1
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Dulic M, Krpan N, Gruic-Sovulj I. Gly56 in the synthetic site of isoleucyl-tRNA synthetase confers specificity and maintains communication with the editing site. FEBS Lett 2023; 597:3114-3124. [PMID: 38015921 DOI: 10.1002/1873-3468.14780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/30/2023] [Accepted: 11/10/2023] [Indexed: 11/30/2023]
Abstract
Isoleucyl-tRNA synthetase (IleRS) links isoleucine to cognate tRNA via the Ile-AMP intermediate. Non-cognate valine is often mistakenly recognized as the IleRS substrate; therefore, to maintain the accuracy of translation, IleRS hydrolyzes Val-AMP within the synthetic site (pre-transfer editing). As this activity is not efficient enough, Val-tRNAIle is formed and hydrolyzed in the distant post-transfer editing site. A strictly conserved synthetic site residue Gly56 was previously shown to safeguard Ile-to-Val discrimination during aminoacyl (aa)-AMP formation. Here, we show that the Gly56Ala variant lost its specificity in pre-transfer editing, confirming that this residue ensures the selectivity of all synthetic site reactions. Moreover, we found that the Gly56Ala mutation affects IleRS interaction with aa-tRNA likely by disturbing tRNA-dependent communication between the two active sites.
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Affiliation(s)
- Morana Dulic
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
| | - Nina Krpan
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
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2
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Byun JK, Vu JA, He SL, Jang JC, Musier-Forsyth K. Plant-exclusive domain of trans-editing enzyme ProXp-ala confers dimerization and enhanced tRNA binding. J Biol Chem 2022; 298:102255. [PMID: 35835222 PMCID: PMC9425024 DOI: 10.1016/j.jbc.2022.102255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/26/2022] Open
Abstract
Faithful translation of the genetic code is critical for the viability of all living organisms. The trans-editing enzyme ProXp-ala prevents Pro to Ala mutations during translation by hydrolyzing misacylated Ala-tRNAPro that has been synthesized by prolyl-tRNA synthetase. Plant ProXp-ala sequences contain a conserved C-terminal domain (CTD) that is absent in other organisms; the origin, structure, and function of this extra domain are unknown. To characterize the plant-specific CTD, we performed bioinformatics and computational analyses that provided a model consistent with a conserved α-helical structure. We also expressed and purified wildtype Arabidopsis thaliana (At) ProXp-ala in Escherichia coli, as well as variants lacking the CTD or containing only the CTD. Circular dichroism spectroscopy confirmed a loss of α-helical signal intensity upon CTD truncation. Size-exclusion chromatography with multiangle laser-light scattering revealed that wildtype At ProXp-ala was primarily dimeric and CTD truncation abolished dimerization in vitro. Furthermore, bimolecular fluorescence complementation assays in At protoplasts support a role for the CTD in homodimerization in vivo. The deacylation rate of Ala-tRNAPro by At ProXp-ala was also significantly reduced in the absence of the CTD, and kinetic assays indicated that the reduction in activity is primarily due to a tRNA binding defect. Overall, these results broaden our understanding of eukaryotic translational fidelity in the plant kingdom. Our study reveals that the plant-specific CTD plays a significant role in substrate binding and canonical editing function. Through its ability to facilitate protein-protein interactions, we propose the CTD may also provide expanded functional potential for trans-editing enzymes in plants.
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Affiliation(s)
- Jun-Kyu Byun
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - John A Vu
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Siou-Luan He
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA; Department of Horticulture and Crop Science and Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Jyan-Chyun Jang
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA; Department of Horticulture and Crop Science and Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio, USA.
| | - Karin Musier-Forsyth
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA.
