1
|
Yakobov N, Debard S, Fischer F, Senger B, Becker HD. Cytosolic aminoacyl-tRNA synthetases: Unanticipated relocations for unexpected functions. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:387-400. [PMID: 29155070 DOI: 10.1016/j.bbagrm.2017.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 12/13/2022]
Abstract
Prokaryotic and eukaryotic cytosolic aminoacyl-tRNA synthetases (aaRSs) are essentially known for their conventional function of generating the full set of aminoacyl-tRNA species that are needed to incorporate each organism's repertoire of genetically-encoded amino acids during ribosomal translation of messenger RNAs. However, bacterial and eukaryotic cytosolic aaRSs have been shown to exhibit other essential nonconventional functions. Here we review all the subcellular compartments that prokaryotic and eukaryotic cytosolic aaRSs can reach to exert either a conventional or nontranslational role. We describe the physiological and stress conditions, the mechanisms and the signaling pathways that trigger their relocation and the new functions associated with these relocating cytosolic aaRS. Finally, given that these relocating pools of cytosolic aaRSs participate to a wide range of cellular pathways beyond translation, but equally important for cellular homeostasis, we mention some of the pathologies and diseases associated with the dis-regulation or malfunctioning of these nontranslational functions.
Collapse
Affiliation(s)
- Nathaniel Yakobov
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Sylvain Debard
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Frédéric Fischer
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Bruno Senger
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Hubert Dominique Becker
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France.
| |
Collapse
|
2
|
Debard S, Bader G, De Craene JO, Enkler L, Bär S, Laporte D, Hammann P, Myslinski E, Senger B, Friant S, Becker HD. Nonconventional localizations of cytosolic aminoacyl-tRNA synthetases in yeast and human cells. Methods 2017; 113:91-104. [DOI: 10.1016/j.ymeth.2016.09.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 09/27/2016] [Accepted: 09/30/2016] [Indexed: 11/26/2022] Open
|
3
|
Nikić I, Estrada Girona G, Kang JH, Paci G, Mikhaleva S, Koehler C, Shymanska NV, Ventura Santos C, Spitz D, Lemke EA. Debugging Eukaryotic Genetic Code Expansion for Site-Specific Click-PAINT Super-Resolution Microscopy. Angew Chem Int Ed Engl 2016; 55:16172-16176. [PMID: 27804198 PMCID: PMC5215487 DOI: 10.1002/anie.201608284] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/20/2016] [Indexed: 01/29/2023]
Abstract
Super‐resolution microscopy (SRM) greatly benefits from the ability to install small photostable fluorescent labels into proteins. Genetic code expansion (GCE) technology addresses this demand, allowing the introduction of small labeling sites, in the form of uniquely reactive noncanonical amino acids (ncAAs), at any residue in a target protein. However, low incorporation efficiency of ncAAs and high background fluorescence limit its current SRM applications. Redirecting the subcellular localization of the pyrrolysine‐based GCE system for click chemistry, combined with DNA‐PAINT microscopy, enables the visualization of even low‐abundance proteins inside mammalian cells. This approach links a versatile, biocompatible, and potentially unbleachable labeling method with residue‐specific precision. Moreover, our reengineered GCE system eliminates untargeted background fluorescence and substantially boosts the expression yield, which is of general interest for enhanced protein engineering in eukaryotes using GCE.
Collapse
Affiliation(s)
- Ivana Nikić
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Present address: Werner Reichardt Centre for Integrative, Neuroscience, University of Tübingen, Tübingen, 72076, Germany
| | - Gemma Estrada Girona
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Jun Hee Kang
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Giulia Paci
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Sofya Mikhaleva
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Christine Koehler
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Nataliia V Shymanska
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Camilla Ventura Santos
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Daniel Spitz
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| |
Collapse
|
4
|
Nikić I, Estrada Girona G, Kang JH, Paci G, Mikhaleva S, Koehler C, Shymanska NV, Ventura Santos C, Spitz D, Lemke EA. Verbesserte Erweiterung des eukaryotischen genetischen Codes für seitenspezifische, hochauflösende Click-PAINT-Mikroskopie. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608284] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ivana Nikić
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
- Aktuelle Adresse: Werner Reichardt Zentrum für integrative Neurowissenschaften; Universität Tübingen; 72076 Tübingen Deutschland
| | - Gemma Estrada Girona
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Jun Hee Kang
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Giulia Paci
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Sofya Mikhaleva
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Christine Koehler
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Nataliia V. Shymanska
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Camilla Ventura Santos
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Daniel Spitz
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Edward A. Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| |
Collapse
|
5
|
Shi Y, Wei N, Yang XL. Studying nuclear functions of aminoacyl tRNA synthetases. Methods 2016; 113:105-110. [PMID: 27664293 DOI: 10.1016/j.ymeth.2016.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/20/2016] [Accepted: 09/20/2016] [Indexed: 01/09/2023] Open
Abstract
Aminoacyl tRNA synthetases (AARSs) are best known for their essential role in translation in the cytoplasm. The concept that AARSs also exist in the nucleus started to draw attention around the turn of the new millennium, when aminoacylated tRNAs were first found in the nuclei of Xenopus oocytes. It is now expected that all cytoplasmic AARSs are present in the nucleus. In addition to tRNA aminoacylation, nuclear AARSs were found to regulate a spectrum of biological processes and responses, with many AARSs functioning through regulation at the level of gene transcription. In this paper, we focus on describing methods that have been successfully implemented to study AARSs in transcriptional regulation. These include a cell fractionation assay to detect nuclear localization, an in vitro DNA-cellulose pull-down assay to determine DNA binding capacity, and a chromatin immunoprecipitation (ChIP)-DNA deep sequencing assay to identify DNA binding sites. Application of these methods would expand our understanding of AARS functions and reveal critical insights on the coordination of gene transcription and translation.
Collapse
Affiliation(s)
- Yi Shi
- Departments of Chemical Physiology and Cell & Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; The School of Medicine, Nankai University, 94 Weijin Road, Tianjin 300071, China.
| | - Na Wei
- Departments of Chemical Physiology and Cell & Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Xiang-Lei Yang
- Departments of Chemical Physiology and Cell & Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
6
|
Marriott AS, Copeland NA, Cunningham R, Wilkinson MC, McLennan AG, Jones NJ. Diadenosine 5', 5'''-P(1),P(4)-tetraphosphate (Ap4A) is synthesized in response to DNA damage and inhibits the initiation of DNA replication. DNA Repair (Amst) 2015. [PMID: 26204256 DOI: 10.1016/j.dnarep.2015.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The level of intracellular diadenosine 5', 5'''-P(1),P(4)-tetraphosphate (Ap4A) increases several fold in mammalian cells treated with non-cytotoxic doses of interstrand DNA-crosslinking agents such as mitomycin C. It is also increased in cells lacking DNA repair proteins including XRCC1, PARP1, APTX and FANCG, while >50-fold increases (up to around 25 μM) are achieved in repair mutants exposed to mitomycin C. Part of this induced Ap4A is converted into novel derivatives, identified as mono- and di-ADP-ribosylated Ap4A. Gene knockout experiments suggest that DNA ligase III is primarily responsible for the synthesis of damage-induced Ap4A and that PARP1 and PARP2 can both catalyze its ADP-ribosylation. Degradative proteins such as aprataxin may also contribute to the increase. Using a cell-free replication system, Ap4A was found to cause a marked inhibition of the initiation of DNA replicons, while elongation was unaffected. Maximum inhibition of 70-80% was achieved with 20 μM Ap4A. Ap3A, Ap5A, Gp4G and ADP-ribosylated Ap4A were without effect. It is proposed that Ap4A acts as an important inducible ligand in the DNA damage response to prevent the replication of damaged DNA.
