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Barai P, Chen J. Beyond protein synthesis: non-translational functions of threonyl-tRNA synthetases. Biochem Soc Trans 2024; 52:661-670. [PMID: 38477373 PMCID: PMC11088916 DOI: 10.1042/bst20230506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024]
Abstract
Aminoacyl-tRNA synthetases (AARSs) play an indispensable role in the translation of mRNAs into proteins. It has become amply clear that AARSs also have non-canonical or non-translational, yet essential, functions in a myriad of cellular and developmental processes. In this mini-review we discuss the current understanding of the roles of threonyl-tRNA synthetase (TARS) beyond protein synthesis and the underlying mechanisms. The two proteins in eukaryotes - cytoplasmic TARS1 and mitochondrial TARS2 - exert their non-canonical functions in the regulation of gene expression, cell signaling, angiogenesis, inflammatory responses, and tumorigenesis. The TARS proteins utilize a range of biochemical mechanisms, including assembly of a translation initiation complex, unexpected protein-protein interactions that lead to activation or inhibition of intracellular signaling pathways, and cytokine-like signaling through cell surface receptors in inflammation and angiogenesis. It is likely that new functions and novel mechanisms will continue to emerge for these multi-talented proteins.
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Affiliation(s)
- Pallob Barai
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Jie Chen
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
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2
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Abstract
We describe a strategy for tracking Mg²⁺-initiated folding of ³²P-labeled tRNA molecules to their native structures based on the capacity for aminoacylation by the cognate aminoacyl-tRNA synthetase enzyme. The approach directly links folding to function, paralleling a common strategy used to study the folding of catalytic RNAs. Incubation of unfolded tRNA with magnesium ions, followed by the addition of aminoacyl-tRNA synthetase and further incubation, yields a rapid burst of aminoacyl-tRNA formation corresponding to the prefolded tRNA fraction. A subsequent slower increase in product formation monitors continued folding in the presence of the enzyme. Further analysis reveals the presence of a parallel fraction of tRNA that folds more rapidly than the majority of the population. The application of the approach to study the influence of post-transcriptional modifications in folding of Escherichia coli tRNA₁(Gln) reveals that the modified bases increase the folding rate but do not affect either the equilibrium between properly folded and misfolded states or the folding pathway. This assay allows the use of ³²P-labeled tRNA in integrated studies combining folding, post-transcriptional processing, and aminoacylation reactions.
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Affiliation(s)
| | | | - John J. Perona
- Department of Chemistry and Biochemistry
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106-9510, USA
- Corresponding author.E-mail .
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3
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Larson ET, Kim JE, Castaneda LJ, Napuli AJ, Zhang Z, Fan E, Zucker FH, Verlinde CL, Buckner FS, Van Voorhis WC, Hol WG, Merritt EA. The double-length tyrosyl-tRNA synthetase from the eukaryote Leishmania major forms an intrinsically asymmetric pseudo-dimer. J Mol Biol 2011; 409:159-76. [PMID: 21420975 DOI: 10.1016/j.jmb.2011.03.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Revised: 03/08/2011] [Accepted: 03/14/2011] [Indexed: 01/07/2023]
Abstract
The single tyrosyl-tRNA synthetase (TyrRS) gene in trypanosomatid genomes codes for a protein that is twice the length of TyrRS from virtually all other organisms. Each half of the double-length TyrRS contains a catalytic domain and an anticodon-binding domain; however, the two halves retain only 17% sequence identity to each other. The structural and functional consequences of this duplication and divergence are unclear. TyrRS normally forms a homodimer in which the active site of one monomer pairs with the anticodon-binding domain from the other. However, crystal structures of Leishmania major TyrRS show that, instead, the two halves of a single molecule form a pseudo-dimer resembling the canonical TyrRS dimer. Curiously, the C-terminal copy of the catalytic domain has lost the catalytically important HIGH and KMSKS motifs characteristic of class I aminoacyl-tRNA synthetases. Thus, the pseudo-dimer contains only one functional active site (contributed by the N-terminal half) and only one functional anticodon recognition site (contributed by the C-terminal half). Despite biochemical evidence for negative cooperativity between the two active sites of the usual TyrRS homodimer, previous structures have captured a crystallographically-imposed symmetric state. As the L. major TyrRS pseudo-dimer is inherently asymmetric, conformational variations observed near the active site may be relevant to understanding how the state of a single active site is communicated across the dimer interface. Furthermore, substantial differences between trypanosomal TyrRS and human homologs are promising for the design of inhibitors that selectively target the parasite enzyme.