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3
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Kuzmishin Nagy AB, Bakhtina M, Musier-Forsyth K. Trans-editing by aminoacyl-tRNA synthetase-like editing domains. Enzymes 2020; 48:69-115. [PMID: 33837712 DOI: 10.1016/bs.enz.2020.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Aminoacyl-tRNA synthetases (aaRS) are ubiquitous enzymes responsible for aminoacyl-tRNA (aa-tRNA) synthesis. Correctly formed aa-tRNAs are necessary for proper decoding of mRNA and accurate protein synthesis. tRNAs possess specific nucleobases that promote selective recognition by cognate aaRSs. Selecting the cognate amino acid can be more challenging because all amino acids share the same peptide backbone and several are isosteric or have similar side chains. Thus, aaRSs can misactivate non-cognate amino acids and produce mischarged aa-tRNAs. If left uncorrected, mischarged aa-tRNAs deliver their non-cognate amino acid to the ribosome resulting in misincorporation into the nascent polypeptide chain. This changes the primary protein sequence and potentially causes misfolding or formation of non-functional proteins that impair cell survival. A variety of proofreading or editing pathways exist to prevent and correct mistakes in aa-tRNA formation. Editing may occur before the amino acid transfer step of aminoacylation via hydrolysis of the aminoacyl-adenylate. Alternatively, post-transfer editing, which occurs after the mischarged aa-tRNA is formed, may be carried out via a distinct editing site on the aaRS where the mischarged aa-tRNA is deacylated. In recent years, it has become clear that most organisms also encode factors that lack aminoacylation activity but resemble aaRS editing domains and function to clear mischarged aa-tRNAs in trans. This review focuses on these trans-editing factors, which are encoded in all three domains of life and function together with editing domains present within aaRSs to ensure that the accuracy of protein synthesis is sufficient for cell survival.
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Affiliation(s)
- Alexandra B Kuzmishin Nagy
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Marina Bakhtina
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States.
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4
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Hu QH, Williams MT, Shulgina I, Fossum CJ, Weeks KM, Adams LM, Reinhardt CR, Musier-Forsyth K, Hati S, Bhattacharyya S. Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase. ACS Catal 2020; 10:10229-10242. [PMID: 34295570 DOI: 10.1021/acscatal.0c02381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Prolyl-tRNA synthetases (ProRSs) catalyze the covalent attachment of proline onto cognate tRNAs, an indispensable step for protein synthesis in all living organisms. ProRSs are modular enzymes and the "prokaryotic-like" ProRSs are distinguished from "eukaryotic-like" ProRSs by the presence of an editing domain (INS) inserted between motifs 2 and 3 of the main catalytic domain. Earlier studies suggested the presence of coupled-domain dynamics could contribute to catalysis; however, the role that the distal, highly mobile INS domain plays in catalysis at the synthetic active site is not completely understood. In the present study, a combination of theoretical and experimental approaches has been used to elucidate the precise role of INS domain dynamics. Quantum mechanical/molecular mechanical simulations were carried out to model catalytic Pro-AMP formation by Enterococcus faecalis ProRS. The energetics of the adenylate formation by the wild-type enzyme was computed and contrasted with variants containing active site mutations, as well as a deletion mutant lacking the INS domain. The combined results revealed that two distinct types of dynamics contribute to the enzyme's catalytic power. One set of motions is intrinsic to the INS domain and leads to conformational preorganization that is essential for catalysis. A second type of motion, stemming from the electrostatic reorganization of active site residues, impacts the height and width of the energy profile and has a critical role in fine tuning the substrate orientation to facilitate reactive collisions. Thus, motions in a distal domain can preorganize the active site of an enzyme to optimize catalysis.
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Affiliation(s)
- Quin H. Hu
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Murphi T. Williams
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Irina Shulgina
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Carl J. Fossum
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Katelyn M. Weeks
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Lauren M. Adams
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Clorice R. Reinhardt
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sanchita Hati
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Sudeep Bhattacharyya
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
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5
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Kaiser F, Krautwurst S, Salentin S, Haupt VJ, Leberecht C, Bittrich S, Labudde D, Schroeder M. The structural basis of the genetic code: amino acid recognition by aminoacyl-tRNA synthetases. Sci Rep 2020; 10:12647. [PMID: 32724042 PMCID: PMC7387524 DOI: 10.1038/s41598-020-69100-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/06/2020] [Indexed: 12/29/2022] Open
Abstract
Storage and directed transfer of information is the key requirement for the development of life. Yet any information stored on our genes is useless without its correct interpretation. The genetic code defines the rule set to decode this information. Aminoacyl-tRNA synthetases are at the heart of this process. We extensively characterize how these enzymes distinguish all natural amino acids based on the computational analysis of crystallographic structure data. The results of this meta-analysis show that the correct read-out of genetic information is a delicate interplay between the composition of the binding site, non-covalent interactions, error correction mechanisms, and steric effects.