Collapse
Affiliation(s)
- Andrew S Marriott
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Nikki A Copeland
- Division of Biomedical and Life Sciences, University of Lancaster, Lancaster LA1 4YG, UK
| | - Ryan Cunningham
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Mark C Wilkinson
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Alexander G McLennan
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Nigel J Jones
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| |
Collapse
|
7
|
Structure and function of collectin liver 1 (CL-L1) and collectin 11 (CL-11, CL-K1). Immunobiology 2012; 217:851-63. [DOI: 10.1016/j.imbio.2011.12.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 12/16/2011] [Accepted: 12/16/2011] [Indexed: 01/25/2023]
|
8
|
Liao CC, Lin CH, Chen SJ, Wang CC. Trans-kingdom rescue of Gln-tRNAGln synthesis in yeast cytoplasm and mitochondria. Nucleic Acids Res 2012; 40:9171-81. [PMID: 22821561 PMCID: PMC3467082 DOI: 10.1093/nar/gks689] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aminoacylation of transfer RNAGln (tRNAGln) is performed by distinct mechanisms in different kingdoms and represents the most diverged route of aminoacyl-tRNA synthesis found in nature. In Saccharomyces cerevisiae, cytosolic Gln-tRNAGln is generated by direct glutaminylation of tRNAGln by glutaminyl-tRNA synthetase (GlnRS), whereas mitochondrial Gln-tRNAGln is formed by an indirect pathway involving charging by a non-discriminating glutamyl-tRNA synthetase and the subsequent transamidation by a specific Glu-tRNAGln amidotransferase. Previous studies showed that fusion of a yeast non-specific tRNA-binding cofactor, Arc1p, to Escherichia coli GlnRS enables the bacterial enzyme to substitute for its yeast homologue in vivo. We report herein that the same fusion enzyme, upon being imported into mitochondria, substituted the indirect pathway for Gln-tRNAGln synthesis as well, despite significant differences in the identity determinants of E. coli and yeast cytosolic and mitochondrial tRNAGln isoacceptors. Fusion of Arc1p to the bacterial enzyme significantly enhanced its aminoacylation activity towards yeast tRNAGln isoacceptors in vitro. Our study provides a mechanism by which trans-kingdom rescue of distinct pathways of Gln-tRNAGln synthesis can be conferred by a single enzyme.
Collapse
Affiliation(s)
- Chih-Chi Liao
- Department of Life Sciences, National Central University, Jung-li 32001, Taiwan, Republic of China
| | | | | | | |
Collapse
|
9
|
Smirnova EV, Lakunina VA, Tarassov I, Krasheninnikov IA, Kamenski PA. Noncanonical functions of aminoacyl-tRNA synthetases. BIOCHEMISTRY (MOSCOW) 2012; 77:15-25. [PMID: 22339629 DOI: 10.1134/s0006297912010026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Aminoacyl-tRNA synthetases, together with their main function of covalent binding of an amino acid to a corresponding tRNA, also perform many other functions. They take part in regulation of gene transcription, apoptosis, translation, and RNA splicing. Some of them function as cytokines or catalyze different reactions in living cells. Noncanonical functions can be mediated by additional domains of these proteins. On the other hand, some of the noncanonical functions are directly associated with the active center of the aminoacylation reaction. In this review we summarize recent data on the noncanonical functions of aminoacyl-tRNA synthetases and on the mechanisms of their action.
Collapse
Affiliation(s)
- E V Smirnova
- Department of Molecular Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | | | | |
Collapse
|
10
|
Biological functions of the novel collectins CL-L1, CL-K1, and CL-P1. J Biomed Biotechnol 2012; 2012:493945. [PMID: 22570530 PMCID: PMC3336186 DOI: 10.1155/2012/493945] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Revised: 02/13/2012] [Accepted: 02/14/2012] [Indexed: 12/17/2022] Open
Abstract
Collectins are characterized by a collagen-like sequence and a carbohydrate recognition domain and are members of the vertebrate C-type lectin superfamily. Recently, “novel collectins”, different from “classical collectins” consisting of mannan-binding lectin (MBL) and surfactant proteins A and D (SP-A and SP-D), have been found by reverse genetics. These “novel collectins” consist of collectin liver 1 (CL-L1), collectin kidney 1 (CL-K1), and collectin placenta 1 (CL-P1) and are encoded by three separate genes. Experimental findings on human and animal collectins have shown that both novel collectins and classical collectins play an important role in innate immunity. Based on our recent results and those of others, in this paper, we summarize the new biological functions of these novel collectins in embryonic morphogenesis and development.
Collapse
|
11
|
Chen SJ, Lee CY, Lin ST, Wang CC. Rescuing a dysfunctional homologue of a yeast glycyl-tRNA synthetase gene. ACS Chem Biol 2011; 6:1182-7. [PMID: 21877692 DOI: 10.1021/cb200240a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The yeast Saccharomyces cerevisiae contains two distinct nuclear glycyl-tRNA synthetase (GlyRS) genes, GRS1 and GRS2. GRS1 is dual functional in that possesses both cytoplasmic and mitochondrial activities, whereas GRS2 is pseudogene-like. GlyRS1 and GlyRS2 are highly similar on the whole but are distinguished by a lysine-rich insertion domain of 44 amino acid residues, present only in GlyRS1. We herein present evidence that whereas the insertion domain is dispensable for the complementary activity of GRS1in vivo, deletion of this domain from GlyRS1 reduced its aminoacylation activity by up to 9-fold. On the other hand, fusion of a constitutive ADH promoter to GRS2 failed to confer a functional phenotype to the gene, but further fusion of ARC1 (a yeast gene encoding a tRNA-binding protein, Arc1p) to this hybrid gene successfully rescued its activity. Most intriguingly, purified GlyRS2 retained a substantial level of aminoacylation activity. Fusion of Arc1p to this enzyme further enhanced its activity and stability. These findings highlight not only the structural integrity of the pseudogene-encoded enzyme but also the necessity of obtaining an auxiliary tRNA-binding domain for functioning of a yeast tRNA synthetase.
