID: 26798630 PMCID: PMC4717488 DOI: 10.15698/mic2016.01.473] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The universal tRNA modification t6A is found at position 37 of nearly
all tRNAs decoding ANN codons. The absence of t6A37 leads
to severe growth defects in baker’s yeast, phenotypes similar to those caused by
defects in mcm5s2U34 synthesis. Mutants in
mcm5s2U34 can be suppressed by
overexpression of tRNALysUUU, but we show t6A
phenotypes could not be suppressed by expressing any individual ANN decoding
tRNA, and t6A and mcm5s2U are not determinants
for each other’s formation. Our results suggest that t6A deficiency,
like mcm5s2U deficiency, leads to protein folding defects,
and show that the absence of t6A led to stress sensitivities (heat,
ethanol, salt) and sensitivity to TOR pathway inhibitors. Additionally,
L-homoserine suppressed the slow growth phenotype seen in
t6A-deficient strains, and proteins aggregates and Advanced Glycation
End-products (AGEs) were increased in the mutants. The global consequences on
translation caused by t6A absence were examined by ribosome
profiling. Interestingly, the absence of t6A did not lead to global
translation defects, but did increase translation initiation at upstream non-AUG
codons and increased frame-shifting in specific genes. Analysis of codon
occupancy rates suggests that one of the major roles of t6A is to
homogenize the process of elongation by slowing the elongation rate at codons
decoded by high abundance tRNAs and I34:C3 pairs while
increasing the elongation rate of rare tRNAs and G34:U3
pairs. This work reveals that the consequences of t6A absence are
complex and multilayered and has set the stage to elucidate the molecular basis
of the observed phenotypes.
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Affiliation(s)
- Patrick C Thiaville
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; Genetics and Genomics Graduate Program, University of Florida, Gainesville, FL 32610, USA; University of Florida Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Bâtiment 400, 91400 Orsay, France
| | - Rachel Legendre
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Bâtiment 400, 91400 Orsay, France
| | - Diego Rojas-Benítez
- Centro de Regulación del Genoma. Facultad de Ciencias - Universidad de Chile, Santiago, Chile
| | - Agnès Baudin-Baillieu
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Bâtiment 400, 91400 Orsay, France
| | - Isabelle Hatin
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Bâtiment 400, 91400 Orsay, France
| | - Guilhem Chalancon
- Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Alvaro Glavic
- Centro de Regulación del Genoma. Facultad de Ciencias - Universidad de Chile, Santiago, Chile
| | - Olivier Namy
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Bâtiment 400, 91400 Orsay, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; University of Florida Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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103
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Shigi N. Sulfur Modifications in tRNA: Function and Implications for Human Disease. MODIFIED NUCLEIC ACIDS IN BIOLOGY AND MEDICINE 2016. [DOI: 10.1007/978-3-319-34175-0_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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104
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Karlsborn T, Mahmud AKMF, Tükenmez H, Byström AS. Loss of ncm 5 and mcm 5 wobble uridine side chains results in an altered metabolic profile. Metabolomics 2016; 12:177. [PMID: 27738410 PMCID: PMC5037161 DOI: 10.1007/s11306-016-1120-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/14/2016] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The Elongator complex, comprising six subunits (Elp1p-Elp6p), is required for formation of 5-carbamoylmethyl (ncm5) and 5-methoxycarbonylmethyl (mcm5) side chains on wobble uridines in 11 out of 42 tRNA species in Saccharomyces cerevisiae. Loss of these side chains reduces the efficiency of tRNA decoding during translation, resulting in pleiotropic phenotypes. Overexpression of hypomodified [Formula: see text], which in wild-type strains are modified with mcm5s2U, partially suppress phenotypes of an elp3Δ strain. OBJECTIVES To identify metabolic alterations in an elp3Δ strain and elucidate whether these metabolic alterations are suppressed by overexpression of hypomodified [Formula: see text]. METHOD Metabolic profiles were obtained using untargeted GC-TOF-MS of a temperature-sensitive elp3Δ strain carrying either an empty low-copy vector, an empty high-copy vector, a low-copy vector harboring the wild-type ELP3 gene, or a high-copy vector overexpressing [Formula: see text]. The temperature sensitive elp3Δ strain derivatives were cultivated at permissive (30 °C) or semi-permissive (34 °C) growth conditions. RESULTS Culturing an elp3Δ strain at 30 or 34 °C resulted in altered metabolism of 36 and 46 %, respectively, of all metabolites detected when compared to an elp3Δ strain carrying the wild-type ELP3 gene. Overexpression of hypomodified [Formula: see text] suppressed a subset of the metabolic alterations observed in the elp3Δ strain. CONCLUSION Our results suggest that the presence of ncm5- and mcm5-side chains on wobble uridines in tRNA are important for metabolic homeostasis.
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Affiliation(s)
- Tony Karlsborn
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | | | - Hasan Tükenmez
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Anders S. Byström
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
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105
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Ladang A, Rapino F, Heukamp LC, Tharun L, Shostak K, Hermand D, Delaunay S, Klevernic I, Jiang Z, Jacques N, Jamart D, Migeot V, Florin A, Göktuna S, Malgrange B, Sansom OJ, Nguyen L, Büttner R, Close P, Chariot A. Elp3 drives Wnt-dependent tumor initiation and regeneration in the intestine. J Exp Med 2015; 212:2057-75. [PMID: 26527802 PMCID: PMC4647259 DOI: 10.1084/jem.20142288] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 09/30/2015] [Indexed: 01/04/2023] Open
Abstract
Ladang et al. report that Elp3, a subunit of the Elongator complex, is induced by Wnt signaling and is required to initiate colon cancer development through the regulation of Sox9 translation. They also show that this mechanism is relevant in radiation-induced intestinal regeneration. Tumor initiation in the intestine can rapidly occur from Lgr5+ crypt columnar stem cells. Dclk1 is a marker of differentiated Tuft cells and, when coexpressed with Lgr5, also marks intestinal cancer stem cells. Here, we show that Elp3, the catalytic subunit of the Elongator complex, is required for Wnt-driven intestinal tumor initiation and radiation-induced regeneration by maintaining a subpool of Lgr5+/Dclk1+/Sox9+ cells. Elp3 deficiency dramatically delayed tumor appearance in Apc-mutated intestinal epithelia and greatly prolonged mice survival without affecting the normal epithelium. Specific ablation of Elp3 in Lgr5+ cells resulted in marked reduction of polyp formation upon Apc inactivation, in part due to a decreased number of Lgr5+/Dclk1+/Sox9+ cells. Mechanistically, Elp3 is induced by Wnt signaling and promotes Sox9 translation, which is needed to maintain the subpool of Lgr5+/Dclk1+ cancer stem cells. Consequently, Elp3 or Sox9 depletion led to similar defects in Dclk1+ cancer stem cells in ex vivo organoids. Finally, Elp3 deficiency strongly impaired radiation-induced intestinal regeneration, in part because of decreased Sox9 protein levels. Together, our data demonstrate the crucial role of Elp3 in maintaining a subpopulation of Lgr5-derived and Sox9-expressing cells needed to trigger Wnt-driven tumor initiation in the intestine.
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Affiliation(s)
- Aurélie Ladang
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Francesca Rapino
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Cancer Signaling, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Lukas C Heukamp
- Institut für Pathologie, University Hospital Cologne, 50937 Cologne, Germany
| | - Lars Tharun
- Institut für Pathologie, University Hospital Cologne, 50937 Cologne, Germany
| | - Kateryna Shostak
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Damien Hermand
- Unité de Recherche en Physiologie Moléculaire-Laboratoire de Génétique Moléculaire, University of Namur, 5000 Namur, Belgium
| | - Sylvain Delaunay
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Cancer Signaling, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Iva Klevernic
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Zheshen Jiang
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Nicolas Jacques
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Diane Jamart
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Cancer Signaling, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Valérie Migeot
- Unité de Recherche en Physiologie Moléculaire-Laboratoire de Génétique Moléculaire, University of Namur, 5000 Namur, Belgium
| | - Alexandra Florin
- Institut für Pathologie, University Hospital Cologne, 50937 Cologne, Germany
| | - Serkan Göktuna
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Brigitte Malgrange
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium GIGA Neurosciences, University of Liège, 4000 Liège, Belgium
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, Scotland, UK
| | - Laurent Nguyen
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium GIGA Neurosciences, University of Liège, 4000 Liège, Belgium Walloon Excellence in Life Sciences and Biotechnology, 1300 Wavre, Belgium
| | - Reinhard Büttner
- Institut für Pathologie, University Hospital Cologne, 50937 Cologne, Germany
| | - Pierre Close
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Cancer Signaling, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Alain Chariot
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium Walloon Excellence in Life Sciences and Biotechnology, 1300 Wavre, Belgium
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106
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Armengod ME, Meseguer S, Villarroya M, Prado S, Moukadiri I, Ruiz-Partida R, Garzón MJ, Navarro-González C, Martínez-Zamora A. Modification of the wobble uridine in bacterial and mitochondrial tRNAs reading NNA/NNG triplets of 2-codon boxes. RNA Biol 2015; 11:1495-507. [PMID: 25607529 DOI: 10.4161/15476286.2014.992269] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Posttranscriptional modification of the uridine located at the wobble position (U34) of tRNAs is crucial for optimization of translation. Defects in the U34 modification of mitochondrial-tRNAs are associated with a group of rare diseases collectively characterized by the impairment of the oxidative phosphorylation system. Retrograde signaling pathways from mitochondria to nucleus are involved in the pathophysiology of these diseases. These pathways may be triggered by not only the disturbance of the mitochondrial (mt) translation caused by hypomodification of tRNAs, but also as a result of nonconventional roles of mt-tRNAs and mt-tRNA-modifying enzymes. The evolutionary conservation of these enzymes supports their importance for cell and organismal functions. Interestingly, bacterial and eukaryotic cells respond to stress by altering the expression or activity of these tRNA-modifying enzymes, which leads to changes in the modification status of tRNAs. This review summarizes recent findings about these enzymes and sets them within the previous data context.