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4
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Larson ET, Kim JE, Zucker FH, Kelley A, Mueller N, Napuli AJ, Verlinde CL, Fan E, Buckner FS, Van Voorhis WC, Merritt EA, Hol WG. Structure of Leishmania major methionyl-tRNA synthetase in complex with intermediate products methionyladenylate and pyrophosphate. Biochimie 2011; 93:570-82. [PMID: 21144880 PMCID: PMC3039092 DOI: 10.1016/j.biochi.2010.11.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 11/29/2010] [Indexed: 01/07/2023]
Abstract
Leishmania parasites cause two million new cases of leishmaniasis each year with several hundreds of millions of people at risk. Due to the paucity and shortcomings of available drugs, we have undertaken the crystal structure determination of a key enzyme from Leishmania major in hopes of creating a platform for the rational design of new therapeutics. Crystals of the catalytic core of methionyl-tRNA synthetase from L. major (LmMetRS) were obtained with the substrates MgATP and methionine present in the crystallization medium. These crystals yielded the 2.0 Å resolution structure of LmMetRS in complex with two products, methionyladenylate and pyrophosphate, along with a Mg(2+) ion that bridges them. This is the first class I aminoacyl-tRNA synthetase (aaRS) structure with pyrophosphate bound. The residues of the class I aaRS signature sequence motifs, KISKS and HIGH, make numerous contacts with the pyrophosphate. Substantial differences between the LmMetRS structure and previously reported complexes of Escherichia coli MetRS (EcMetRS) with analogs of the methionyladenylate intermediate product are observed, even though one of these analogs only differs by one atom from the intermediate. The source of these structural differences is attributed to the presence of the product pyrophosphate in LmMetRS. Analysis of the LmMetRS structure in light of the Aquifex aeolicus MetRS-tRNA(Met) complex shows that major rearrangements of multiple structural elements of enzyme and/or tRNA are required to allow the CCA acceptor triplet to reach the methionyladenylate intermediate in the active site. Comparison with sequences of human cytosolic and mitochondrial MetRS reveals interesting differences near the ATP- and methionine-binding regions of LmMetRS, suggesting that it should be possible to obtain compounds that selectively inhibit the parasite enzyme.
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Affiliation(s)
- Eric T. Larson
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA,Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org
| | - Jessica E. Kim
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA,Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org
| | - Frank H. Zucker
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA,Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org
| | - Angela Kelley
- Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org,Department of Medicine, University of Washington, Seattle, WA 98195-7185, USA
| | - Natascha Mueller
- Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org,Department of Medicine, University of Washington, Seattle, WA 98195-7185, USA
| | - Alberto J. Napuli
- Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org,Department of Medicine, University of Washington, Seattle, WA 98195-7185, USA
| | - Christophe L.M.J. Verlinde
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA,Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org
| | - Erkang Fan
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA,Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org
| | - Frederick S. Buckner
- Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org,Department of Medicine, University of Washington, Seattle, WA 98195-7185, USA
| | - Wesley C. Van Voorhis
- Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org,Department of Medicine, University of Washington, Seattle, WA 98195-7185, USA
| | - Ethan A. Merritt
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA,Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org
| | - Wim G.J. Hol
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA,Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org,Corresponding author.