Collapse
Affiliation(s)
- Shun-Jia Chen
- Department of Life Sciences, National Central University, 300 Jung-da Rd., Jung-li 32001, Taiwan
| | - Chih-Ying Lee
- Department of Life Sciences, National Central University, 300 Jung-da Rd., Jung-li 32001, Taiwan
| | - Szu-Ting Lin
- Department of Life Sciences, National Central University, 300 Jung-da Rd., Jung-li 32001, Taiwan
| | - Chien-Chia Wang
- Department of Life Sciences, National Central University, 300 Jung-da Rd., Jung-li 32001, Taiwan
| |
Collapse
|
12
|
Lin CH, Lin G, Chang CP, Wang CC. A tryptophan-rich peptide acts as a transcription activation domain. BMC Mol Biol 2010; 11:85. [PMID: 21078206 PMCID: PMC2992532 DOI: 10.1186/1471-2199-11-85] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2010] [Accepted: 11/16/2010] [Indexed: 11/23/2022] Open
Abstract
Background Eukaryotic transcription activators normally consist of a sequence-specific DNA-binding domain (DBD) and a transcription activation domain (AD). While many sequence patterns and motifs have been defined for DBDs, ADs do not share easily recognizable motifs or structures. Results We report herein that the N-terminal domain of yeast valyl-tRNA synthetase can function as an AD when fused to a DNA-binding protein, LexA, and turn on reporter genes with distinct LexA-responsive promoters. The transcriptional activity was mainly attributed to a five-residue peptide, WYDWW, near the C-terminus of the N domain. Remarkably, the pentapeptide per se retained much of the transcriptional activity. Mutations which substituted tryptophan residues for both of the non-tryptophan residues in the pentapeptide (resulting in W5) significantly enhanced its activity (~1.8-fold), while mutations which substituted aromatic residues with alanine residues severely impaired its activity. Accordingly, a much more active peptide, pentatryptophan (W7), was produced, which elicited ~3-fold higher activity than that of the native pentapeptide and the N domain. Further study indicated that W7 mediates transcription activation through interacting with the general transcription factor, TFIIB. Conclusions Since W7 shares no sequence homology or features with any known transcription activators, it may represent a novel class of AD.
Collapse
Affiliation(s)
- Chen-Huan Lin
- Department of Life Science, National Central University, Jung-li 32001, Taiwan
| | | | | | | |
Collapse
|
13
|
Brown MV, Reader JS, Tzima E. Mammalian aminoacyl-tRNA synthetases: Cell signaling functions of the protein translation machinery. Vascul Pharmacol 2010; 52:21-6. [DOI: 10.1016/j.vph.2009.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 11/20/2009] [Accepted: 11/29/2009] [Indexed: 12/01/2022]
|
14
|
Chiu WC, Chang CP, Wang CC. Evolutionary basis of converting a bacterial tRNA synthetase into a yeast cytoplasmic or mitochondrial enzyme. J Biol Chem 2009; 284:23954-60. [PMID: 19574213 DOI: 10.1074/jbc.m109.031047] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Previous studies showed that cytoplasmic and mitochondrial forms of yeast valyl-tRNA synthetase (ValRS) are specified by the VAS1 gene through alternative initiation of translation. Sequence comparison suggests that the yeast cytoplasmic (or mature mitochondrial) ValRS contains an N-terminal appendage that acts in cis as a nonspecific tRNA-binding domain (TRBD) and is absent from its bacterial relatives. We show here that Escherichia coli ValRS can substitute for the mitochondrial and cytoplasmic functions of VAS1 by fusion of a mitochondrial targeting signal and a TRBD, respectively. In addition, the bacterial ValRS gene can be converted into a dual functional yeast gene encoding both cytoplasmic and mitochondrial activities by fusion of a DNA sequence specifying both the mitochondrial targeting signal and TRBD. In vitro assays suggested that fusion of a nonspecific TRBD to the bacterial enzyme significantly enhanced its yeast tRNA-binding and aminoacylation activities. These results not only underscore the necessity of retaining a TRBD for functioning of a tRNA synthetase in yeast cytoplasm, but also provide insights into the evolution of tRNA synthetase genes.
Collapse
Affiliation(s)
- Wen-Chih Chiu
- Department of Life Science, National Central University, Jung-li 32001, Taiwan
| | | | | |
Collapse
|
15
|
Ryckelynck M, A. Paulus C, Frugier M. Post-Translational Modifications Guard Yeast from Misaspartylation. Biochemistry 2008. [DOI: 10.1021/bi800931x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michaël Ryckelynck
- Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg Cedex, France, and ISIS-ULP, Laboratoire de Biologie Chimique, 8 allée Gaspard Monge, BP 70028, 67083 Strasbourg Cedex, France
| | - Caroline A. Paulus
- Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg Cedex, France, and ISIS-ULP, Laboratoire de Biologie Chimique, 8 allée Gaspard Monge, BP 70028, 67083 Strasbourg Cedex, France
| | - Magali Frugier
- Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg Cedex, France, and ISIS-ULP, Laboratoire de Biologie Chimique, 8 allée Gaspard Monge, BP 70028, 67083 Strasbourg Cedex, France
| |
Collapse
|
16
|
Chang CP, Lin G, Chen SJ, Chiu WC, Chen WH, Wang CC. Promoting the formation of an active synthetase/tRNA complex by a nonspecific tRNA-binding domain. J Biol Chem 2008; 283:30699-706. [PMID: 18755686 DOI: 10.1074/jbc.m805339200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Previous studies showed that valyl-tRNA synthetase of Saccharomyces cerevisiae contains an N-terminal polypeptide extension of 97 residues, which is absent from its bacterial relatives, but is conserved in its mammalian homologues. We showed herein that this appended domain and its human counterpart are both nonspecific tRNA-binding domains (K(d) approximately 0.5 microm). Deletion of the appended domain from the yeast enzyme severely impaired its tRNA binding, aminoacylation, and complementation activities. This N-domain-deleted yeast valyl-tRNA synthetase mutant could be rescued by fusion of the equivalent domain from its human homologue. Moreover, fusion of the N-domain of the yeast enzyme or its human counterpart to Escherichia coli glutaminyl-tRNA synthetase enabled the otherwise "inactive" prokaryotic enzyme to function as a yeast enzyme in vivo. Different from the native yeast enzyme, which showed different affinities toward mixed tRNA populations, the fusion enzyme exhibited similar binding affinities for all yeast tRNAs. These results not only underscore the significance of nonspecific tRNA binding in aminoacylation, but also provide insights into the mechanism of the formation of aminoacyl-tRNAs.