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Affiliation(s)
- Florian Kaiser
- Biotechnology Center (BIOTEC), TU Dresden, 01307, Dresden, Germany. .,PharmAI GmbH, Tatzberg 47, 01307, Dresden, Germany.
| | - Sarah Krautwurst
- University of Applied Sciences Mittweida, 09648, Mittweida, Germany
| | | | - V Joachim Haupt
- Biotechnology Center (BIOTEC), TU Dresden, 01307, Dresden, Germany.,PharmAI GmbH, Tatzberg 47, 01307, Dresden, Germany
| | | | | | - Dirk Labudde
- University of Applied Sciences Mittweida, 09648, Mittweida, Germany
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6
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Tawfik DS, Gruic-Sovulj I. How evolution shapes enzyme selectivity - lessons from aminoacyl-tRNA synthetases and other amino acid utilizing enzymes. FEBS J 2020; 287:1284-1305. [PMID: 31891445 DOI: 10.1111/febs.15199] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 12/08/2019] [Accepted: 12/30/2019] [Indexed: 12/21/2022]
Abstract
Aminoacyl-tRNA synthetases (AARSs) charge tRNA with their cognate amino acids. Many other enzymes use amino acids as substrates, yet discrimination against noncognate amino acids that threaten the accuracy of protein translation is a hallmark of AARSs. Comparing AARSs to these other enzymes allowed us to recognize patterns in molecular recognition and strategies used by evolution for exercising selectivity. Overall, AARSs are 2-3 orders of magnitude more selective than most other amino acid utilizing enzymes. AARSs also reveal the physicochemical limits of molecular discrimination. For example, amino acids smaller by a single methyl moiety present a discrimination ceiling of ~200, while larger ones can be discriminated by up to 105 -fold. In contrast, substrates larger by a hydroxyl group challenge AARS selectivity, due to promiscuous H-bonding with polar active site groups. This 'hydroxyl paradox' is resolved by editing. Indeed, when the physicochemical discrimination limits are reached, post-transfer editing - hydrolysis of tRNAs charged with noncognate amino acids, evolved. The editing site often selectively recognizes the edited noncognate substrate using the very same feature that the synthetic site could not efficiently discriminate against. Finally, the comparison to other enzymes also reveals that the selectivity of AARSs is an explicitly evolved trait, showing some clear examples of how selection acted not only to optimize catalytic efficiency with the target substrate, but also to abolish activity with noncognate threat substrates ('negative selection').
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Affiliation(s)
- Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
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7
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Bilus M, Semanjski M, Mocibob M, Zivkovic I, Cvetesic N, Tawfik DS, Toth-Petroczy A, Macek B, Gruic-Sovulj I. On the Mechanism and Origin of Isoleucyl-tRNA Synthetase Editing against Norvaline. J Mol Biol 2019; 431:1284-1297. [PMID: 30711543 DOI: 10.1016/j.jmb.2019.01.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/20/2019] [Accepted: 01/22/2019] [Indexed: 11/17/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs), the enzymes responsible for coupling tRNAs to their cognate amino acids, minimize translational errors by intrinsic hydrolytic editing. Here, we compared norvaline (Nva), a linear amino acid not coded for protein synthesis, to the proteinogenic, branched valine (Val) in their propensity to mistranslate isoleucine (Ile) in proteins. We show that in the synthetic site of isoleucyl-tRNA synthetase (IleRS), Nva and Val are activated and transferred to tRNA at similar rates. The efficiency of the synthetic site in pre-transfer editing of Nva and Val also appears to be similar. Post-transfer editing was, however, more rapid with Nva and consequently IleRS misaminoacylates Nva-tRNAIle at slower rate than Val-tRNAIle. Accordingly, an Escherichia coli strain lacking IleRS post-transfer editing misincorporated Nva and Val in the proteome to a similar extent and at the same Ile positions. However, Nva mistranslation inflicted higher toxicity than Val, in agreement with IleRS editing being optimized for hydrolysis of Nva-tRNAIle. Furthermore, we found that the evolutionary-related IleRS, leucyl- and valyl-tRNA synthetases (I/L/VRSs), all efficiently hydrolyze Nva-tRNAs even when editing of Nva seems redundant. We thus hypothesize that editing of Nva-tRNAs had already existed in the last common ancestor of I/L/VRSs, and that the editing domain of I/L/VRSs had primarily evolved to prevent infiltration of Nva into modern proteins.