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5
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Merritt EA, Arakaki TL, Gillespie JR, Larson ET, Kelley A, Mueller N, Napuli AJ, Kim J, Zhang L, Verlinde CLMJ, Fan E, Zucker F, Buckner FS, Van Voorhis WC, Hol WGJ. Crystal structures of trypanosomal histidyl-tRNA synthetase illuminate differences between eukaryotic and prokaryotic homologs. J Mol Biol 2010; 397:481-94. [PMID: 20132829 PMCID: PMC2834879 DOI: 10.1016/j.jmb.2010.01.051] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 01/11/2010] [Accepted: 01/24/2010] [Indexed: 01/07/2023]
Abstract
Crystal structures of histidyl-tRNA synthetase (HisRS) from the eukaryotic parasites Trypanosoma brucei and Trypanosoma cruzi provide a first structural view of a eukaryotic form of this enzyme and reveal differences from bacterial homologs. HisRSs in general contain an extra domain inserted between conserved motifs 2 and 3 of the Class II aminoacyl-tRNA synthetase catalytic core. The current structures show that the three-dimensional topology of this domain is very different in bacterial and archaeal/eukaryotic forms of the enzyme. Comparison of apo and histidine-bound trypanosomal structures indicates substantial active-site rearrangement upon histidine binding but relatively little subsequent rearrangement after reaction of histidine with ATP to form the enzyme's first reaction product, histidyladenylate. The specific residues involved in forming the binding pocket for the adenine moiety differ substantially both from the previously characterized binding site in bacterial structures and from the homologous residues in human HisRSs. The essentiality of the single HisRS gene in T. brucei is shown by a severe depression of parasite growth rate that results from even partial suppression of expression by RNA interference.
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Affiliation(s)
- Ethan A Merritt
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA,Corresponding author: Phone: 206-543-1421 Fax: 206-685-7002,
| | - Tracy L Arakaki
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
| | - J Robert Gillespie
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Eric T Larson
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
| | - Angela Kelley
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Natascha Mueller
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Alberto J Napuli
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Jessica Kim
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
| | - Li Zhang
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
| | - Christophe L M J Verlinde
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
| | - Erkang Fan
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
| | - Frank Zucker
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
| | - Frederick S Buckner
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Wesley C Van Voorhis
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Wim G J Hol
- Medical Structural Genomics of Pathogenic Protozoa http://www.msgpp.org, Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
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6
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Charrière F, Helgadóttir S, Horn EK, Söll D, Schneider A. Dual targeting of a single tRNA(Trp) requires two different tryptophanyl-tRNA synthetases in Trypanosoma brucei. Proc Natl Acad Sci U S A 2006; 103:6847-52. [PMID: 16636268 PMCID: PMC1458982 DOI: 10.1073/pnas.0602362103] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mitochondrion of Trypanosoma brucei does not encode any tRNAs. This deficiency is compensated for by the import of a small fraction of nearly all of its cytosolic tRNAs. Most trypanosomal aminoacyl-tRNA synthetases are encoded by single-copy genes, suggesting the use of the same enzyme in the cytosol and mitochondrion. However, the T. brucei genome contains two distinct genes for eukaryotic tryptophanyl-tRNA synthetase (TrpRS). RNA interference analysis established that both TrpRS1 and TrpRS2 are essential for growth and required for cytosolic and mitochondrial tryptophanyl-tRNA formation, respectively. Decoding the mitochondrial tryptophan codon UGA requires mitochondria-specific C-->U RNA editing in the anticodon of the imported tRNA(Trp). In vitro charging assays with recombinant TrpRS enzymes demonstrated that the edited anticodon and the mitochondria-specific thiolation of U33 in the imported tRNA(Trp) act as antideterminants for the cytosolic TrpRS1. The existence of two TrpRS enzymes, therefore, can be explained by the need for a mitochondrial synthetase with extended substrate specificity to achieve aminoacylation of the imported thiolated and edited tRNA(Trp). Thus, the notion that, in an organism, all nuclear-encoded tRNAs assigned to a given amino acid are charged by a single aminoacyl-tRNA synthetase, is not universally valid.