Collapse
Affiliation(s)
- Chia-Pei Chang
- Department of Life Science, National Central University, Jung-li, 32001 Taiwan
| | | | | | | | | | | |
Collapse
|
17
|
Frugier M, Ryckelynck M, Giegé R. tRNA-balanced expression of a eukaryal aminoacyl-tRNA synthetase by an mRNA-mediated pathway. EMBO Rep 2006; 6:860-5. [PMID: 16113655 PMCID: PMC1369159 DOI: 10.1038/sj.embor.7400481] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Revised: 06/09/2005] [Accepted: 06/09/2005] [Indexed: 11/09/2022] Open
Abstract
Aminoacylation of transfer RNAs is a key step during translation. It is catalysed by the aminoacyl-tRNA synthetases (aaRSs) and requires the specific recognition of their cognate substrates, one or several tRNAs, ATP and the amino acid. Whereas the control of certain aaRS genes is well known in prokaryotes, little is known about the regulation of eukaryotic aaRS genes. Here, it is shown that expression of AspRS is regulated in yeast by a feedback mechanism that necessitates the binding of AspRS to its messenger RNA. This regulation leads to a synchronized expression of AspRS and tRNA(Asp). The correlation between AspRS expression and mRNA(AspRS) and tRNA(Asp) concentrations, as well as the presence of AspRS in the nucleus, suggests an original regulation mechanism. It is proposed that the surplus of AspRS, not sequestered by tRNA(Asp), is imported into the nucleus where it binds to mRNA(AspRS) and thus inhibits its accumulation.
Collapse
Affiliation(s)
- Magali Frugier
- Département Machineries Traductionnelles, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, 67084 Strasbourg Cedex, France.
| | | | | |
Collapse
|
18
|
Hogenkamp A, van Eijk M, van Dijk A, van Asten AJAM, Veldhuizen EJA, Haagsman HP. Characterization and expression sites of newly identified chicken collectins. Mol Immunol 2005; 43:1604-16. [PMID: 16289291 DOI: 10.1016/j.molimm.2005.09.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Accepted: 09/24/2005] [Indexed: 11/17/2022]
Abstract
Collectins are members of the family of vertebrate C-type lectins. They have been found almost exclusively in mammals, with the exception of chicken MBL. Because of their important role in innate immunity, we sought to identify other collectins in chicken. Using the amino acid sequences of known collectins, the EST database was searched and related to the chicken genome. Three chicken collectins were found and designated chicken Collectin 1 (cCL-1), chicken Collectin 2 (cCL-2), and chicken Collectin 3 (cCL-3), which resemble the mammalian proteins Collectin Liver 1, Collectin 11 and Collectin Placenta 1, respectively. Additionally, a lectin was found which resembled Surfactant Protein A, but lacked the collagen domain. Therefore, it was named chicken Lung Lectin (cLL). Tissue distribution analysis showed cCL-1, cCL-2 and cCL-3 are expressed in a wide range of tissues throughout the digestive, the reproductive and the lymphatic system. Similar to SP-A, cLL is mainly localized in lung tissue. Phylogenetic analysis indicates that cCL-1, cCL-2 and cCL-3 represent new subgroups within the collectin family. The newly found collectins may have an important function in avian host defence. Elucidation of the role of these pattern-recognition molecules could lead to strategies that thwart infectious diseases in poultry, which could also be beneficial for public health.
Collapse
Affiliation(s)
- Astrid Hogenkamp
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Graduate School of Animal Health, Utrecht University, P.O. Box 80.165, 3508 TD Utrecht, The Netherlands
| | | | | | | | | | | |
Collapse
|
19
|
Tang HL, Yeh LS, Chen NK, Ripmaster T, Schimmel P, Wang CC. Translation of a yeast mitochondrial tRNA synthetase initiated at redundant non-AUG codons. J Biol Chem 2004; 279:49656-63. [PMID: 15358761 DOI: 10.1074/jbc.m408081200] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although initiation of translation at non-AUG codons occurs occasionally in prokaryotes and higher eukaryotes, it has not been reported in yeast until very recently. Evidence presented here shows that redundant ACG codons are recognized as alternative translation start sites for ALA1, the only gene in Saccharomyces cerevisiae coding for alanyl-tRNA synthetase. ALA1 is shown to be a bifunctional gene that provides both cytoplasmic and mitochondrial activities. Unlike most bifunctional genes that contain alternative in-frame AUG initiators, there is only one AUG codon, designated AUG1, close to the 5'-end of the ALA1 open reading frame. Transcriptional mapping identified three overlapping transcripts, with 5'-ends at positions 54, 105, and 117 nucleotides upstream of AUG1, respectively. Site-specific mutagenesis demonstrated that the cytoplasmic and mitochondrial functions of ALA1 are provided by two protein isoforms with distinct amino termini; that is, a short cytoplasmic form initiated at AUG1 and a longer mitochondrial isoform initiated at two upstream in-frame ACG codons, i.e. ACG(-25) and ACG(-24). These two ACG codons function redundantly in initiation of translation. Either codon can function in the absence of the other. The short transcript appears to serve as the template for the cytoplasmic form, whereas the longer transcripts are likely to code for both isoforms via alternative initiation. Because yeast ribosomes in general cannot efficiently recognize a non-AUG initiator, this unique feature of redundancy of non-AUG initiators in a single mRNA may in itself represent a novel paradigm for translation initiation from poor initiators.
Collapse
Affiliation(s)
- Huei-Lin Tang
- Department of Life Science, National Central University, Jung-li, Taiwan 32054
| | | | | | | | | | | |
Collapse
|
20
|
Wolfe CL, Warrington JA, Davis S, Green S, Norcum MT. Isolation and characterization of human nuclear and cytosolic multisynthetase complexes and the intracellular distribution of p43/EMAPII. Protein Sci 2004; 12:2282-90. [PMID: 14500886 PMCID: PMC2366922 DOI: 10.1110/ps.03147903] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this study, the human multienzyme aminoacyl-tRNA synthetase "core" complex has been isolated from the nuclear and cytosolic compartments of human cells and purified to near homogeneity. It is clear from the polypeptide compositions, stoichiometries, and three-dimensional structures that the cytosolic and nuclear particles are very similar to each other and to the particle obtained from rabbit reticulocytes. The most significant difference observed via aminoacylation activity assays and densitometric analysis of electrophoretic band patterns is a lower amount of glutaminyl-tRNA synthetase in the human particles. However, this is not enough to cause major changes in the three-dimensional structures calculated from samples negatively stained with either uranyl acetate or methylamine vanadate. Indeed, the latter samples produce volumes that are highly similar to an initial structure previously calculated from a frozen hydrated sample of the rabbit multisynthetase complex. New structures in this study reveal that the three major structural domains have discrete subsections. This information is an important step toward determination of specific protein interactions and arrangements within the multisynthetase core complex and understanding of the particle's cellular function(s). Finally, gel filtration and immunoblot analysis demonstrate that a major biological role for the cytokine precursor p43 is as an integral part of the multisynthetase complex.