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Affiliation(s)
- Mirna Bilus
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia
| | - Maja Semanjski
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen 72076, Germany
| | - Marko Mocibob
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia
| | - Igor Zivkovic
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia
| | - Nevena Cvetesic
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, and the MRC London Institute of Medical Sciences, London, W12 0NN, United Kingdom
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Agnes Toth-Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Boris Macek
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen 72076, Germany
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia.
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8
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Kaiser F, Bittrich S, Salentin S, Leberecht C, Haupt VJ, Krautwurst S, Schroeder M, Labudde D. Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases. PLoS Comput Biol 2018; 14:e1006101. [PMID: 29659563 PMCID: PMC5919687 DOI: 10.1371/journal.pcbi.1006101] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 04/26/2018] [Accepted: 03/20/2018] [Indexed: 12/22/2022] Open
Abstract
The origin of the machinery that realizes protein biosynthesis in all organisms is still unclear. One key component of this machinery are aminoacyl tRNA synthetases (aaRS), which ligate tRNAs to amino acids while consuming ATP. Sequence analyses revealed that these enzymes can be divided into two complementary classes. Both classes differ significantly on a sequence and structural level, feature different reaction mechanisms, and occur in diverse oligomerization states. The one unifying aspect of both classes is their function of binding ATP. We identified Backbone Brackets and Arginine Tweezers as most compact ATP binding motifs characteristic for each Class. Geometric analysis shows a structural rearrangement of the Backbone Brackets upon ATP binding, indicating a general mechanism of all Class I structures. Regarding the origin of aaRS, the Rodin-Ohno hypothesis states that the peculiar nature of the two aaRS classes is the result of their primordial forms, called Protozymes, being encoded on opposite strands of the same gene. Backbone Brackets and Arginine Tweezers were traced back to the proposed Protozymes and their more efficient successors, the Urzymes. Both structural motifs can be observed as pairs of residues in contemporary structures and it seems that the time of their addition, indicated by their placement in the ancient aaRS, coincides with the evolutionary trace of Proto- and Urzymes. Aminoacyl tRNA synthetases (aaRS) are primordial enzymes essential for interpretation and transfer of genetic information. Understanding the origin of the peculiarities observed with aaRS can explain what constituted the earliest life forms and how the genetic code was established. The increasing amount of experimentally determined three-dimensional structures of aaRS opens up new avenues for high-throughput analyses of molecular mechanisms. In this study, we present an exhaustive structural analysis of ATP binding motifs. We unveil an oppositional implementation of enzyme substrate binding in each aaRS Class. While Class I binds via interactions mediated by backbone hydrogen bonds, Class II uses a pair of arginine residues to establish salt bridges to its ATP ligand. We show how nature realized the binding of the same ligand species with completely different mechanisms. In addition, we demonstrate that sequence or even structure analysis for conserved residues may miss important functional aspects which can only be revealed by ligand interaction studies. Additionally, the placement of those key residues in the structure supports a popular hypothesis, which states that prototypic aaRS were once coded on complementary strands of the same gene.