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Affiliation(s)
- M Eugenia Armengod
- a Laboratory of RNA Modification and Mitochondrial Diseases ; Centro de Investigación Príncipe Felipe ; Valencia , Spain
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107
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Karlsborn T, Tükenmez H, Mahmud AKMF, Xu F, Xu H, Byström AS. Elongator, a conserved complex required for wobble uridine modifications in eukaryotes. RNA Biol 2015; 11:1519-28. [PMID: 25607684 DOI: 10.4161/15476286.2014.992276] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Elongator is a 6 subunit protein complex highly conserved in eukaryotes. The role of this complex has been controversial as the pleiotropic phenotypes of Elongator mutants have implicated the complex in several cellular processes. However, in yeast there is convincing evidence that the primary and probably only role of this complex is in formation of the 5-methoxycarbonylmethyl (mcm(5)) and 5-carbamoylmethyl (ncm(5)) side chains on uridines at wobble position in tRNA. In this review we summarize the cellular processes that have been linked to the Elongator complex and discuss its role in tRNA modification and regulation of translation. We also describe additional gene products essential for formation of ncm(5) and mcm(5) side chains at U34 and their influence on Elongator activity.
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Affiliation(s)
- Tony Karlsborn
- a Department of Molecular Biology ; Umeå University; Umeå , Sweden
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108
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Xu H, Bygdell J, Wingsle G, Byström AS. Yeast Elongator protein Elp1p does not undergo proteolytic processing in exponentially growing cells. Microbiologyopen 2015; 4:867-78. [PMID: 26407534 PMCID: PMC4694139 DOI: 10.1002/mbo3.285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/27/2015] [Accepted: 07/30/2015] [Indexed: 01/09/2023] Open
Abstract
In eukaryotic organisms, Elongator is a six-subunit protein complex required for the formation of 5-carbamoylmethyl (ncm(5) ) and 5-methylcarboxymethyl (mcm(5) ) side chains on uridines present at the wobble position (U34 ) of tRNA. The open reading frame encoding the largest Elongator subunit Elp1p has two in-frame 5' AUG methionine codons separated by 48 nucleotides. Here, we show that the second AUG acts as the start codon of translation. Furthermore, Elp1p was previously shown to exist in two major forms of which one was generated by proteolysis of full-length Elp1p and this proteolytic cleavage was suggested to regulate Elongator complex activity. In this study, we found that the vacuolar protease Prb1p was responsible for the cleavage of Elp1p. The cleavage occurs between residues 203 (Lys) and 204 (Ala) as shown by amine reactive Tandem Mass Tag followed by LC-MS/MS (liquid chromatography mass spectrometry) analysis. However, using a modified protein extraction procedure, including trichloroacetic acid, only full-length Elp1p was observed, showing that truncation of Elp1p is an artifact occurring during protein extraction. Consequently, our results indicate that N-terminal truncation of Elp1p is not likely to regulate Elongator complex activity.
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Affiliation(s)
- Hao Xu
- Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| | - Joakim Bygdell
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 87, Umeå, Sweden
| | - Gunnar Wingsle
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 87, Umeå, Sweden
| | - Anders S Byström
- Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
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109
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Guy MP, Shaw M, Weiner CL, Hobson L, Stark Z, Rose K, Kalscheuer VM, Gecz J, Phizicky EM. Defects in tRNA Anticodon Loop 2'-O-Methylation Are Implicated in Nonsyndromic X-Linked Intellectual Disability due to Mutations in FTSJ1. Hum Mutat 2015; 36:1176-87. [PMID: 26310293 DOI: 10.1002/humu.22897] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/12/2015] [Indexed: 01/18/2023]
Abstract
tRNA modifications are crucial for efficient and accurate protein synthesis, and modification defects are frequently associated with disease. Yeast trm7Δ mutants grow poorly due to lack of 2'-O-methylated C32 (Cm32 ) and Gm34 on tRNA(Phe) , catalyzed by Trm7-Trm732 and Trm7-Trm734, respectively, which in turn results in loss of wybutosine at G37 . Mutations in human FTSJ1, the likely TRM7 homolog, cause nonsyndromic X-linked intellectual disability (NSXLID), but the role of FTSJ1 in tRNA modification is unknown. Here, we report that tRNA(Phe) from two genetically independent cell lines of NSXLID patients with loss-of-function FTSJ1 mutations nearly completely lacks Cm32 and Gm34 , and has reduced peroxywybutosine (o2yW37 ). Additionally, tRNA(Phe) from an NSXLID patient with a novel FTSJ1-p.A26P missense allele specifically lacks Gm34 , but has normal levels of Cm32 and o2yW37 . tRNA(Phe) from the corresponding Saccharomyces cerevisiae trm7-A26P mutant also specifically lacks Gm34 , and the reduced Gm34 is not due to weaker Trm734 binding. These results directly link defective 2'-O-methylation of the tRNA anticodon loop to FTSJ1 mutations, suggest that the modification defects cause NSXLID, and may implicate Gm34 of tRNA(Phe) as the critical modification. These results also underscore the widespread conservation of the circuitry for Trm7-dependent anticodon loop modification of eukaryotic tRNA(Phe) .
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Affiliation(s)
- Michael P Guy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York, 14642
| | - Marie Shaw
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia 5000, Australia.,School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, South Australia 5000, Australia
| | - Catherine L Weiner
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York, 14642
| | - Lynne Hobson
- SA Pathology, Women's and Children's Hospital, Adelaide, South Australia 5006, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria 3052, Australia
| | - Katherine Rose
- Monash Health, Special Medicine Centre, Monash Medical Centre, Clayton, Victoria 3168, Australia
| | - Vera M Kalscheuer
- Department Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin D14195, Germany
| | - Jozef Gecz
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia 5000, Australia.,School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, South Australia 5000, Australia
| | - Eric M Phizicky
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York, 14642
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110
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Tükenmez H, Xu H, Esberg A, Byström AS. The role of wobble uridine modifications in +1 translational frameshifting in eukaryotes. Nucleic Acids Res 2015; 43:9489-99. [PMID: 26283182 PMCID: PMC4627075 DOI: 10.1093/nar/gkv832] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/06/2015] [Indexed: 12/31/2022] Open
Abstract
In Saccharomyces cerevisiae, 11 out of 42 tRNA species contain 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U), 5-methoxycarbonylmethyluridine (mcm(5)U), 5-carbamoylmethyluridine (ncm(5)U) or 5-carbamoylmethyl-2'-O-methyluridine (ncm(5)Um) nucleosides in the anticodon at the wobble position (U34). Earlier we showed that mutants unable to form the side chain at position 5 (ncm(5) or mcm(5)) or lacking sulphur at position 2 (s(2)) of U34 result in pleiotropic phenotypes, which are all suppressed by overexpression of hypomodified tRNAs. This observation suggests that the observed phenotypes are due to inefficient reading of cognate codons or an increased frameshifting. The latter may be caused by a ternary complex (aminoacyl-tRNA*eEF1A*GTP) with a modification deficient tRNA inefficiently being accepted to the ribosomal A-site and thereby allowing an increased peptidyl-tRNA slippage and thus a frameshift error. In this study, we have investigated the role of wobble uridine modifications in reading frame maintenance, using either the Renilla/Firefly luciferase bicistronic reporter system or a modified Ty1 frameshifting site in a HIS4A::lacZ reporter system. We here show that the presence of mcm(5) and s(2) side groups at wobble uridines are important for reading frame maintenance and thus the aforementioned mutant phenotypes might partly be due to frameshift errors.
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Affiliation(s)
- Hasan Tükenmez
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Hao Xu
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Anders Esberg
- Department of Odontology/Cariology, Umeå University, Umeå, 901 87, Sweden
| | - Anders S Byström
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
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111
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Tigano M, Ruotolo R, Dallabona C, Fontanesi F, Barrientos A, Donnini C, Ottonello S. Elongator-dependent modification of cytoplasmic tRNALysUUU is required for mitochondrial function under stress conditions. Nucleic Acids Res 2015; 43:8368-80. [PMID: 26240381 PMCID: PMC4787798 DOI: 10.1093/nar/gkv765] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 07/15/2015] [Indexed: 11/12/2022] Open
Abstract
To gain a wider view of the pathways that regulate mitochondrial function, we combined the effect of heat stress on respiratory capacity with the discovery potential of a genome-wide screen in Saccharomyces cerevisiae. We identified 105 new genes whose deletion impairs respiratory growth at 37°C by interfering with processes such as transcriptional regulation, ubiquitination and cytosolic tRNA wobble uridine modification via 5-methoxycarbonylmethyl-2-thiouridine formation. The latter process, specifically required for efficient decoding of AA-ending codons under stress conditions, was covered by multiple genes belonging to the Elongator (e.g. ELP3) and urmylation (e.g., NCS6) pathways. ELP3 or NCS6 deletants had impaired mitochondrial protein synthesis. Their respiratory deficiency was selectively rescued by overexpression of tRNA(Lys) UUU as well by overexpression of genes (BCK1 and HFM1) with a strong bias for the AAA codon read by this tRNA. These data extend the mitochondrial regulome, demonstrate that heat stress can impair respiration by disturbing cytoplasmic translation of proteins critically involved in mitochondrial function and document, for the first time, the involvement in such process of the Elongator and urmylation pathways. Given the conservation of these pathways, the present findings may pave the way to a better understanding of the human mitochondrial regulome in health and disease.
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Affiliation(s)
- Marco Tigano
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | - Roberta Ruotolo
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | | | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Antoni Barrientos
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA Department of Neurology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Claudia Donnini
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | - Simone Ottonello
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
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112
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Fina JP, Casati P. HAG3, a Histone Acetyltransferase, Affects UV-B Responses by Negatively Regulating the Expression of DNA Repair Enzymes and Sunscreen Content in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2015; 56:1388-400. [PMID: 25907565 DOI: 10.1093/pcp/pcv054] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/02/2015] [Indexed: 05/23/2023]
Abstract
Histone acetylation is regulated by histone acetyltransferases and deacetylases. In Arabidopsis, there are 12 histone acetyltransferases and 18 deacetylases. Histone acetyltransferases are organized in four families: the GNAT/HAG, the MYST, the p300/CBP and the TAFII250 families. Previously, we demonstrated that Arabidopsis mutants in the two members of the MYST acetyltransferase family show increased DNA damage after UV-B irradiation. To investigate further the role of other histone acetyltransferases in UV-B responses, a putative role for enzymes of the GNAT family, HAG1, HAG2 and HAG3, was analyzed. HAG transcripts are not UV-B regulated; however, hag3 RNA interference (RNAi) transgenic plants show a lower inhibition of leaf and root growth by UV-B, higher levels of UV-B-absorbing compounds and less UV-B-induced DNA damage than Wassilewskija (Ws) plants, while hag1 RNAi transgenic plants and hag2 mutants do not show significant differences from wild-type plants. Transcripts for UV-B-regulated genes are highly expressed under control conditions in the absence of UV-B in hag3 RNAi transgenic plants, suggesting that the higher UV-B tolerance may be due to increased levels of proteins that participate in UV-B responses. Together, our data provide evidence that HAG3, directly or indirectly, participates in UV-B-induced DNA damage repair and signaling.