Collapse
Affiliation(s)
- Cindy L Wolfe
- Biology Department, Tougaloo College, Tougaloo, Mississippi 39174, USA
| | | | | | | | | |
Collapse
|
21
|
Chang KJ, Wang CC. Translation initiation from a naturally occurring non-AUG codon in Saccharomyces cerevisiae. J Biol Chem 2004; 279:13778-85. [PMID: 14734560 DOI: 10.1074/jbc.m311269200] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although previous studies have already shown that both cytoplasmic and mitochondrial activities of glycyl-tRNA synthetase are provided by a single gene, GRS1,in the yeast Saccharomyces cerevisiae, the mechanism by which this occurs remains unclear. Evidence presented here indicates that this bifunctional property is actually a result of two distinct translational products alternatively generated from a single transcript of this gene. Except for an amino-terminal 23-amino acid extension, these two isoforms have the same polypeptide sequence and function exclusively in their respective compartments under normal conditions. Reporter gene assays further suggest that this leader peptide can function independently as a mitochondrial targeting signal and plays the major role in the subcellular localization of the isoforms. Additionally, whereas the short protein is translationally initiated from a traditional AUG triplet, the longer isoform is generated from an upstream inframe UUG codon. To our knowledge, GRS1 appears to be the first example in the yeast wherein a functional protein isoform is initiated from a naturally occurring non-AUG codon. The results suggest that non-AUG initiation might be a mechanism existing throughout all kingdoms.
Collapse
Affiliation(s)
- Kuang-Jung Chang
- Department of Life Science, National Central University, 300 Jung-da, Jung-li, Taiwan 32054
| | | |
Collapse
|
22
|
Yiadom KPAB, Hammamieh R, Ukpabi N, Tsang P, Yang DCH. A peptide from the extension of Lys-tRNA synthetase binds to transfer RNA and DNA. Peptides 2003; 24:987-98. [PMID: 14499277 DOI: 10.1016/s0196-9781(03)00188-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Eukaryotic aminoacyl-tRNA synthetases have dispensable extensions appended at the amino- or carboxyl-terminus as compared to their bacterial counterparts. While a synthetic peptide corresponding to the basic amino-terminal extension in yeast Asp-tRNA synthetase binds to DNA, the extension in the intact protein evidently binds to tRNA and enhances the tRNA specificity of Asp-tRNA synthetase. On the other hand, the amino-terminal extension in human Asp-tRNA synthetase, both within the intact protein and as a synthetic peptide, binds to tRNA. Here, the tRNA binding of a synthetic peptide, hKRS(Arg(25)-Glu(42)), corresponding to the amino-terminal extension of human Lys-tRNA synthetase (hKRS) was analyzed. This basic peptide bound to tRNA(Phe) and the apparent-binding constant increased with increasing concentrations of Mg(2+). The hKRS peptide also bound to DNA and polyphosphate; however, the apparent DNA-binding constants decreased at increasing concentrations of Mg(2+). The ability of the hKRS peptide to adopt alpha-helical conformation was demonstrated by NMR and circular dichroism. A Lys-rich peptide derived from the elongation factor 1alpha was also examined and bound to DNA but not to tRNA.
Collapse
MESH Headings
- Amino Acid Sequence
- Cations, Divalent/chemistry
- Circular Dichroism
- DNA/chemistry
- DNA/metabolism
- DNA-Binding Proteins/chemical synthesis
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/metabolism
- Humans
- Hydrogen-Ion Concentration
- Lysine-tRNA Ligase/chemistry
- Magnesium Chloride/chemistry
- Magnetic Resonance Spectroscopy
- Models, Molecular
- Molecular Sequence Data
- Molecular Weight
- Peptide Elongation Factor 1/chemistry
- Peptides/chemical synthesis
- Peptides/chemistry
- Peptides/metabolism
- Polyphosphates/chemistry
- Protein Binding
- Protein Structure, Secondary
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/metabolism
- RNA-Binding Proteins/chemical synthesis
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/metabolism
- Sodium Chloride/chemistry
- Spectrometry, Fluorescence
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Trifluoroethanol/chemistry
Collapse
|
23
|
Rho SB, Lincecum TL, Martinis SA. An inserted region of leucyl-tRNA synthetase plays a critical role in group I intron splicing. EMBO J 2002; 21:6874-81. [PMID: 12486008 PMCID: PMC139092 DOI: 10.1093/emboj/cdf671] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Yeast mitochondrial leucyl-tRNA synthetase (LeuRS) binds to the bI4 intron and collaborates with the bI4 maturase to aid excision of the group I intron. Deletion analysis isolated the inserted LeuRS CP1 domain as a critical factor in the protein's splicing activity. Protein fragments comprised of just the LeuRS CP1 region rescued complementation of a yeast strain that expressed a splicing-defective LeuRS. Three-hybrid analysis determined that these CP1-containing LeuRS fragments, ranging from 214 to 375 amino acids, bound to the bI4 intron. In each case, interactions with only the LeuRS protein fragment specifically stimulated bI4 intron splicing activity. Substitution of a homologous CP1 domain from isoleucyl-tRNA synthetase or mutation within the LeuRS CP1 region of the smallest protein fragment abolished RNA binding and splicing activity. The CP1 domain is best known for its amino acid editing activity. However, these results suggest that elements within the LeuRS CP1 domain also play a novel role, independent of the full-length tRNA synthetase, in binding the bI4 group I intron and facilitating its self-splicing activity.
Collapse
Affiliation(s)
- Seung Bae Rho
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
Present address: Samsung Medical Center Annex 8F, 50, Ilwon-dong, Kangnam-ku, Seoul, Korea 135-710 Corresponding author e-mail:
| | | | - Susan A. Martinis
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
Present address: Samsung Medical Center Annex 8F, 50, Ilwon-dong, Kangnam-ku, Seoul, Korea 135-710 Corresponding author e-mail:
| |
Collapse
|
24
|
Affiliation(s)
- George Simos
- Biochemie-Zentrum Heidelberg (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | | | | |
Collapse
|
25
|
Galani K, Großhans H, Deinert K, Hurt EC, Simos G. The intracellular location of two aminoacyl-tRNA synthetases depends on complex formation with Arc1p. EMBO J 2001; 20:6889-98. [PMID: 11726524 PMCID: PMC125769 DOI: 10.1093/emboj/20.23.6889] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In yeast, two aminoacyl-tRNA synthetases, MetRS and GluRS, are associated with Arc1p. We have studied the mechanism of this complex formation and found that the non-catalytic N-terminally appended domains of MetRS and GluRS are necessary and sufficient for binding to Arc1p. Similarly, it is the N-terminal domain of Arc1p that contains distinct but overlapping binding sites for MetRS and GluRS. Localization of Arc1p, MetRS and GluRS in living cells using green fluorescent protein showed that these three proteins are cytoplasmic and largely excluded from the nucleus. However, when their assembly into a complex is inhibited, significant amounts of MetRS, GluRS and Arc1p can enter the nucleus. We suggest that the organization of aminoacyl-tRNA synthetases into a multimeric complex not only affects catalysis, but is also a means of segregating the tRNA- aminoacylation machinery mainly to the cytoplasmic compartment.