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Affiliation(s)
- Florian Kaiser
- University of Applied Sciences Mittweida, Mittweida, Germany
- Biotechnology Center (BIOTEC), TU Dresden, Dresden, Germany
- * E-mail:
| | - Sebastian Bittrich
- University of Applied Sciences Mittweida, Mittweida, Germany
- Biotechnology Center (BIOTEC), TU Dresden, Dresden, Germany
| | | | - Christoph Leberecht
- University of Applied Sciences Mittweida, Mittweida, Germany
- Biotechnology Center (BIOTEC), TU Dresden, Dresden, Germany
| | | | | | | | - Dirk Labudde
- University of Applied Sciences Mittweida, Mittweida, Germany
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9
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Dulic M, Cvetesic N, Zivkovic I, Palencia A, Cusack S, Bertosa B, Gruic-Sovulj I. Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase. J Mol Biol 2018; 430:1-16. [DOI: 10.1016/j.jmb.2017.10.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/02/2017] [Accepted: 10/08/2017] [Indexed: 10/18/2022]
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10
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Bacusmo JM, Kuzmishin AB, Cantara WA, Goto Y, Suga H, Musier-Forsyth K. Quality control by trans-editing factor prevents global mistranslation of non-protein amino acid α-aminobutyrate. RNA Biol 2017; 15:576-585. [PMID: 28737471 DOI: 10.1080/15476286.2017.1353846] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Accuracy in protein biosynthesis is maintained through multiple pathways, with a critical checkpoint occurring at the tRNA aminoacylation step catalyzed by aminoacyl-tRNA synthetases (ARSs). In addition to the editing functions inherent to some synthetases, single-domain trans-editing factors, which are structurally homologous to ARS editing domains, have evolved as alternative mechanisms to correct mistakes in aminoacyl-tRNA synthesis. To date, ARS-like trans-editing domains have been shown to act on specific tRNAs that are mischarged with genetically encoded amino acids. However, structurally related non-protein amino acids are ubiquitous in cells and threaten the proteome. Here, we show that a previously uncharacterized homolog of the bacterial prolyl-tRNA synthetase (ProRS) editing domain edits a known ProRS aminoacylation error, Ala-tRNAPro, but displays even more robust editing of tRNAs misaminoacylated with the non-protein amino acid α-aminobutyrate (2-aminobutyrate, Abu) in vitro and in vivo. Our results indicate that editing by trans-editing domains such as ProXp-x studied here may offer advantages to cells, especially under environmental conditions where concentrations of non-protein amino acids may challenge the substrate specificity of ARSs.
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Affiliation(s)
- Jo Marie Bacusmo
- a Department of Chemistry and Biochemistry , The Ohio State University , Columbus , OH , USA.,b Center for RNA Biology , The Ohio State University , Columbus , OH , USA
| | - Alexandra B Kuzmishin
- a Department of Chemistry and Biochemistry , The Ohio State University , Columbus , OH , USA.,b Center for RNA Biology , The Ohio State University , Columbus , OH , USA
| | - William A Cantara
- a Department of Chemistry and Biochemistry , The Ohio State University , Columbus , OH , USA.,b Center for RNA Biology , The Ohio State University , Columbus , OH , USA
| | - Yuki Goto
- c Department of Chemistry , Graduate School of Science, The University of Tokyo , Bunkyo , Tokyo , Japan
| | - Hiroaki Suga
- c Department of Chemistry , Graduate School of Science, The University of Tokyo , Bunkyo , Tokyo , Japan
| | - Karin Musier-Forsyth
- a Department of Chemistry and Biochemistry , The Ohio State University , Columbus , OH , USA.,b Center for RNA Biology , The Ohio State University , Columbus , OH , USA
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11
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Discovery of a novel prolyl-tRNA synthetase inhibitor and elucidation of its binding mode to the ATP site in complex with l-proline. Biochem Biophys Res Commun 2017; 488:393-399. [PMID: 28501621 DOI: 10.1016/j.bbrc.2017.05.064] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 05/10/2017] [Indexed: 11/23/2022]
Abstract