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Affiliation(s)
- Julieta P Fina
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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113
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Nedialkova DD, Leidel SA. Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity. Cell 2015; 161:1606-18. [PMID: 26052047 PMCID: PMC4503807 DOI: 10.1016/j.cell.2015.05.022] [Citation(s) in RCA: 421] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 02/28/2015] [Accepted: 04/10/2015] [Indexed: 01/15/2023]
Abstract
Proteins begin to fold as they emerge from translating ribosomes. The kinetics of ribosome transit along a given mRNA can influence nascent chain folding, but the extent to which individual codon translation rates impact proteome integrity remains unknown. Here, we show that slower decoding of discrete codons elicits widespread protein aggregation in vivo. Using ribosome profiling, we find that loss of anticodon wobble uridine (U34) modifications in a subset of tRNAs leads to ribosome pausing at their cognate codons in S. cerevisiae and C. elegans. Cells lacking U34 modifications exhibit gene expression hallmarks of proteotoxic stress, accumulate aggregates of endogenous proteins, and are severely compromised in clearing stress-induced protein aggregates. Overexpression of hypomodified tRNAs alleviates ribosome pausing, concomitantly restoring protein homeostasis. Our findings demonstrate that modified U34 is an evolutionarily conserved accelerator of decoding and reveal an unanticipated role for tRNA modifications in maintaining proteome integrity. tRNA anticodon modification loss slows translation at cognate codons in vivo Codon-specific translational pausing triggers protein misfolding in yeast and worms Codon translation rates and protein homeostasis are restored by tRNA overexpression
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Affiliation(s)
- Danny D Nedialkova
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Strasse 54, 48149 Muenster, Germany; Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Strasse 54, 48149 Muenster, Germany; Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany; Faculty of Medicine, University of Muenster, Albert-Schweitzer-Campus 1, 48149 Muenster, Germany.
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114
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Fang X, Cui Y, Li Y, Qi Y. Transcription and processing of primary microRNAs are coupled by Elongator complex in Arabidopsis. NATURE PLANTS 2015; 1:15075. [PMID: 27250010 DOI: 10.1038/nplants.2015.75] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 04/27/2015] [Indexed: 06/05/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that play important regulatory roles in gene expression in plants and animals. The biogenesis of miRNAs involves the transcription of primary miRNAs (pri-miRNAs) by RNA polymerase II (RNAPII) and subsequent processing by Dicer or Dicer-like (DCL) proteins. Here we show that the Elongator complex is involved in miRNA biogenesis in Arabidopsis. Disruption of Elongator reduces RNAPII occupancy at miRNA loci and pri-miRNA transcription. We also show that Elongator interacts with the DCL1-containing Dicing complex and lack of Elongator impairs DCL1 localization in the nuclear Dicing body. Finally, we show that pri-miRNA transcripts as well as DCL1 associate with the chromatin of miRNA genes and the chromatin association of DCL1 is compromised in the absence of Elongator. Our results suggest that Elongator functions in both transcription and processing of pri-miRNAs and probably couples these two processes.
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Affiliation(s)
- Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yuwei Cui
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yaoxi Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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115
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The Elp2 subunit is essential for elongator complex assembly and functional regulation. Structure 2015; 23:1078-86. [PMID: 25960406 DOI: 10.1016/j.str.2015.03.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 03/20/2015] [Accepted: 03/25/2015] [Indexed: 01/24/2023]
Abstract
Elongator is a highly conserved multiprotein complex composed of six subunits (Elp1-6). Elongator has been associated with various cellular activities and has attracted clinical attention because of its role in certain neurodegenerative diseases. Here, we present the crystal structure of the Elp2 subunit revealing two seven-bladed WD40 β propellers, and show by structure-guided mutational analyses that the WD40 fold integrity of Elp2 is necessary for its binding to Elp1 and Elp3 subunits in multiple species. The detailed biochemical experiments indicate that Elp2 binds microtubules through its conserved alkaline residues in vitro and in vivo. We find that both the mutually independent Elp2-mediated Elongator assembly and the cytoskeleton association are important for yeast viability. In addition, mutation of Elp2 greatly affects the histone H3 acetylation activity of Elongator in vivo. Our results indicate that Elp2 is a necessary component for functional Elongator and acts as a hub in the formation of various complexes.
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116
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Leitner J, Retzer K, Malenica N, Bartkeviciute R, Lucyshyn D, Jäger G, Korbei B, Byström A, Luschnig C. Meta-regulation of Arabidopsis auxin responses depends on tRNA maturation. Cell Rep 2015; 11:516-26. [PMID: 25892242 PMCID: PMC4416960 DOI: 10.1016/j.celrep.2015.03.054] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 03/02/2015] [Accepted: 03/25/2015] [Indexed: 12/30/2022] Open
Abstract
Polar transport of the phytohormone auxin throughout plants shapes morphogenesis and is subject to stringent and specific control. Here, we identify basic cellular activities connected to translational control of gene expression as sufficient to specify auxin-mediated development. Mutants in subunits of Arabidopsis Elongator, a protein complex modulating translational efficiency via maturation of tRNAs, exhibit defects in auxin-controlled developmental processes, associated with reduced abundance of PIN-formed (PIN) auxin transport proteins. Similar anomalies are observed upon interference with tRNA splicing by downregulation of RNA ligase (AtRNL), pointing to a general role of tRNA maturation in auxin signaling. Elongator Protein 6 (ELP6) and AtRNL expression patterns underline an involvement in adjusting PIN protein levels, whereas rescue of mutant defects by auxin indicates rate-limiting activities in auxin-controlled organogenesis. This emphasizes mechanisms in which auxin serves as a bottleneck for plant morphogenesis, translating common cellular activities into defined developmental readouts.
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Affiliation(s)
- Johannes Leitner
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Wien, Austria
| | - Katarzyna Retzer
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Wien, Austria
| | - Nenad Malenica
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Wien, Austria
| | - Rasa Bartkeviciute
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Wien, Austria
| | - Doris Lucyshyn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Wien, Austria
| | - Gunilla Jäger
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Barbara Korbei
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Wien, Austria
| | - Anders Byström
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Christian Luschnig
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Wien, Austria.
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117
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Tyagi K, Pedrioli PGA. Protein degradation and dynamic tRNA thiolation fine-tune translation at elevated temperatures. Nucleic Acids Res 2015; 43:4701-12. [PMID: 25870413 PMCID: PMC4482078 DOI: 10.1093/nar/gkv322] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/30/2015] [Indexed: 01/15/2023] Open
Abstract
Maintenance of protein quality control has implications in various processes such as neurodegeneration and ageing. To investigate how environmental insults affect this process, we analysed the proteome of yeast continuously exposed to mild heat stress. In agreement with previous transcriptomics studies, amongst the most marked changes, we found up-regulation of cytoprotective factors; a shift from oxidative phosphorylation to fermentation; and down-regulation of translation. Importantly, we also identified a novel, post-translationally controlled, component of the heat shock response. The abundance of Ncs2p and Ncs6p, two members of the URM1 pathway responsible for the thiolation of wobble uridines in cytoplasmic tRNAs tKUUU, tQUUG and tEUUC, is down-regulated in a proteasomal dependent fashion. Using random forests we show that this results in differential translation of transcripts with a biased content for the corresponding codons. We propose that the role of this pathway in promoting catabolic and inhibiting anabolic processes, affords cells with additional time and resources needed to attain proper protein folding under periods of stress.
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Affiliation(s)
- Kshitiz Tyagi
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Patrick G A Pedrioli
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK The Swiss Federal Institute of Technology, The Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, 8092 Zurich, Switzerland
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118
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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: 4.8] [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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119
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Sharma S, Langhendries JL, Watzinger P, Kötter P, Entian KD, Lafontaine DLJ. Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine acetyltransferases that modify tRNAs assisted by the adaptor Tan1/THUMPD1. Nucleic Acids Res 2015; 43:2242-58. [PMID: 25653167 PMCID: PMC4344512 DOI: 10.1093/nar/gkv075] [Citation(s) in RCA: 252] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/20/2015] [Accepted: 01/20/2015] [Indexed: 01/05/2023] Open
Abstract
The function of RNA is subtly modulated by post-transcriptional modifications. Here, we report an important crosstalk in the covalent modification of two classes of RNAs. We demonstrate that yeast Kre33 and human NAT10 are RNA cytosine acetyltransferases with, surprisingly, specificity toward both 18S rRNA and tRNAs. tRNA acetylation requires the intervention of a specific and conserved adaptor: yeast Tan1/human THUMPD1. In budding and fission yeasts, and in human cells, we found two acetylated cytosines on 18S rRNA, one in helix 34 important for translation accuracy and another in helix 45 near the decoding site. Efficient 18S rRNA acetylation in helix 45 involves, in human cells, the vertebrate-specific box C/D snoRNA U13, which, we suggest, exposes the substrate cytosine to modification through Watson-Crick base pairing with 18S rRNA precursors during small subunit biogenesis. Finally, while Kre33 and NAT10 are essential for pre-rRNA processing reactions leading to 18S rRNA synthesis, we demonstrate that rRNA acetylation is dispensable to yeast cells growth. The inactivation of NAT10 was suggested to suppress nuclear morphological defects observed in laminopathic patient cells through loss of microtubules modification and cytoskeleton reorganization. We rather propose the effects of NAT10 on laminopathic cells are due to reduced ribosome biogenesis or function.