Collapse
Affiliation(s)
| | - Helge Großhans
- Biochemie-Zentrum Heidelberg (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
Present address: MCDB Department, KBT 940 Yale University, PO Box 208103, 266 Whitney Avenue, New Haven, CT 06520, USA Present address: Laboratory of Biochemistry, School of Medicine, University of Thessaly, 22 Papakiriazi str., 41222 Larissa, Greece Corresponding author e-mail:
| | | | | | - George Simos
- Biochemie-Zentrum Heidelberg (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
Present address: MCDB Department, KBT 940 Yale University, PO Box 208103, 266 Whitney Avenue, New Haven, CT 06520, USA Present address: Laboratory of Biochemistry, School of Medicine, University of Thessaly, 22 Papakiriazi str., 41222 Larissa, Greece Corresponding author e-mail:
| |
Collapse
|
26
|
Azad AK, Stanford DR, Sarkar S, Hopper AK. Role of nuclear pools of aminoacyl-tRNA synthetases in tRNA nuclear export. Mol Biol Cell 2001; 12:1381-92. [PMID: 11359929 PMCID: PMC34591 DOI: 10.1091/mbc.12.5.1381] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Reports of nuclear tRNA aminoacylation and its role in tRNA nuclear export (Lund and Dahlberg, 1998; Sarkar et al., 1999; Grosshans et al., 20001) have led to the prediction that there should be nuclear pools of aminoacyl-tRNA synthetases. We report that in budding yeast there are nuclear pools of tyrosyl-tRNA synthetase, Tys1p. By sequence alignments we predicted a Tys1p nuclear localization sequence and showed it to be sufficient for nuclear location of a passenger protein. Mutations of this nuclear localization sequence in endogenous Tys1p reduce nuclear Tys1p pools, indicating that the motif is also important for nucleus location. The mutations do not significantly affect catalytic activity, but they do cause defects in export of tRNAs to the cytosol. Despite export defects, the cells are viable, indicating that nuclear tRNA aminoacylation is not required for all tRNA nuclear export paths. Because the tRNA nuclear exportin, Los1p, is also unessential, we tested whether tRNA aminoacylation and Los1p operate in alternative tRNA nuclear export paths. No genetic interactions between aminoacyl-tRNA synthetases and Los1p were detected, indicating that tRNA nuclear aminoacylation and Los1p operate in the same export pathway or there are more than two pathways for tRNA nuclear export.
Collapse
Affiliation(s)
- A K Azad
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
| | | | | | | |
Collapse
|
27
|
Deinert K, Fasiolo F, Hurt EC, Simos G. Arc1p organizes the yeast aminoacyl-tRNA synthetase complex and stabilizes its interaction with the cognate tRNAs. J Biol Chem 2001; 276:6000-8. [PMID: 11069915 DOI: 10.1074/jbc.m008682200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic aminoacyl-tRNA synthetases, in contrast to their prokaryotic counterparts, are often part of high molecular weight complexes. In yeast, two enzymes, the methionyl- and glutamyl-tRNA synthetases associate in vivo with the tRNA-binding protein Arc1p. To study the assembly and function of this complex, we have reconstituted it in vitro from individually purified recombinant proteins. Our results show that Arc1p can readily bind to either or both of the two enzymes, mediating the formation of the respective binary or ternary complexes. Under competition conditions, Arc1p alone exhibits broad specificity and interacts with a defined set of tRNA species. Nevertheless, the in vitro reconstituted Arc1p-containing enzyme complexes can bind only to their cognate tRNAs and tighter than the corresponding monomeric enzymes. These results demonstrate that the organization of aminoacyl-tRNA synthetases with general tRNA-binding proteins into multimeric complexes can stimulate their catalytic efficiency and, therefore, offer a significant advantage to the eukaryotic cell.
Collapse
Affiliation(s)
- K Deinert
- Biochemie-Zentrum Heidelberg (BZH), University of Heidelberg, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | | | | | | |
Collapse
|
28
|
Ko YG, Kim EY, Kim T, Park H, Park HS, Choi EJ, Kim S. Glutamine-dependent antiapoptotic interaction of human glutaminyl-tRNA synthetase with apoptosis signal-regulating kinase 1. J Biol Chem 2001; 276:6030-6. [PMID: 11096076 DOI: 10.1074/jbc.m006189200] [Citation(s) in RCA: 154] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Glutamine has been known to be an apoptosis suppressor, since it blocks apoptosis induced by heat shock, irradiation, and c-Myc overexpression. Here, we demonstrated that HeLa cells were susceptible to Fas-mediated apoptosis under the condition of glutamine deprivation. Fas ligation activated apoptosis signal-regulating kinase 1 (ASK1) and c-Jun N-terminal kinase (JNK; also known as stress-activated protein kinase (SAPK)) in Gln-deprived cells but not in normal cells, suggesting that Gln might be involved in the activity control of ASK1 and JNK/SAPK. As one of the possible mechanisms for the suppressive effect of Gln on ASK1, we investigated the molecular interaction between human glutaminyl-tRNA synthetase (QRS) and ASK1 and found the Gln-dependent association of the two molecules. While their association was enhanced by the elevation of Gln concentration, they were dissociated by Fas ligation within 5 min. The association involved the catalytic domains of the two enzymes. The ASK1 activity was inhibited by the interaction with QRS as determined by in vitro kinase and transcription assays. Finally, we have shown that QRS inhibited the cell death induced by ASK1, and this antiapoptotic function of QRS was weakened by the deprivation of Gln. Thus, the antiapoptotic interaction of QRS with ASK1 is controlled positively by the cellular concentration of Gln and negatively by Fas ligation. The results of this work provide one possible explanation for the working mechanism of the antiapoptotic activity of Gln and suggest a novel function of mammalian ARSs.
Collapse
Affiliation(s)
- Y G Ko
- National Creative Research Initiatives Center for ARS Network, Sung Kyun Kwan University, Suwon, Kyunggido 440-746, Korea
| | | | | | | | | | | | | |
Collapse
|
29
|
Metzler DE, Metzler CM, Sauke DJ. Ribosomes and the Synthesis of Proteins. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50032-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
30
|
Nathanson L, Deutscher MP. Active aminoacyl-tRNA synthetases are present in nuclei as a high molecular weight multienzyme complex. J Biol Chem 2000; 275:31559-62. [PMID: 10930398 DOI: 10.1074/jbc.c000385200] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recent studies suggest that aminoacylation of tRNA may play an important role in the transport of these molecules from the nucleus to the cytoplasm. However, there is almost no information regarding the status of active aminoacyl-tRNA synthetases within the nuclei of eukaryotic cells. Here we show that at least 13 active aminoacyl-tRNA synthetases are present in purified nuclei of both Chinese hamster ovary and rabbit kidney cells, although their steady-state levels represent only a small percentage of those found in the cytoplasm. Most interestingly, all the nuclear aminoacyl-tRNA synthetases examined can be isolated as part of a multienzyme complex that is more stable, and consequently larger, than the comparable complex isolated from the cytoplasm. These data directly demonstrate the presence of active aminoacyl-tRNA synthetases in mammalian cell nuclei. Moreover, their unexpected structural organization raises important questions about the functional significance of these multienzyme complexes and whether they might play a more direct role in nuclear to cytoplasmic transport of tRNAs.