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Affiliation(s)
- Fabien Charrière
- *Department of Biology/Cell and Developmental Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland; and Departments of
| | | | - Elke K. Horn
- *Department of Biology/Cell and Developmental Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland; and Departments of
| | - Dieter Söll
- Molecular Biophysics and Biochemistry and
- Chemistry, Yale University, New Haven, CT 06520-8114
| | - André Schneider
- *Department of Biology/Cell and Developmental Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland; and Departments of
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Copela LA, Chakshusmathi G, Sherrer RL, Wolin SL. The La protein functions redundantly with tRNA modification enzymes to ensure tRNA structural stability. RNA 2006; 12:644-54. [PMID: 16581807 PMCID: PMC1421099 DOI: 10.1261/rna.2307206] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Although the La protein stabilizes nascent pre-tRNAs from nucleases, influences the pathway of pre-tRNA maturation, and assists correct folding of certain pre-tRNAs, it is dispensable for growth in both budding and fission yeast. Here we show that the Saccharomyces cerevisiae La shares functional redundancy with both tRNA modification enzymes and other proteins that contact tRNAs during their biogenesis. La is important for growth in the presence of mutations in either the arginyl tRNA synthetase or the tRNA modification enzyme Trm1p. In addition, two pseudouridine synthases, PUS3 and PUS4, are important for growth in strains carrying a mutation in tRNA(Arg)(CCG) and are essential when La is deleted in these strains. Depletion of Pus3p results in accumulation of the aminoacylated mutant tRNA(Arg)(CCG) in nuclei, while depletion of Pus4p results in decreased stability of the mutant tRNA. Interestingly, the degradation of mutant unstable forms of tRNA(Arg)(CCG) does not require the Trf4p poly(A) polymerase, suggesting that yeast cells possess multiple pathways for tRNA decay. These data demonstrate that La functions redundantly with both tRNA modifications and proteins that associate with tRNAs to achieve tRNA structural stability and efficient biogenesis.
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Affiliation(s)
- Laura A Copela
- Department of Cell Biology, Howard Hughes Medical Institute, Yale University School of Medicine, 295 Congress Avenue, New Haven, Connecticut 06536, USA
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Abstract
The recent discovery of an alternate pathway for indirectly charging tRNA(Cys) has stimulated a re-examination of the evolutionary history of Cys-tRNA(Cys) formation. In the first step of the pathway, O-phosphoseryl-tRNA synthetase charges tRNA(Cys) with O-phosphoserine (Sep), a precursor of the cognate amino acid. In the following step, Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep to Cys in a tRNA-dependent reaction. The existence of such a pathway raises several evolutionary questions, including whether the indirect pathway is a recent evolutionary invention, as might be implied from its localization to the Euryarchaea, or, as evidence presented here indicates, whether this pathway is more ancient, perhaps already in existence at the time of the last universal common ancestral state. A comparative phylogenetic approach is used, combining evolutionary information from protein sequences and structures, that takes both the signature of horizontal gene transfer and the recurrence of the full canonical phylogenetic pattern into account, to document the complete evolutionary history of cysteine coding and understand the nature of this process in the last universal common ancestral state. Resulting from the historical study of tRNA(Cys) aminoacylation and the integrative perspective of sequence, structure, and function are 3D models of O-phosphoseryl-tRNA synthetase and SepCysS, which provide experimentally testable predictions regarding the identity and function of key active-site residues in these proteins. The model of SepCysS is used to suggest a sulfhydrylation reaction mechanism, which is predicted to occur at the interface of a SepCysS dimer.
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Affiliation(s)
- Patrick O'Donoghue
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Iwaki J, Suzuki R, Fujimoto Z, Momma M, Kuno A, Hasegawa T. Overexpression, purification and crystallization of tyrosyl-tRNA synthetase from the hyperthermophilic archaeon Aeropyrum pernix K1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:1003-5. [PMID: 16511219 PMCID: PMC1978129 DOI: 10.1107/s1744309105033245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Accepted: 10/17/2005] [Indexed: 11/10/2022]
Abstract
Hyperthermophilic archaeal tyrosyl-tRNA synthetase from Aeropyrum pernix K1 was cloned and overexpressed in Escherichia coli. The expressed protein was purified by Cibacron Blue affinity chromatography following heat treatment at 363 K. Crystals suitable for X-ray diffraction studies were obtained under optimized crystallization conditions in the presence of 1.5 M ammonium sulfate using the hanging-drop vapour-diffusion method. The crystals belonged to the tetragonal space group P4(3)2(1)2, with unit-cell parameters a = b = 66.1, c = 196.2 A, and diffracted to beyond 2.15 A resolution at 100 K.