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MESH Headings
- Acetylation
- Acetyltransferases/chemistry
- Acetyltransferases/metabolism
- Amino Acid Sequence
- Cell Line
- Conserved Sequence
- Cytosine/metabolism
- Humans
- N-Terminal Acetyltransferase E/chemistry
- N-Terminal Acetyltransferase E/metabolism
- N-Terminal Acetyltransferases
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- RNA, Plant/chemistry
- RNA, Plant/metabolism
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/metabolism
- RNA, Small Nucleolar/metabolism
- RNA, Transfer/metabolism
- RNA-Binding Proteins/metabolism
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/metabolism
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Affiliation(s)
- Sunny Sharma
- Institute of Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany RNA Molecular Biology, F.R.S./FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium
| | - Jean-Louis Langhendries
- RNA Molecular Biology, F.R.S./FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium
| | - Peter Watzinger
- Institute of Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Peter Kötter
- Institute of Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Karl-Dieter Entian
- Institute of Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Denis L J Lafontaine
- RNA Molecular Biology, F.R.S./FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium Center for Microscopy and Molecular Imaging, B-6041 Charleroi-Gosselies, Belgium
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120
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Cheng WWC, Tang CSM, Gui HS, So MT, Lui VCH, Tam PKH, Garcia-Barcelo MM. Depletion of the IKBKAP ortholog in zebrafish leads to hirschsprung disease-like phenotype. World J Gastroenterol 2015; 21:2040-2046. [PMID: 25717236 PMCID: PMC4326138 DOI: 10.3748/wjg.v21.i7.2040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 08/01/2014] [Accepted: 09/16/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the role of IKBKAP (inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein) in the development of enteric nervous system (ENS) and Hirschsprung disease (HSCR).
METHODS: In this study, we injected a morpholino that blocked the translation of ikbkap protein to 1-cell stage zebrafish embryos. The phenotype in the ENS was analysed by antibody staining of the pan-neuronal marker HuC/D followed by enteric neuron counting. The mean numbers of enteric neurons were compared between the morphant and the control. We also studied the expressions of ret and phox2bb, which are involved in ENS development, in the ikbkap morpholino injected embryos by quantitative reverse transcriptase polymerase chain reaction and compared them with the control.
RESULTS: We observed aganglionosis (χ2, P < 0.01) and a reduced number of enteric neurons (38.8 ± 9.9 vs 50.2 ± 17.3, P < 0.05) in the zebrafish embryos injected with ikbkap translation-blocking morpholino (morphant) when compared with the control embryos. Specificity of the morpholino was confirmed by similar results obtained using a second non-overlapping morpholino that blocked the translation of ikbkap. We further studied the morphant by analysing the expression levels of genes involved in ENS development such as ret, phox2bb and sox10, and found that phox2bb, the ortholog of human PHOX2B, was significantly down-regulated (0.51 ± 0.15 vs 1.00 ± 0, P < 0.05). Although we also observed a reduction in the expression of ret, the difference was not significant.
CONCLUSION: Loss of IKBKAP contributed to HSCR as demonstrated by functional analysis in zebrafish embryos.
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121
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Rectifier of aberrant mRNA splicing recovers tRNA modification in familial dysautonomia. Proc Natl Acad Sci U S A 2015; 112:2764-9. [PMID: 25675486 DOI: 10.1073/pnas.1415525112] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Familial dysautonomia (FD), a hereditary sensory and autonomic neuropathy, is caused by missplicing of exon 20, resulting from an intronic mutation in the inhibitor of kappa light polypeptide gene enhancer in B cells, kinase complex-associated protein (IKBKAP) gene encoding IKK complex-associated protein (IKAP)/elongator protein 1 (ELP1). A newly established splicing reporter assay allowed us to visualize pathogenic splicing in cells and to screen small chemicals for the ability to correct the aberrant splicing of IKBKAP. Using this splicing reporter, we screened our chemical libraries and identified a compound, rectifier of aberrant splicing (RECTAS), that rectifies the aberrant IKBKAP splicing in cells from patients with FD. Here, we found that the levels of modified uridine at the wobble position in cytoplasmic tRNAs are reduced in cells from patients with FD and that treatment with RECTAS increases the expression of IKAP and recovers the tRNA modifications. These findings suggest that the missplicing of IKBKAP results in reduced tRNA modifications in patients with FD and that RECTAS is a promising therapeutic drug candidate for FD.
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122
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Kolaj-Robin O, McEwen AG, Cavarelli J, Séraphin B. Structure of the Elongator cofactor complex Kti11/Kti13 provides insight into the role of Kti13 in Elongator-dependent tRNA modification. FEBS J 2015; 282:819-33. [PMID: 25604895 DOI: 10.1111/febs.13199] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/12/2015] [Accepted: 01/14/2015] [Indexed: 12/26/2022]
Abstract
UNLABELLED Modification of wobble uridines of many eukaryotic tRNAs requires the Elongator complex, a highly conserved six-subunit eukaryotic protein assembly, as well as the Killer toxin-insensitive (Kti) proteins 11-14. Kti11 was additionally shown to be implicated in the biosynthesis of diphthamide, a post-translationally modified histidine of translation elongation factor 2. Recent data indicate that iron-bearing Kti11 functions as an electron donor to the [4Fe-4S] cluster of radical S-Adenosylmethionine enzymes, triggering the subsequent radical reaction. We show here that recombinant yeast Kti11 forms a stable 1 : 1 complex with Kti13. To obtain insights into the function of this heterodimer, the Kti11/Kti13 complex was purified to homogeneity, crystallized, and its structure determined at 1.45 Å resolution. The importance of several residues mediating complex formation was confirmed by mutagenesis. Kti13 adopts a fold characteristic of RCC1-like proteins. The seven-bladed β-propeller consists of a unique mixture of four- and three-stranded blades. In the complex, Kti13 orients Kti11 and restricts access to its electron-carrying iron atom, constraining the electron transfer capacity of Kti11. Based on these findings, we propose a role for Kti13, and discuss the possible functional implications of complex formation. DATABASE Structural data have been submitted to the Protein Data Bank under accession number 4X33.
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Affiliation(s)
- Olga Kolaj-Robin
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de Recherche Scientifique UMR 7104/Institut National de Santé et de Recherche Médicale U964/Université de Strasbourg, Illkirch, France
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123
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Alings F, Sarin LP, Fufezan C, Drexler HCA, Leidel SA. An evolutionary approach uncovers a diverse response of tRNA 2-thiolation to elevated temperatures in yeast. RNA (NEW YORK, N.Y.) 2015; 21:202-12. [PMID: 25505025 PMCID: PMC4338348 DOI: 10.1261/rna.048199.114] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Chemical modifications of transfer RNA (tRNA) molecules are evolutionarily well conserved and critical for translation and tRNA structure. Little is known how these nucleoside modifications respond to physiological stress. Using mass spectrometry and complementary methods, we defined tRNA modification levels in six yeast species in response to elevated temperatures. We show that 2-thiolation of uridine at position 34 (s(2)U34) is impaired at temperatures exceeding 30°C in the commonly used Saccharomyces cerevisiae laboratory strains S288C and W303, and in Saccharomyces bayanus. Upon stress relief, thiolation levels recover and we find no evidence that modified tRNA or s(2)U34 nucleosides are actively removed. Our results suggest that loss of 2-thiolation follows accumulation of newly synthesized tRNA that lack s(2)U34 modification due to temperature sensitivity of the URM1 pathway in S. cerevisiae and S. bayanus. Furthermore, our analysis of the tRNA modification pattern in selected yeast species revealed two alternative phenotypes. Most strains moderately increase their tRNA modification levels in response to heat, possibly constituting a common adaptation to high temperatures. However, an overall reduction of nucleoside modifications was observed exclusively in S288C. This surprising finding emphasizes the importance of studies that utilize the power of evolutionary biology, and highlights the need for future systematic studies on tRNA modifications in additional model organisms.
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Affiliation(s)
- Fiona Alings
- RNA Biology Laboratory, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany
| | - L Peter Sarin
- RNA Biology Laboratory, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany
| | - Christian Fufezan
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Münster, Germany
| | - Hannes C A Drexler
- Bioanalytical Mass Spectrometry Unit, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany
| | - Sebastian A Leidel
- RNA Biology Laboratory, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany Faculty of Medicine, University of Münster, 48149 Münster, Germany
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124
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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: 5.4] [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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Abstract
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Long
known for their role in histone acetylation, recent studies
have demonstrated that lysine acetyltransferases also carry out distinct
“orphan” functions. These activities impact a wide range
of biological phenomena including metabolism, RNA modification, nuclear
morphology, and mitochondrial function. Here, we review the discovery
and characterization of orphan lysine acetyltransferase functions.
In addition to highlighting the evidence and biological role for these
functions in human disease, we discuss the part emerging chemical
tools may play in investigating this versatile enzyme superfamily.
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Affiliation(s)
- David C. Montgomery
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
| | - Alexander W. Sorum
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
| | - Jordan L. Meier
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
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126
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Zhu M, Li Y, Chen G, Ren L, Xie Q, Zhao Z, Hu Z. Silencing SlELP2L, a tomato Elongator complex protein 2-like gene, inhibits leaf growth, accelerates leaf, sepal senescence, and produces dark-green fruit. Sci Rep 2015; 5:7693. [PMID: 25573793 PMCID: PMC4287726 DOI: 10.1038/srep07693] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 11/28/2014] [Indexed: 11/12/2022] Open
Abstract
The multi-subunit complex Elongator interacts with elongating RNA polymerase II (RNAPII) and is thought to facilitate transcription through histone acetylation. Elongator is highly conserved in eukaryotes, yet has multiple kingdom-specific functions in diverse organisms. Recent genetic studies performed in Arabidopsis have demonstrated that Elongator functions in plant growth and development, and in response to biotic and abiotic stress. However, little is known about its roles in other plant species. Here, we study the function of an Elongator complex protein 2-like gene in tomato, here designated as SlELP2L, through RNAi-mediated gene silencing. Silencing SlELP2L in tomato inhibits leaf growth, accelerates leaf and sepal senescence, and produces dark-green fruit with reduced GA and IAA contents in leaves, and increased chlorophyll accumulation in pericarps. Gene expression analysis indicated that SlELP2L-silenced plants had reduced transcript levels of ethylene- and ripening-related genes during fruit ripening with slightly decreased carotenoid content in fruits, while the expression of DNA methyltransferase genes was up-regulated, indicating that SlELP2L may modulate DNA methylation in tomato. Besides, silencing SlELP2L increases ABA sensitivity in inhibiting seedling growth. These results suggest that SlELP2L plays important roles in regulating plant growth and development, as well as in response to ABA in tomato.