Collapse
Affiliation(s)
- L Nathanson
- Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami, Florida 33136, USA
| | | |
Collapse
|
31
|
Abstract
Despite being known for over 30 years, the functions of the dinucleoside polyphosphates, such as diadenosine 5',5"'-P(1), P(4)-tetraphosphate (Ap(4)A) and diadenosine 5',5"'-P(1), P(3)-triphosphate (Ap(3)A), are still unclear. On the one hand, they may have important signalling functions, both inside and outside the cell (friend), while on the other hand, they may simply be the unavoidable by-products of certain biochemical reactions, which, if allowed to accumulate, would be potentially toxic through their structural similarity to ATP and other essential mononucleotides (foe). Here, the occurrence, synthesis, degradation, and proposed functions of these compounds are briefly reviewed, along with some new data and recent evidence supporting roles for Ap(3)A and Ap(4)A in the cellular decision making processes leading to proliferation, quiescence, differentiation, and apoptosis. Hypotheses are forwarded for the involvement of Ap(4)A in the intra-S phase DNA damage checkpoint and for Ap(3)A and the pFhit (fragile histidine triad gene product) protein in tumour suppression. It is concluded that the roles of friend and foe are not incompatible, but are distinguished by the concentration range of nucleotide achieved under different circumstances.
Collapse
Affiliation(s)
- A G McLennan
- School of Biological Sciences, Life Sciences Building, University of Liverpool, Crown Street, L69 7ZB, Liverpool, UK.
| |
Collapse
|
32
|
Frugier M, Moulinier L, Giegé R. A domain in the N-terminal extension of class IIb eukaryotic aminoacyl-tRNA synthetases is important for tRNA binding. EMBO J 2000; 19:2371-80. [PMID: 10811628 PMCID: PMC384352 DOI: 10.1093/emboj/19.10.2371] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cytoplasmic aspartyl-tRNA synthetase (AspRS) from Saccharomyces cerevisiae is a homodimer of 64 kDa subunits. Previous studies have emphasized the high sensitivity of the N-terminal region to proteolytic cleavage, leading to truncated species that have lost the first 20-70 residues but that retain enzymatic activity and dimeric structure. In this work, we demonstrate that the N-terminal extension in yeast AspRS participates in tRNA binding and we generalize this finding to eukaryotic class IIb aminoacyl-tRNA synthetases. By gel retardation studies and footprinting experiments on yeast tRNA(Asp), we show that the extension, connected to the anticodon-binding module of the synthetase, contacts tRNA on the minor groove side of its anticodon stem. Sequence comparison of eukaryotic class IIb synthetases identifies a lysine-rich 11 residue sequence ((29)LSKKALKKLQK(39) in yeast AspRS with the consensus xSKxxLKKxxK in class IIb synthetases) that is important for this binding. Direct proof of the role of this sequence comes from a mutagenesis analysis and from binding studies using the isolated peptide.
Collapse
Affiliation(s)
- M Frugier
- Département 'Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse', UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, 67084 Strasbourg Cedex, France
| | | | | |
Collapse
|
33
|
Ko YG, Kang YS, Kim EK, Park SG, Kim S. Nucleolar localization of human methionyl-tRNA synthetase and its role in ribosomal RNA synthesis. J Cell Biol 2000; 149:567-74. [PMID: 10791971 PMCID: PMC2174846 DOI: 10.1083/jcb.149.3.567] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Human aminoacyl-tRNA synthetases (ARSs) are normally located in cytoplasm and are involved in protein synthesis. In the present work, we found that human methionyl-tRNA synthetase (MRS) was translocated to nucleolus in proliferative cells, but disappeared in quiescent cells. The nucleolar localization of MRS was triggered by various growth factors such as insulin, PDGF, and EGF. The presence of MRS in nucleoli depended on the integrity of RNA and the activity of RNA polymerase I in the nucleolus. The ribosomal RNA synthesis was specifically decreased by the treatment of anti-MRS antibody as determined by nuclear run-on assay and immunostaining with anti-Br antibody after incorporating Br-UTP into nascent RNA. Thus, human MRS plays a role in the biogenesis of rRNA in nucleoli, while it is catalytically involved in protein synthesis in cytoplasm.
Collapse
Affiliation(s)
- Young-Gyu Ko
- National Creative Research Initiatives Center for ARS Network, Sung Kyun Kwan University, Jangangu, Suwon, Kyunggido 440-746, Korea
| | - Young-Sun Kang
- National Creative Research Initiatives Center for ARS Network, Sung Kyun Kwan University, Jangangu, Suwon, Kyunggido 440-746, Korea
| | - Eun-Kyoung Kim
- National Creative Research Initiatives Center for ARS Network, Sung Kyun Kwan University, Jangangu, Suwon, Kyunggido 440-746, Korea
| | - Sang Gyu Park
- National Creative Research Initiatives Center for ARS Network, Sung Kyun Kwan University, Jangangu, Suwon, Kyunggido 440-746, Korea
| | - Sunghoon Kim
- National Creative Research Initiatives Center for ARS Network, Sung Kyun Kwan University, Jangangu, Suwon, Kyunggido 440-746, Korea
| |
Collapse
|
34
|
Grosshans H, Simos G, Hurt E. Review: transport of tRNA out of the nucleus-direct channeling to the ribosome? J Struct Biol 2000; 129:288-94. [PMID: 10806079 DOI: 10.1006/jsbi.2000.4226] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although tRNA was the first substrate whose export from the nuclei of eukaryotic cells had been shown to be carrier-mediated and active, it has only been in the last 2 years that the first mechanistic details of this nucleocytoplasmic transport pathway have begun to emerge. A member of the importin/karyopherin beta superfamily, Los1p in yeast and Xpo-t in vertebrates, has been shown to export tRNA in cooperation with the small GTPase Ran (Gsp1p) from the nucleus into the cytoplasm, where tRNA becomes available for translation. However, Los1p is not essential for viability in yeast cells, suggesting that alternative tRNA export pathways exist. Recent results show that aminoacylation and a translation factor are also required for efficient nuclear tRNA export. Thus, protein translation and nuclear export of tRNA appear to be coupled processes.