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Affiliation(s)
- Jun Iwaki
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
- Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Ryuichiro Suzuki
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
- Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
- Research Centre for Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan
| | - Zui Fujimoto
- Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Mitsuru Momma
- Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Atsushi Kuno
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
- Research Centre for Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan
| | - Tsunemi Hasegawa
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
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Park SG, Kim HJ, Min YH, Choi EC, Shin YK, Park BJ, Lee SW, Kim S. Human lysyl-tRNA synthetase is secreted to trigger proinflammatory response. Proc Natl Acad Sci U S A 2005; 102:6356-61. [PMID: 15851690 PMCID: PMC1088368 DOI: 10.1073/pnas.0500226102] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2005] [Indexed: 01/09/2023] Open
Abstract
Although aminoacyl-tRNA synthetases (ARSs) are essential for protein synthesis, they also function as regulators and signaling molecules in diverse biological processes. Here, we screened 11 different human ARSs to identify the enzyme that is secreted as a signaling molecule. Among them, we found that lysyl-tRNA synthetase (KRS) was secreted from intact human cells, and its secretion was induced by TNF-alpha. The secreted KRS bound to macrophages and peripheral blood mononuclear cells to enhance the TNF-alpha production and their migration. The mitogen-activated protein kinases, extracellular signal-regulated kinase and p38 mitogen-activated protein kinase, and Galphai were determined to be involved in the signal transduction triggered by KRS. All of these activities demonstrate that human KRS may work as a previously uncharacterized signaling molecule, inducing immune response through the activation of monocyte/macrophages.
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Affiliation(s)
- Sang Gyu Park
- National Creative Research Initiatives Center for ARS Network, College of Pharmacy, Seoul National University, Seoul 151-742, Korea
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11
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Chen X, Mohr G, Lambowitz AM. The Neurospora crassa CYT-18 protein C-terminal RNA-binding domain helps stabilize interdomain tertiary interactions in group I introns. RNA 2004; 10:634-644. [PMID: 15037773 PMCID: PMC1370554 DOI: 10.1261/rna.5212604] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2003] [Accepted: 12/18/2003] [Indexed: 05/24/2023]
Abstract
The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) promotes the splicing of group I introns by stabilizing the catalytically active RNA structure. To accomplish this, CYT-18 recognizes conserved structural features of group I intron RNAs using regions of the N-terminal nucleotide-binding fold, intermediate alpha-helical, and C-terminal RNA-binding domains that also function in binding tRNA(Tyr). Curiously, whereas the splicing of the N. crassa mitochondrial large subunit rRNA intron is completely dependent on CYT-18's C-terminal RNA-binding domain, all other group I introns tested thus far are spliced efficiently by a truncated protein lacking this domain. To investigate the function of the C-terminal domain, we used an Escherichia coli genetic assay to isolate mutants of the Saccharomyces cerevisiae mitochondrial large subunit rRNA and phage T4 td introns that can be spliced in vivo by the wild-type CYT-18 protein, but not by the C-terminally truncated protein. Mutations that result in dependence on CYT-18's C-terminal domain include those disrupting two long-range GNRA tetraloop/receptor interactions: L2-P8, which helps position the P1 helix containing the 5'-splice site, and L9-P5, which helps establish the correct relative orientation of the P4-P6 and P3-P9 domains of the group I intron catalytic core. Our results indicate that different structural mutations in group I intron RNAs can result in dependence on different regions of CYT-18 for RNA splicing.
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Affiliation(s)
- Xin Chen
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, and Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, Texas 78712, USA
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12
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Tardif KD, Horowitz J. Functional group recognition at the aminoacylation and editing sites of E. coli valyl-tRNA synthetase. RNA 2004; 10:493-503. [PMID: 14970394 PMCID: PMC1370944 DOI: 10.1261/rna.5166704] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2003] [Accepted: 11/07/2003] [Indexed: 05/24/2023]
Abstract
To correct misactivation and misacylation errors, Escherichia coli valyl-tRNA synthetase (ValRS) catalyzes a tRNA(Val)-dependent editing reaction at a site distinct from its aminoacylation site. Here we examined the effects of replacing the conserved 3'-adenosine of tRNA(Val) with nucleoside analogs, to identify structural elements of the 3'-terminal nucleoside necessary for tRNA function at the aminoacylation and editing sites of ValRS. The results show that the exocyclic amino group (N6) is not essential: purine riboside-substituted tRNA(Val) is active in aminoacylation and in stimulating editing. Presence of an O6 substituent (guanosine, inosine, xanthosine) interferes with aminoacylation as well as posttransfer and total editing (pre- plus posttransfer editing). Because ValRS does not recognize substituents at the 6-position, these results suggest that an unprotonated N1, capable of acting as an H-bond acceptor, is an essential determinant for both the aminoacylation and editing reactions. Substituents at the 2-position of the purine ring, either a 2-amino group (2-aminopurine, 2,6-diaminopurine, guanosine, and 7-deazaguanosine) or a 2-keto group (xanthosine, isoguanosine), strongly inhibit both aminoacylation and editing. Although aminoacylation by ValRS is at the 2'-OH, substitution of the 3'-terminal adenosine of tRNA(Val) with 3'-deoxyadenosine reduces the efficiency of valine acceptance and of posttransfer editing, demonstrating that the 3'-terminal hydroxyl group contributes to tRNA recognition at both the aminoacylation and editing sites. Our results show a strong correlation between the amino acid accepting activity of tRNA and its ability to stimulate editing, suggesting misacylated tRNA is a transient intermediate in the editing reaction, and editing by ValRS requires a posttransfer step.