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Affiliation(s)
- Mingku Zhu
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Yali Li
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Guoping Chen
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Lijun Ren
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Qiaoli Xie
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Zhiping Zhao
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Zongli Hu
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
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127
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Abdel-Fattah W, Jablonowski D, Di Santo R, Thüring KL, Scheidt V, Hammermeister A, ten Have S, Helm M, Schaffrath R, Stark MJR. Phosphorylation of Elp1 by Hrr25 is required for elongator-dependent tRNA modification in yeast. PLoS Genet 2015; 11:e1004931. [PMID: 25569479 PMCID: PMC4287497 DOI: 10.1371/journal.pgen.1004931] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 12/01/2014] [Indexed: 12/26/2022] Open
Abstract
Elongator is a conserved protein complex comprising six different polypeptides that has been ascribed a wide range of functions, but which is now known to be required for modification of uridine residues in the wobble position of a subset of tRNAs in yeast, plants, worms and mammals. In previous work, we showed that Elongator's largest subunit (Elp1; also known as Iki3) was phosphorylated and implicated the yeast casein kinase I Hrr25 in Elongator function. Here we report identification of nine in vivo phosphorylation sites within Elp1 and show that four of these, clustered close to the Elp1 C-terminus and adjacent to a region that binds tRNA, are important for Elongator's tRNA modification function. Hrr25 protein kinase directly modifies Elp1 on two sites (Ser-1198 and Ser-1202) and through analyzing non-phosphorylatable (alanine) and acidic, phosphomimic substitutions at Ser-1198, Ser-1202 and Ser-1209, we provide evidence that phosphorylation plays a positive role in the tRNA modification function of Elongator and may regulate the interaction of Elongator both with its accessory protein Kti12 and with Hrr25 kinase. tRNA molecules function as adapters in protein synthesis, bringing amino acids to the ribosome and reading the genetic code through codon-anticodon base pairing. When the tRNA contains a uridine residue in the “wobble position” of its anticodon, which base-pairs with purine residues in the third position of a cognate codon, it is almost always chemically modified and modification is required for efficient decoding. In eukaryotic cells, these wobble uridine modifications require a conserved protein complex called Elongator. Our work shows that Elp1, Elongator's largest subunit, is phosphorylated on several sites. By blocking phosphorylation at these positions using mutations, we identified four phosphorylation sites that are important for Elongator's role in tRNA modification. We have also shown that Hrr25 protein kinase, a member of the casein kinase I (CKI) family, is responsible for modification of two of the sites that are important for Elongator function. Phosphorylation appears to affect interaction of the Elongator complex both with its kinase (Hrr25) and with Kti12, an accessory protein previously implicated in Elongator function. Our studies imply that Elp1 phosphorylation plays a positive role in Elongator-mediated tRNA modification and raise the possibility that wobble uridine modification may be regulated, representing a potential translational control mechanism.
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Affiliation(s)
- Wael Abdel-Fattah
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Germany
| | | | - Rachael Di Santo
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Kathrin L. Thüring
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Germany
| | - Viktor Scheidt
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Germany
| | | | - Sara ten Have
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mark Helm
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Germany
| | - Raffael Schaffrath
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Germany
- Department of Genetics, University of Leicester, Leicester, United Kingdom
- * E-mail: (RS); (MJRS)
| | - Michael J. R. Stark
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
- * E-mail: (RS); (MJRS)
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128
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Thiaville PC, de Crécy-Lagard V. The emerging role of complex modifications of tRNA LysUUU in signaling pathways. MICROBIAL CELL 2015; 2:1-4. [PMID: 25821779 PMCID: PMC4374736 DOI: 10.15698/mic2015.01.185] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Coordination of cell growth with nutrient availability, in particular amino acids, is a central problem that has been solved by the implementation of complex regulatory cascades. Although the specific regulatory mechanisms differ between kingdoms and species, a common theme is the use of tRNA molecules as sensors and transducers of amino acid starvation. In many bacteria, amino acid starvation leads to high levels of uncharged tRNAs, a signal for the synthesis of the stringent response’s alarmones, halting transcription of stable RNAs and inducing the synthesis of amino acid synthesis pathways 1. In gram-positive Bacteria (as well as the Deinococcus-Thermus clade), uncharged tRNAs bind structures (T-boxes) in the leader sequences of mRNA encoding gene, activating the expression of genes involved in amino acid metabolism 2. In eukaryotes, the conserved General Amino Acid Control (GAAC) response is triggered by shortage of amino acids that leads to the binding of uncharged tRNAs to Gcn2 kinase and, through a cascade of events, to the activation of the central activator of amino acid synthesis genes, Gcn4 3. As the study by Scheidt et al. 4 and several other recent studies in this field reveal, variations in charging levels are not the only mechanism by which tRNAs play a role in amino acid starvation responses; levels of post-transcriptional modifications also seem to play major roles.
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Affiliation(s)
- Patrick C Thiaville
- Genetics and Genomics Graduate Program, University of Florida, Gainesville, Florida, USA. ; University of Florida Genetics Institute, Gainesville, Florida, USA. ; Institut de Génétique et Microbiologie, Université of Paris-Sud, Orsay, France. ; Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Valérie de Crécy-Lagard
- University of Florida Genetics Institute, Gainesville, Florida, USA. ; Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
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129
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Guy MP, Phizicky EM. Conservation of an intricate circuit for crucial modifications of the tRNAPhe anticodon loop in eukaryotes. RNA (NEW YORK, N.Y.) 2015; 21:61-74. [PMID: 25404562 PMCID: PMC4274638 DOI: 10.1261/rna.047639.114] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Post-transcriptional tRNA modifications are critical for efficient and accurate translation, and have multiple different roles. Lack of modifications often leads to different biological consequences in different organisms, and in humans is frequently associated with neurological disorders. We investigate here the conservation of a unique circuitry for anticodon loop modification required for healthy growth in the yeast Saccharomyces cerevisiae. S. cerevisiae Trm7 interacts separately with Trm732 and Trm734 to 2'-O-methylate three substrate tRNAs at anticodon loop residues C₃₂ and N₃₄, and these modifications are required for efficient wybutosine formation at m(1)G₃₇ of tRNA(Phe). Moreover, trm7Δ and trm732Δ trm734Δ mutants grow poorly due to lack of functional tRNA(Phe). It is unknown if this circuitry is conserved and important for tRNA(Phe) modification in other eukaryotes, but a likely human TRM7 ortholog is implicated in nonsyndromic X-linked intellectual disability. We find that the distantly related yeast Schizosaccharomyces pombe has retained this circuitry for anticodon loop modification, that S. pombe trm7Δ and trm734Δ mutants have more severe phenotypes than the S. cerevisiae mutants, and that tRNA(Phe) is the major biological target. Furthermore, we provide evidence that Trm7 and Trm732 function is widely conserved throughout eukaryotes, since human FTSJ1 and THADA, respectively, complement growth defects of S. cerevisiae trm7Δ and trm732Δ trm734Δ mutants by modifying C₃₂ of tRNA(Phe), each working with the corresponding S. cerevisiae partner protein. These results suggest widespread importance of 2'-O-methylation of the tRNA anticodon loop, implicate tRNA(Phe) as the crucial substrate, and suggest that this modification circuitry is important for human neuronal development.
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Affiliation(s)
- Michael P Guy
- 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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130
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Ding Y, Mou Z. Elongator and its epigenetic role in plant development and responses to abiotic and biotic stresses. FRONTIERS IN PLANT SCIENCE 2015; 6:296. [PMID: 25972888 PMCID: PMC4413731 DOI: 10.3389/fpls.2015.00296] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 04/13/2015] [Indexed: 05/20/2023]
Abstract
Elongator, a six-subunit protein complex, was initially isolated as an interactor of hyperphosphorylated RNA polymerase II in yeast, and was subsequently identified in animals and plants. Elongator has been implicated in multiple cellular activities or biological processes including tRNA modification, histone modification, DNA demethylation or methylation, tubulin acetylation, and exocytosis. Studies in the model plant Arabidopsis thaliana suggest that the structure of Elongator and its functions are highly conserved between plants and yeast. Disruption of the Elongator complex in plants leads to aberrant growth and development, resistance to abiotic stresses, and susceptibility to plant pathogens. The morphological and physiological phenotypes of Arabidopsis Elongator mutants are associated with decreased histone acetylation and/or altered DNA methylation. This review summarizes recent findings related to the epigenetic function of Elongator in plant development and responses to abiotic and biotic stresses.
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Affiliation(s)
| | - Zhonglin Mou
- *Correspondence: Zhonglin Mou, Department of Microbiology and Cell Science, University of Florida, Museum Road, Building 981, Gainesville, FL 32611, USA
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131
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Glatt S, Zabel R, Vonkova I, Kumar A, Netz DJ, Pierik AJ, Rybin V, Lill R, Gavin AC, Balbach J, Breunig KD, Müller CW. Structure of the Kti11/Kti13 heterodimer and its double role in modifications of tRNA and eukaryotic elongation factor 2. Structure 2014; 23:149-160. [PMID: 25543256 DOI: 10.1016/j.str.2014.11.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 12/14/2022]
Abstract
The small, highly conserved Kti11 alias Dph3 protein encoded by the Kluyveromyces lactis killer toxin insensitive gene KTI11/DPH3 is involved in the diphthamide modification of eukaryotic elongation factor 2 and, together with Kti13, in Elongator-dependent tRNA wobble base modifications, thereby affecting the speed and accuracy of protein biosynthesis through two distinct mechanisms. We have solved the crystal structures of Saccharomyces cerevisiae Kti13 and the Kti11/Kti13 heterodimer at 2.4 and 2.9 Å resolution, respectively, and validated interacting residues through mutational analysis in vitro and in vivo. We show that metal coordination by Kti11 and its heterodimerization with Kti13 are essential for both translational control mechanisms. Our structural and functional analyses identify Kti13 as an additional component of the diphthamide modification pathway and provide insight into the molecular mechanisms that allow the Kti11/Kti13 heterodimer to coregulate two consecutive steps in ribosomal protein synthesis.
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Affiliation(s)
- Sebastian Glatt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Rene Zabel
- Martin-Luther-Universität Halle-Wittenberg, Institut für Biologie, Weinbergweg 10, 06120 Halle (Saale), Germany
| | - Ivana Vonkova
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Amit Kumar
- Martin-Luther-Universität Halle-Wittenberg, Institut für Physik, Betty-Heimann-Straße 7, 06120 Halle (Saale), Germany
| | - Daili J Netz
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Straße 6, 35037 Marburg, Germany
| | - Antonio J Pierik
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Straße 6, 35037 Marburg, Germany
| | - Vladimir Rybin
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Straße 6, 35037 Marburg, Germany; LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Hans-Meerwein-Straße, 35043 Marburg, Germany
| | - Anne-Claude Gavin
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jochen Balbach
- Martin-Luther-Universität Halle-Wittenberg, Institut für Physik, Betty-Heimann-Straße 7, 06120 Halle (Saale), Germany
| | - Karin D Breunig
- Martin-Luther-Universität Halle-Wittenberg, Institut für Biologie, Weinbergweg 10, 06120 Halle (Saale), Germany.