Collapse
Affiliation(s)
- H Grosshans
- Biochemie-Zentrum Heidelberg (BZH), University of Heidelberg, Im Neuenheimer Feld 328, Heidelberg, D-69120, Germany
| | | | | |
Collapse
|
35
|
Grosshans H, Hurt E, Simos G. An aminoacylation-dependent nuclear tRNA export pathway in yeast. Genes Dev 2000. [DOI: 10.1101/gad.14.7.830] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Yeast Los1p, the homolog of human exportin-t, mediates nuclear export of tRNA. Using fluorescence in situ hybridization, we could show that the export of some intronless tRNA species is not detectably affected by the disruption of LOS1. To find other factors that facilitate tRNA export, we performed a suppressor screen of a synthetically lethal los1 mutant and identified the essential translation elongation factor eEF-1A. Mutations in eEF-1A impaired nuclear export of all tRNAs tested, which included both spliced and intronless species. An even stronger defect in nuclear exit of tRNA was observed under conditions that inhibited tRNA aminoacylation. In all cases, inhibition of tRNA export led to nucleolar accumulation of mature tRNAs. Our data show that tRNA aminoacylation and eEF-1A are required for efficient nuclear tRNA export in yeast and suggest coordination between the protein translation and the nuclear tRNA processing and transport machineries.
Collapse
|
36
|
Krzyzaniak A, Siatecka M, Szyk A, Mucha P, Rekowski P, Kupryszewski G, Barciszewski J. Specific induction of Z-DNA conformation by a nuclear localization signal peptide of lupin glutaminyl tRNA synthetase. Mol Biol Rep 2000; 27:51-4. [PMID: 10939526 DOI: 10.1023/a:1007146516710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Recently we have sequenced cDNA of plant glutaminyl-tRNA synthetase (GlnRS) from Lupinus luteus. At the N terminal part the protein contains a lysine rich polypeptide (KPKKKKEK), which is identical to a nuclear localization signal (NLS). In this paper we showed that two synthetic peptides (20 and 8 amino acids long), which were derived from lupin GlnRS containing the NLS sequence interact with DNA, but one of them (8aa long) changing its conformation from the B to the Z form. This observation clearly suggests that the presence of the NLS polypeptide in a leader sequence of GlnRS is required not only for protein transport into nucleus but also for regulation of a gene expression. This is the first report suggesting a role of the NLS signal peptide in structural changes of DNA.
Collapse
Affiliation(s)
- A Krzyzaniak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznañ
| | | | | | | | | | | | | |
Collapse
|
37
|
Stanford DR, Martin NC, Hopper AK. ADEPTs: information necessary for subcellular distribution of eukaryotic sorting isozymes resides in domains missing from eubacterial and archaeal counterparts. Nucleic Acids Res 2000; 28:383-92. [PMID: 10606634 PMCID: PMC102526 DOI: 10.1093/nar/28.2.383] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/1999] [Revised: 11/22/1999] [Accepted: 11/22/1999] [Indexed: 11/14/2022] Open
Abstract
Sorting isozymes are encoded by single genes, but the encoded proteins are distributed to multiple subcellular compartments. We surveyed the predicted protein sequences of several nucleic acid interacting sorting isozymes from the eukaryotic taxonomic domain and compared them with their homologs in the archaeal and eubacterial domains. Here, we summarize the data showing that the eukaryotic sorting isozymes often possess sequences not present in the archaeal and eubacterial counterparts and that the additional sequences can act to target the eukaryotic proteins to their appropriate subcellular locations. Therefore, we have named these protein domains ADEPTs (Additional Domains for Eukaryotic Protein Targeting). Identification of additional domains by phylogenetic comparisons should be generally useful for locating candidate sequences important for subcellular distribution of eukaryotic proteins.
Collapse
Affiliation(s)
- D R Stanford
- Department of Biochemistry, Pennsylvania State University College of Medicine, H171, 500 University Drive, Hershey, PA 17033, USA
| | | | | |
Collapse
|
38
|
Szymanski M, Barciszewski J. Aminoacyl-tRNA synthetases database Y2K. Nucleic Acids Res 2000; 28:326-8. [PMID: 10592262 PMCID: PMC102446 DOI: 10.1093/nar/28.1.326] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/1999] [Revised: 10/08/1999] [Accepted: 10/08/1999] [Indexed: 11/14/2022] Open
Abstract
The aminoacyl-tRNA synthetases (AARS) are a diverse group of enzymes that ensure the fidelity of transfer of genetic information from DNA into protein. They catalyse the attachment of amino acids to transfer RNAs and thereby establish the rules of the genetic code by virtue of matching the nucleotide triplet of the anticodon with its cognate amino acid. Currently, 818 AARS primary structures have been reported from archaebacteria, eubacteria, mitochondria, chloro-plasts and eukaryotic cells. The database is a compilation of the amino acid sequences of all AARSs, known to date, which are available as separate entries or alignments of related proteins via the WWW at http://rose.man.poznan.pl/aars/index.html
Collapse
Affiliation(s)
- M Szymanski
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | | |
Collapse
|
39
|
Sarkar S, Azad AK, Hopper AK. Nuclear tRNA aminoacylation and its role in nuclear export of endogenous tRNAs in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 1999; 96:14366-71. [PMID: 10588711 PMCID: PMC24442 DOI: 10.1073/pnas.96.25.14366] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nuclear tRNA aminoacylation was proposed to provide a proofreading step in Xenopus oocytes, ensuring nuclear export of functional tRNAs [Lund, E. & Dahlberg, J. E. (1998) Science 282, 2082-2085]. Herein, it is documented that tRNA aminoacylation also occurs in yeast nuclei and is important for tRNA export. We propose that tRNA aminoacylation functions in one of at least two parallel paths of tRNA export in yeast. Alteration of one aminoacyl-tRNA synthetase affects export of only cognate tRNA, whereas alterations of two other aminoacyl-tRNA synthetases affect export of both cognate and noncognate tRNAs. Saturation of tRNA export pathway is a possible explanation of this phenomenon.
Collapse
Affiliation(s)
- S Sarkar
- Department of Biochemistry, Pennsylvania State University, College of Medicine, Hershey, PA, 17033, USA
| | | | | |
Collapse
|
40
|
Martinis SA, Plateau P, Cavarelli J, Florentz C. Aminoacyl-tRNA synthetases: a new image for a classical family. Biochimie 1999; 81:683-700. [PMID: 10492015 DOI: 10.1016/s0300-9084(99)80126-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The aminoacyl-tRNA synthetases (aaRSs) are a family of enzymes well known for their role in protein synthesis. More recent investigations have discovered that this classic family of enzymes is actually capable of a broad repertoire of functions which not only impact protein synthesis, but extend to a number of other critical cellular activities. Specific aaRSs play roles in cellular fidelity, tRNA processing, RNA splicing, RNA trafficking, apoptosis, transcriptional and translational regulation. A recent EMBO workshop entitled 'Structure and Function of Aminoacyl-tRNA Synthetases' (Mittelwihr, France, October 10-15, 1998), highlighted the diversity of the aaRSs' role within the cell. These novel activities as well as significant advances in delineating mechanisms of substrate specificity and the aminoacylation reaction affirm the family of aaRSs as pharmaceutical targets.
Collapse
Affiliation(s)
- S A Martinis
- Department of Biology and Biochemistry, University of Houston, TX 77204-5513, USA
| | | | | | | |
Collapse
|