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Affiliation(s)
- Keith D Tardif
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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Fukai S, Nureki O, Sekine SI, Shimada A, Vassylyev DG, Yokoyama S. Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase. RNA 2003; 9:100-111. [PMID: 12554880 PMCID: PMC1370374 DOI: 10.1261/rna.2760703] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2002] [Accepted: 09/23/2002] [Indexed: 05/24/2023]
Abstract
The molecular interactions between valyl-tRNA synthetase (ValRS) and tRNA(Val), with the C34-A35-C36 anticodon, from Thermus thermophilus were studied by crystallographic analysis and structure-based mutagenesis. In the ValRS-bound structure of tRNA(Val), the successive A35-C36 residues (the major identity elements) of tRNA(Val) are base-stacked upon each other, and fit into a pocket on the alpha-helix bundle domain of ValRS. Hydrogen bonds are formed between ValRS and A35-C36 of tRNA(Val) in a base-specific manner. The C-terminal coiled-coil domain of ValRS interacts electrostatically with A20 and hydrophobically with the G19*C56 tertiary base pair. The loss of these interactions by the deletion of the coiled-coil domain of ValRS increased the K(M) value for tRNA(Val) 28-fold and decreased the k(cat) value 19-fold in the aminoacylation. The tRNA(Val) K(M) and k(cat) values were increased 21-fold and decreased 32-fold, respectively, by the disruption of the G18*U55 and G19*C56 tertiary base pairs, which associate the D- and T-loops for the formation of the L-shaped tRNA structure. Therefore, the coiled-coil domain of ValRS is likely to stabilize the L-shaped tRNA structure during the aminoacylation reaction.
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Affiliation(s)
- Shuya Fukai
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Japan
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García-Lozano JR, González-Escribano MF, Rodríguez R, Rodriguez-Sanchez JL, Targoff IN, Wichmann I, Núñez-Roldán A. Detection of anti-PL-12 autoantibodies by ELISA using a recombinant antigen; study of the immunoreactive region. Clin Exp Immunol 1998; 114:161-5. [PMID: 9822271 PMCID: PMC1905094 DOI: 10.1046/j.1365-2249.1998.00720.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Autoantibodies to aminoacyl-tRNA synthetases are highly associated with myositis and detection is important in clinical diagnosis; however, current methods of screening limit its clinical utility. In the present study, alanyl-tRNA synthetase (PL-12) recombinant protein was obtained by immunological screening of a HeLa expression library and used in an ELISA with 22 anti-PL-12 sera, 200 autoimmune sera negative for PL-12 and 100 healthy individual sera. Sensitivity of the method was 95% (21/22) and specificity 100%. Mapping of the immunoreactive region was carried out using three anti-PL-12 sera and different recombinant protein-derived peptides. Results show that the same conformational epitope located within amino acids 730-951 of the PL-12 antigen outside the catalytic region was recognized by the three anti-PL-12 sera tested. We conclude that ELISA using recombinant protein is an effective and useful method for routine screening for anti-PL-12 autoantibodies.
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Affiliation(s)
- J R García-Lozano
- Servicio de Inmunología, Hospital Universitario Virgen del Rocío, Sevilla, Spain
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