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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132
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Iron-sulfur proteins responsible for RNA modifications. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1272-83. [PMID: 25533083 DOI: 10.1016/j.bbamcr.2014.12.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 12/22/2022]
Abstract
RNA molecules are decorated with various chemical modifications, which are introduced post-transcriptionally by RNA-modifying enzymes. These modifications are required for proper RNA function. Among more than 100 known species of RNA modifications, several modified bases in tRNAs and rRNAs are introduced by RNA-modifying enzymes containing iron-sulfur (Fe/S) clusters. Most Fe/S-containing RNA-modifying enzymes contain radical SAM domains that catalyze a variety of chemical reactions, including methylation, methylthiolation, carboxymethylation, tricyclic purine formation, and deazaguanine formation. Lack of these modifications can cause pathological consequences. Here, we review recent studies on the biogenesis and function of RNA modifications mediated by Fe/S proteins. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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133
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Scheidt V, Jüdes A, Bär C, Klassen R, Schaffrath R. Loss of wobble uridine modification in tRNA anticodons interferes with TOR pathway signaling. MICROBIAL CELL 2014; 1:416-424. [PMID: 28357221 PMCID: PMC5349137 DOI: 10.15698/mic2014.12.179] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Previous work in yeast has suggested that modification of tRNAs, in particular uridine bases in the anticodon wobble position (U34), is linked to TOR (target of rapamycin) signaling. Hence, U34 modification mutants were found to be hypersensitive to TOR inhibition by rapamycin. To study whether this involves inappropriate TOR signaling, we examined interaction between mutations in TOR pathway genes (tip41∆, sap190∆, ppm1∆, rrd1∆) and U34 modification defects (elp3∆, kti12∆, urm1∆, ncs2∆) and found the rapamycin hypersensitivity in the latter is epistatic to drug resistance of the former. Epistasis, however, is abolished in tandem with a gln3∆ deletion, which inactivates transcription factor Gln3 required for TOR-sensitive activation of NCR (nitrogen catabolite repression) genes. In line with nuclear import of Gln3 being under control of TOR and dephosphorylation by the Sit4 phosphatase, we identify novel TOR-sensitive sit4 mutations that confer rapamycin resistance and importantly, mislocalise Gln3 when TOR is inhibited. This is similar to gln3∆ cells, which abolish the rapamycin hypersensitivity of U34 modification mutants, and suggests TOR deregulation due to tRNA undermodification operates through Gln3. In line with this, loss of U34 modifications (elp3∆, urm1∆) enhances nuclear import of and NCR gene activation (MEP2, GAP1) by Gln3 when TOR activity is low. Strikingly, this stimulatory effect onto Gln3 is suppressed by overexpression of tRNAs that usually carry the U34 modifications. Collectively, our data suggest that proper TOR signaling requires intact tRNA modifications and that loss of U34 modifications impinges on the TOR-sensitive NCR branch via Gln3 misregulation.
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Affiliation(s)
- Viktor Scheidt
- Institut für Biologie, Abteilung Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany
| | - André Jüdes
- Institut für Biologie, Abteilung Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany
| | - Christian Bär
- Institut für Biologie, Abteilung Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany. ; Present address: Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Melchor Fernandez Almagro 3, Madrid, Spain
| | - Roland Klassen
- Institut für Biologie, Abteilung Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany
| | - Raffael Schaffrath
- Institut für Biologie, Abteilung Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany
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134
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Damon JR, Pincus D, Ploegh HL. tRNA thiolation links translation to stress responses in Saccharomyces cerevisiae. Mol Biol Cell 2014; 26:270-82. [PMID: 25392298 PMCID: PMC4294674 DOI: 10.1091/mbc.e14-06-1145] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The URM1 pathway functions in a tRNA thiolation reaction that is required for synthesis of the mcm5s2U34 nucleoside found in tRNAs. Growth of Saccharomyces cerevisiae cells at an elevated temperature results in altered levels of modification enzymes, and this leads to decreased levels of tRNA thiolation. tRNA thiolation is tied to cellular stress responses. Although tRNA modifications have been well catalogued, the precise functions of many modifications and their roles in mediating gene expression are still being elucidated. Whereas tRNA modifications were long assumed to be constitutive, it is now apparent that the modification status of tRNAs changes in response to different environmental conditions. The URM1 pathway is required for thiolation of the cytoplasmic tRNAs tGluUUC, tGlnUUG, and tLysUUU in Saccharomyces cerevisiae. We demonstrate that URM1 pathway mutants have impaired translation, which results in increased basal activation of the Hsf1-mediated heat shock response; we also find that tRNA thiolation levels in wild-type cells decrease when cells are grown at elevated temperature. We show that defects in tRNA thiolation can be conditionally advantageous, conferring resistance to endoplasmic reticulum stress. URM1 pathway proteins are unstable and hence are more sensitive to changes in the translational capacity of cells, which is decreased in cells experiencing stresses. We propose a model in which a stress-induced decrease in translation results in decreased levels of URM1 pathway components, which results in decreased tRNA thiolation levels, which further serves to decrease translation. This mechanism ensures that tRNA thiolation and translation are tightly coupled and coregulated according to need.
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Affiliation(s)
- Jadyn R Damon
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - David Pincus
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - Hidde L Ploegh
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
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135
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Karlsborn T, Tükenmez H, Chen C, Byström AS. Familial dysautonomia (FD) patients have reduced levels of the modified wobble nucleoside mcm5s2U in tRNA. Biochem Biophys Res Commun 2014; 454:441-5. [DOI: 10.1016/j.bbrc.2014.10.116] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 10/21/2014] [Indexed: 12/30/2022]
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136
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Meseguer S, Martínez-Zamora A, García-Arumí E, Andreu AL, Armengod ME. The ROS-sensitive microRNA-9/9* controls the expression of mitochondrial tRNA-modifying enzymes and is involved in the molecular mechanism of MELAS syndrome. Hum Mol Genet 2014; 24:167-84. [PMID: 25149473 DOI: 10.1093/hmg/ddu427] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Mitochondrial dysfunction activates mitochondria-to-nucleus signaling pathways whose components are mostly unknown. Identification of these components is important to understand the molecular mechanisms underlying mitochondrial diseases and to discover putative therapeutic targets. MELAS syndrome is a rare neurodegenerative disease caused by mutations in mitochondrial (mt) DNA affecting mt-tRNA(Leu(UUR)). Patient and cybrid cells exhibit elevated oxidative stress. Moreover, mutant mt-tRNAs(Leu(UUR)) lack the taurine-containing modification normally present at the wobble uridine (U34) of wild-type mt-tRNA(Leu(UUR)), which is considered an etiology of MELAS. However, the molecular mechanism is still unclear. We found that MELAS cybrids exhibit a significant decrease in the steady-state levels of several mt-tRNA-modification enzymes, which is not due to transcriptional regulation. We demonstrated that oxidative stress mediates an NFkB-dependent induction of microRNA-9/9*, which acts as a post-transcriptional negative regulator of the mt-tRNA-modification enzymes GTPBP3, MTO1 and TRMU. Down-regulation of these enzymes by microRNA-9/9* affects the U34 modification status of non-mutant tRNAs and contributes to the MELAS phenotype. Anti-microRNA-9 treatments of MELAS cybrids reverse the phenotype, whereas miR-9 transfection of wild-type cells mimics the effects of siRNA-mediated down-regulation of GTPBP3, MTO1 and TRMU. Our data represent the first evidence that an mt-DNA disease can directly affect microRNA expression. Moreover, we demonstrate that the modification status of mt-tRNAs is dynamic and that cells respond to stress by modulating the expression of mt-tRNA-modifying enzymes. microRNA-9/9* is a crucial player in mitochondria-to-nucleus signaling as it regulates expression of nuclear genes in response to changes in the functional state of mitochondria.
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Affiliation(s)
- Salvador Meseguer
- Laboratory of RNA Modification and Mitochondrial Diseases, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain
| | - Ana Martínez-Zamora
- Laboratory of RNA Modification and Mitochondrial Diseases, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain
| | - Elena García-Arumí
- Hospital Universitari Vall d'Hebron, Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona 08035, Spain Biomedical Research Networking Centre for Rare Diseases (CIBERER) (node U701), Barcelona, Spain and
| | - Antonio L Andreu
- Hospital Universitari Vall d'Hebron, Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona 08035, Spain Biomedical Research Networking Centre for Rare Diseases (CIBERER) (node U701), Barcelona, Spain and
| | - M-Eugenia Armengod
- Laboratory of RNA Modification and Mitochondrial Diseases, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain CIBERER (node U721), Valencia, Spain
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137
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Di Santo R, Bandau S, Stark MJR. A conserved and essential basic region mediates tRNA binding to the Elp1 subunit of the Saccharomyces cerevisiae Elongator complex. Mol Microbiol 2014; 92:1227-42. [PMID: 24750273 PMCID: PMC4150532 DOI: 10.1111/mmi.12624] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2014] [Indexed: 12/25/2022]
Abstract
Elongator is a conserved, multi-protein complex discovered in Saccharomyces cerevisiae, loss of which confers a range of pleiotropic phenotypes. Elongator in higher eukaryotes is required for normal growth and development and a mutation in the largest subunit of human Elongator (Elp1) causes familial dysautonomia, a severe recessive neuropathy. Elongator promotes addition of mcm(5) and ncm(5) modifications to uridine in the tRNA anticodon 'wobble' position in both yeast and higher eukaryotes. Since these modifications are required for the tRNAs to function efficiently, a translation defect caused by hypomodified tRNAs may therefore underlie the variety of phenotypes associated with Elongator dysfunction. The Elp1 carboxy-terminal domain contains a highly conserved arginine/lysine-rich region that resembles a nuclear localization sequence (NLS). Using alanine substitution mutagenesis, we show that this region is essential for Elongator's function in tRNA wobble uridine modification. However, rather than acting to determine the nucleo-cytoplasmic distribution of Elongator, we find that the basic region plays a critical role in a novel interaction between tRNA and the Elp1 carboxy-terminal domain. Thus the conserved basic region in Elp1 may be essential for tRNA wobble uridine modification by acting as tRNA binding motif.
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Affiliation(s)
- Rachael Di Santo
- Centre for Gene Regulation & Expression, College of Life Sciences, MSI/WTB Complex, University of DundeeDundee, DD1 5EH, Scotland, UK
| | | | - Michael J R Stark
- Centre for Gene Regulation & Expression, College of Life Sciences, MSI/WTB Complex, University of DundeeDundee, DD1 5EH, Scotland, UK
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138
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Björk GR, Hagervall TG. Transfer RNA Modification: Presence, Synthesis, and Function. EcoSal Plus 2014; 6. [PMID: 26442937 DOI: 10.1128/ecosalplus.esp-0007-2013] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Indexed: 06/05/2023]
Abstract
Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica serovar Typhimurium contains 33 different modified nucleosides, which are all, except one (Queuosine [Q]), synthesized on an oligonucleotide precursor, which by specific enzymes later matures into tRNA. The structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The synthesis of the tRNA-modifying enzymes is not regulated similarly, and it is not coordinated to that of their substrate, the tRNA. The synthesis of some of them (e.g., several methylated derivatives) is catalyzed by one enzyme, which is position and base specific, whereas synthesis of some has a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N 6-cyclicthreonyladenosine [ct6A], and Q). Several of the modified nucleosides are essential for viability (e.g., lysidin, ct6A, 1-methylguanosine), whereas the deficiency of others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those that are present in the body of the tRNA primarily have a stabilizing effect on the tRNA. Thus, the ubiquitous presence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.
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Affiliation(s)
- Glenn R Björk
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
| | - Tord G Hagervall
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
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139
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Cheishvili D, Dietrich P, Maayan C, Even A, Weil M, Dragatsis I, Razin A. IKAP deficiency in an FD mouse model and in oligodendrocyte precursor cells results in downregulation of genes involved in oligodendrocyte differentiation and myelin formation. PLoS One 2014; 9:e94612. [PMID: 24760006 PMCID: PMC3997429 DOI: 10.1371/journal.pone.0094612] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/17/2014] [Indexed: 02/05/2023] Open
Abstract
The splice site mutation in the IKBKAP gene coding for IKAP protein leads to the tissue-specific skipping of exon 20, with concomitant reduction in IKAP protein production. This causes the neurodevelopmental, autosomal-recessive genetic disorder - Familial Dysautonomia (FD). The molecular hallmark of FD is the severe reduction of IKAP protein in the nervous system that is believed to be the main reason for the devastating symptoms of this disease. Our recent studies showed that in the brain of two FD patients, genes linked to oligodendrocyte differentiation and/or myelin formation are significantly downregulated, implicating IKAP in the process of myelination. However, due to the scarcity of FD patient tissues, these results awaited further validation in other models. Recently, two FD mouse models that faithfully recapitulate FD were generated, with two types of mutations resulting in severely low levels of IKAP expression. Here we demonstrate that IKAP deficiency in these FD mouse models affects a similar set of genes as in FD patients' brains. In addition, we identified two new IKAP target genes involved in oligodendrocyte cells differentiation and myelination, further underscoring the essential role of IKAP in this process. We also provide proof that IKAP expression is needed cell-autonomously for the regulation of expression of genes involved in myelin formation since knockdown of IKAP in the Oli-neu oligodendrocyte precursor cell line results in similar deficiencies. Further analyses of these two experimental models will compensate for the lack of human postmortem tissues and will advance our understanding of the role of IKAP in myelination and the disease pathology.
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Affiliation(s)
- David Cheishvili
- Familial Dysautonomia Centre, Pediatric Department Hadassah Hospital Hebrew University Hadassah Medical School, Jerusalem, Israel
- Department of Developmental Biology and Cancer Research, Institute of Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Paula Dietrich
- Department of Physiology, College of Medicine, The University of Tennessee, Health Science Center, Memphis, Tennessee, United States of America
| | - Channa Maayan
- Familial Dysautonomia Centre, Pediatric Department Hadassah Hospital Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Aviel Even
- Laboratory for Neurodegenerative Diseases and Personalized Medicine, Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, The Sagol School of Neurosciences, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Miguel Weil
- Laboratory for Neurodegenerative Diseases and Personalized Medicine, Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, The Sagol School of Neurosciences, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Ioannis Dragatsis
- Department of Physiology, College of Medicine, The University of Tennessee, Health Science Center, Memphis, Tennessee, United States of America
| | - Aharon Razin
- Department of Developmental Biology and Cancer Research, Institute of Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem, Israel
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140
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Shigi N. Biosynthesis and functions of sulfur modifications in tRNA. Front Genet 2014; 5:67. [PMID: 24765101 PMCID: PMC3980101 DOI: 10.3389/fgene.2014.00067] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 03/17/2014] [Indexed: 12/19/2022] Open
Abstract
Sulfur is an essential element for a variety of cellular constituents in all living organisms. In tRNA molecules, there are many sulfur-containing nucleosides, such as the derivatives of 2-thiouridine (s2U), 4-thiouridine (s4U), 2-thiocytidine (s2C), and 2-methylthioadenosine (ms2A). Earlier studies established the functions of these modifications for accurate and efficient translation, including proper recognition of the codons in mRNA or stabilization of tRNA structure. In many cases, the biosynthesis of these sulfur modifications starts with cysteine desulfurases, which catalyze the generation of persulfide (an activated form of sulfur) from cysteine. Many sulfur-carrier proteins are responsible for delivering this activated sulfur to each biosynthesis pathway. Finally, specific “modification enzymes” activate target tRNAs and then incorporate sulfur atoms. Intriguingly, the biosynthesis of 2-thiouridine in all domains of life is functionally and evolutionarily related to the ubiquitin-like post-translational modification system of cellular proteins in eukaryotes. This review summarizes the recent characterization of the biosynthesis of sulfur modifications in tRNA and the novel roles of this modification in cellular functions in various model organisms, with a special emphasis on 2-thiouridine derivatives. Each biosynthesis pathway of sulfur-containing molecules is mutually modulated via sulfur trafficking, and 2-thiouridine and codon usage bias have been proposed to control the translation of specific genes.
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Affiliation(s)
- Naoki Shigi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology Tokyo, Japan
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141
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Cheishvili D, Laiba E, Rekhtman D, Claman A, Razin A, Maayan C. Dynamic changes in IKBKAP mRNA levels during crisis of familial dysautonomia patients. Auton Neurosci 2014; 180:59-65. [DOI: 10.1016/j.autneu.2013.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Revised: 09/29/2013] [Accepted: 10/24/2013] [Indexed: 11/27/2022]
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142
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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: 1.3] [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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143
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Sarin LP, Leidel SA. Modify or die?--RNA modification defects in metazoans. RNA Biol 2014; 11:1555-67. [PMID: 25692999 PMCID: PMC4615230 DOI: 10.4161/15476286.2014.992279] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/06/2014] [Accepted: 11/10/2014] [Indexed: 12/21/2022] Open
Abstract
Chemical RNA modifications are present in all kingdoms of life and many of these post-transcriptional modifications are conserved throughout evolution. However, most of the research has been performed on single cell organisms, whereas little is known about how RNA modifications contribute to the development of metazoans. In recent years, the identification of RNA modification genes in genome wide association studies (GWAS) has sparked new interest in previously neglected genes. In this review, we summarize recent findings that connect RNA modification defects and phenotypes in higher eukaryotes. Furthermore, we discuss the implications of aberrant tRNA modification in various human diseases including metabolic defects, mitochondrial dysfunctions, neurological disorders, and cancer. As the molecular mechanisms of these diseases are being elucidated, we will gain first insights into the functions of RNA modifications in higher eukaryotes and finally understand their roles during development.
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MESH Headings
- Amyotrophic Lateral Sclerosis/genetics
- Amyotrophic Lateral Sclerosis/metabolism
- Amyotrophic Lateral Sclerosis/pathology
- Animals
- Dysautonomia, Familial/genetics
- Dysautonomia, Familial/metabolism
- Dysautonomia, Familial/pathology
- Epilepsy, Rolandic/genetics
- Epilepsy, Rolandic/metabolism
- Epilepsy, Rolandic/pathology
- Genome-Wide Association Study
- Humans
- Intellectual Disability/genetics
- Intellectual Disability/metabolism
- Intellectual Disability/pathology
- Mutation
- Neoplasms/genetics
- Neoplasms/metabolism
- Neoplasms/pathology
- Nucleic Acid Conformation
- Phenotype
- RNA/genetics
- RNA/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Mitochondrial
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- tRNA Methyltransferases/genetics
- tRNA Methyltransferases/metabolism
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Affiliation(s)
- L Peter Sarin
- Max Planck Institute for Molecular Biomedicine; Münster, Germany
| | - Sebastian A Leidel
- Max Planck Institute for Molecular Biomedicine; Münster, Germany
- Faculty of Medicine; University of Münster; Münster, Germany
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144
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Iben JR, Maraia RJ. tRNA gene copy number variation in humans. Gene 2013; 536:376-84. [PMID: 24342656 DOI: 10.1016/j.gene.2013.11.049] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 11/12/2013] [Accepted: 11/20/2013] [Indexed: 11/29/2022]
Abstract
The human tRNAome consists of more than 500 interspersed tRNA genes comprising 51 anticodon families of largely unequal copy number. We examined tRNA gene copy number variation (tgCNV) in six individuals; two kindreds of two parents and a child, using high coverage whole genome sequence data. Such differences may be important because translation of some mRNAs is sensitive to the relative amounts of tRNAs and because tRNA competition determines translational efficiency vs. fidelity and production of native vs. misfolded proteins. We identified several tRNA gene clusters with CNV, which in some cases were part of larger iterations. In addition there was an isolated tRNALysCUU gene that was absent as a homozygous deletion in one of the parents. When assessed by semiquantitative PCR in 98 DNA samples representing a wide variety of ethnicities, this allele was found deleted in hetero- or homozygosity in all groups at ~50% frequency. This is the first report of copy number variation of human tRNA genes. We conclude that tgCNV exists at significant levels among individual humans and discuss the results in terms of genetic diversity and prior genome wide association studies (GWAS) that suggest the importance of the ratio of tRNALys isoacceptors in Type-2 diabetes.
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Affiliation(s)
- James R Iben
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard J Maraia
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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145
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Skylar A, Matsuwaka S, Wu X. ELONGATA3 is required for shoot meristem cell cycle progression in Arabidopsis thaliana seedlings. Dev Biol 2013; 382:436-45. [DOI: 10.1016/j.ydbio.2013.08.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 08/09/2013] [Accepted: 08/12/2013] [Indexed: 11/26/2022]
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146
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Zinshteyn B, Gilbert WV. Loss of a conserved tRNA anticodon modification perturbs cellular signaling. PLoS Genet 2013; 9:e1003675. [PMID: 23935536 PMCID: PMC3731203 DOI: 10.1371/journal.pgen.1003675] [Citation(s) in RCA: 162] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 06/12/2013] [Indexed: 11/29/2022] Open
Abstract
Transfer RNA (tRNA) modifications enhance the efficiency, specificity and fidelity of translation in all organisms. The anticodon modification mcm(5)s(2)U(34) is required for normal growth and stress resistance in yeast; mutants lacking this modification have numerous phenotypes. Mutations in the homologous human genes are linked to neurological disease. The yeast phenotypes can be ameliorated by overexpression of specific tRNAs, suggesting that the modifications are necessary for efficient translation of specific codons. We determined the in vivo ribosome distributions at single codon resolution in yeast strains lacking mcm(5)s(2)U. We found accumulations at AAA, CAA, and GAA codons, suggesting that translation is slow when these codons are in the ribosomal A site, but these changes appeared too small to affect protein output. Instead, we observed activation of the GCN4-mediated stress response by a non-canonical pathway. Thus, loss of mcm(5)s(2)U causes global effects on gene expression due to perturbation of cellular signaling.
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Affiliation(s)
- Boris Zinshteyn
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Wendy V. Gilbert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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147
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Fernández-Vázquez J, Vargas-Pérez I, Sansó M, Buhne K, Carmona M, Paulo E, Hermand D, Rodríguez-Gabriel M, Ayté J, Leidel S, Hidalgo E. Modification of tRNA(Lys) UUU by elongator is essential for efficient translation of stress mRNAs. PLoS Genet 2013; 9:e1003647. [PMID: 23874237 PMCID: PMC3715433 DOI: 10.1371/journal.pgen.1003647] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 06/04/2013] [Indexed: 12/25/2022] Open
Abstract
The Elongator complex, including the histone acetyl transferase Sin3/Elp3, was isolated as an RNA polymerase II-interacting complex, and cells deficient in Elongator subunits display transcriptional defects. However, it has also been shown that Elongator mediates the modification of some tRNAs, modulating translation efficiency. We show here that the fission yeast Sin3/Elp3 is important for oxidative stress survival. The stress transcriptional program, governed by the Sty1-Atf1-Pcr1 pathway, is affected in mutant cells, but not severely. On the contrary, cells lacking Sin3/Elp3 cannot modify the uridine wobble nucleoside of certain tRNAs, and other tRNA modifying activities such as Ctu1-Ctu2 are also essential for normal tolerance to H2O2. In particular, a plasmid over-expressing the tRNALysUUU complements the stress-related phenotypes of Sin3/Elp3 mutant cells. We have determined that the main H2O2-dependent genes, including those coding for the transcription factors Atf1 and Pcr1, are highly expressed mRNAs containing a biased number of lysine-coding codons AAA versus AAG. Thus, their mRNAs are poorly translated after stress in cells lacking Sin3/Elp3 or Ctu2, whereas a mutated atf1 transcript with AAA-to-AAG lysine codons is efficiently translated in all strain backgrounds. Our study demonstrates that the lack of a functional Elongator complex results in stress phenotypes due to its contribution to tRNA modification and subsequent translation inefficiency of certain stress-induced, highly expressed mRNAs. These results suggest that the transcriptional defects of these strain backgrounds may be a secondary consequence of the deficient expression of a transcription factor, Atf1-Pcr1, and other components of the transcriptional machinery. The success of a biological event such as cellular adaptation to environmental changes requires the complex process of protein expression to be carried out with high efficiency and fidelity. Thus, not only transcription but also mRNA homeostasis and translation have to be performed with maximum efficiency, or survival would be hampered. Our study demonstrates that the role of Elongator, a putative Pol II-associated complex, in survival to stress is to optimize translation efficiency by modifying some particular tRNAs. We show here that Sin3/Elp3, an Elongator component, participates in the modification of the anticodon of the low copy number tRNALysUUU, which probably favours codon recognition. This tRNA recognizes one of the two codons for lysine, which is down-represented in highly expressed constitutive genes. The stress mRNAs, highly-expressed upon stress conditions, have not adapted their lysine codon usage from AAA-to-AAG, and proper tRNALysUUU modification by Elongator is an alternative strategy to accomplish efficient translation of these AAA-containing, abundant stress mRNAs.
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Affiliation(s)
- Jorge Fernández-Vázquez
- Oxidative Stress and Cell Cycle Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Itzel Vargas-Pérez
- Oxidative Stress and Cell Cycle Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Miriam Sansó
- Oxidative Stress and Cell Cycle Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Karin Buhne
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Mercè Carmona
- Oxidative Stress and Cell Cycle Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Esther Paulo
- Oxidative Stress and Cell Cycle Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Damien Hermand
- Namur Research College (NARC), The University of Namur, Namur, Belgium
| | - Miguel Rodríguez-Gabriel
- Centro de Biología Molecular “Severo Ochoa”, Universidad Autónoma de Madrid (UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Sebastian Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
- * E-mail:
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148
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Laxman S, Sutter BM, Wu X, Kumar S, Guo X, Trudgian DC, Mirzaei H, Tu BP. Sulfur amino acids regulate translational capacity and metabolic homeostasis through modulation of tRNA thiolation. Cell 2013; 154:416-29. [PMID: 23870129 PMCID: PMC3757545 DOI: 10.1016/j.cell.2013.06.043] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Revised: 03/15/2013] [Accepted: 06/25/2013] [Indexed: 02/06/2023]
Abstract
Protein translation is an energetically demanding process that must be regulated in response to changes in nutrient availability. Herein, we report that intracellular methionine and cysteine availability directly controls the thiolation status of wobble-uridine (U34) nucleotides present on lysine, glutamine, or glutamate tRNAs to regulate cellular translational capacity and metabolic homeostasis. tRNA thiolation is important for growth under nutritionally challenging environments and required for efficient translation of genes enriched in lysine, glutamine, and glutamate codons, which are enriched in proteins important for translation and growth-specific processes. tRNA thiolation is downregulated during sulfur starvation in order to decrease sulfur consumption and growth, and its absence leads to a compensatory increase in enzymes involved in methionine, cysteine, and lysine biosynthesis. Thus, tRNA thiolation enables cells to modulate translational capacity according to the availability of sulfur amino acids, establishing a functional significance for this conserved tRNA nucleotide modification in cell growth control.
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Affiliation(s)
- Sunil Laxman
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9038, USA
| | - Benjamin M. Sutter
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9038, USA
| | - Xi Wu
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9038, USA
| | - Sujai Kumar
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, EH9 3JT UK
| | - Xiaofeng Guo
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9038, USA
| | - David C. Trudgian
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9038, USA
| | - Hamid Mirzaei
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9038, USA
| | - Benjamin P. Tu
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9038, USA
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149
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Lin FJ, Shen L, Jang CW, Falnes PØ, Zhang Y. Ikbkap/Elp1 deficiency causes male infertility by disrupting meiotic progression. PLoS Genet 2013; 9:e1003516. [PMID: 23717213 PMCID: PMC3662645 DOI: 10.1371/journal.pgen.1003516] [Citation(s) in RCA: 44] [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: 12/06/2012] [Accepted: 04/04/2013] [Indexed: 12/28/2022] Open
Abstract
Mouse Ikbkap gene encodes IKAP—one of the core subunits of Elongator—and is thought to be involved in transcription. However, the biological function of IKAP, particularly within the context of an animal model, remains poorly characterized. We used a loss-of-function approach in mice to demonstrate that Ikbkap is essential for meiosis during spermatogenesis. Absence of Ikbkap results in defects in synapsis and meiotic recombination, both of which result in increased apoptosis and complete arrest of gametogenesis. In Ikbkap-mutant testes, a few meiotic genes are down-regulated, suggesting IKAP's role in transcriptional regulation. In addition, Ikbkap-mutant testes exhibit defects in wobble uridine tRNA modification, supporting a conserved tRNA modification function from yeast to mammals. Thus, our study not only reveals a novel function of IKAP in meiosis, but also suggests that IKAP contributes to this process partly by exerting its effect on transcription and tRNA modification. The process of meiosis is responsible for gamete formation and ensures that offspring will inherit a complete set of chromosomes from each parent. Errors arising during this process generally result in spontaneous abortions, birth defects, or infertility. Many genes that are essential in regulating meiosis have also been implicated in DNA repair. Importantly, defects in DNA repair are common causes of cancers. Therefore, identification of genes important for normal meiosis contributes not only to the field of reproduction but also to the field of cancer biology. We studied the effects of deleting mouse Ikbkap, a gene that encodes one of the subunit of the Elongator complex initially described as an RNA polymerase II–associated transcription elongation factor. We demonstrate that Ikbkap mutant mice exhibit infertility and defects in meiotic progression. Specifically, homologous and sex chromosomes fail to synapse (become associated), DNA double-strand breaks are inefficiently repaired, and DNA crossovers are significantly decreased in Ikbkap males. We also demonstrate that the requirement for Elongator in tRNA modification, which has been shown in lower eukaryotes, is conserved in mammals. Our findings suggest novel roles for Ikbkap in meiosis progression and tRNA modification, which have not been reported previously.
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Affiliation(s)
- Fu-Jung Lin
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Li Shen
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Chuan-Wei Jang
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pål Ø. Falnes
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Yi Zhang
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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Abstract
Elongator is required for the synthesis of the mcm(5)s(2) modification found on tRNAs recognizing AA-ending codons. In order to obtain a global picture of the role of Elongator in translation, we used reverse protein arrays to screen the fission yeast proteome for translation defects. Unexpectedly, this revealed that Elongator inactivation mainly affected three specific functional groups including proteins implicated in cell division. The absence of Elongator results in a delay in mitosis onset and cytokinesis defects. We demonstrate that the kinase Cdr2, which is a central regulator of mitosis and cytokinesis, is under translational control by Elongator due to the Lysine codon usage bias of the cdr2 coding sequence. These findings uncover a mechanism by which the codon usage, coupled to tRNA modifications, fundamentally contributes to gene expression and cellular functions.
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