Prolyl-tRNA synthetase (PRS) is a member of the aminoacyl-tRNA synthetase family of enzymes and catalyzes the synthesis of prolyl-tRNAPro using ATP, l-proline, and tRNAPro as substrates. An ATP-dependent PRS inhibitor, halofuginone, was shown to suppress autoimmune responses, suggesting that the inhibition of PRS is a potential therapeutic approach for inflammatory diseases. Although a few PRS inhibitors have been derivatized from natural sources or substrate mimetics, small-molecule human PRS inhibitors have not been reported. In this study, we discovered a novel series of pyrazinamide PRS inhibitors from a compound library using pre-transfer editing activity of human PRS enzyme. Steady-state biochemical analysis on the inhibitory mode revealed its distinctive characteristics of inhibition with proline uncompetition and ATP competition. The binding activity of a representative compound was time-dependently potentiated by the presence of l-proline with Kd of 0.76 nM. Thermal shift assays demonstrated the stabilization of PRS in complex with l-proline and pyrazinamide PRS inhibitors. The binding mode of the PRS inhibitor to the ATP site of PRS enzyme was elucidated using the ternary complex crystal structure with l-proline. The results demonstrated the different inhibitory and binding mode of pyrazinamide PRS inhibitors from preceding halofuginone. Furthermore, the PRS inhibitor inhibited intracellular protein synthesis via a different mode than halofuginone. In conclusion, we have identified a novel drug-like PRS inhibitor with a distinctive binding mode. This inhibitor was effective in a cellular context. Thus, the series of PRS inhibitors are considered to be applicable to further development with differentiation from preceding halofuginone.
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12
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Kartvelishvili E, Tworowski D, Vernon H, Moor N, Wang J, Wong LJ, Chrzanowska-Lightowlers Z, Safro M. Kinetic and structural changes in HsmtPheRS, induced by pathogenic mutations in human FARS2. Protein Sci 2017; 26:1505-1516. [PMID: 28419689 PMCID: PMC5521548 DOI: 10.1002/pro.3176] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/11/2017] [Accepted: 04/11/2017] [Indexed: 12/13/2022]
Abstract
Mutations in the mitochondrial aminoacyl-tRNA synthetases (mtaaRSs) can cause profound clinical presentations, and have manifested as diseases with very selective tissue specificity. To date most of the mtaaRS mutations could be phenotypically recognized, such that clinicians could identify the affected mtaaRS from the symptoms alone. Among the recently reported pathogenic variants are point mutations in FARS2 gene, encoding the human mitochondrial PheRS. Patient symptoms range from spastic paraplegia to fatal infantile Alpers encephalopathy. How clinical manifestations of these mutations relate to the changes in three-dimensional structures and kinetic characteristics remains unclear, although impaired aminoacylation has been proposed as possible etiology of diseases. Here, we report four crystal structures of HsmtPheRS mutants, and extensive MD simulations for wild-type and nine mutants to reveal the structural changes on dynamic trajectories of HsmtPheRS. Using steady-state kinetic measurements of phenylalanine activation and tRNAPhe aminoacylation, we gained insight into the structural and kinetic effects of mitochondrial disease-related mutations in FARS2 gene.
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Affiliation(s)
| | - Dmitry Tworowski
- Department of Structural Biology, Weizmann Institute of Science, Israel
| | - Hilary Vernon
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore
| | - Nina Moor
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Jing Wang
- Ambry Genetics, California.,Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Lee-Jun Wong
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Mark Safro
- Department of Structural Biology, Weizmann Institute of Science, Israel
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13
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Wei W, Gauld JW, Monard G. Pretransfer Editing in Threonyl-tRNA Synthetase: Roles of Differential Solvent Accessibility and Intermediate Stabilization. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Wanlei Wei
- Department
of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - James W. Gauld
- Department
of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Gerald Monard
- Université de Lorraine, UMR 7565 SRSMC, Boulevard des Aiguillettes B.P. 70239, F-54506 Vandoeuvre-les-Nancy, France
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14
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Cvetesic N, Gruic-Sovulj I. Synthetic and editing reactions of aminoacyl-tRNA synthetases using cognate and non-cognate amino acid substrates. Methods 2016; 113:13-26. [PMID: 27713080 DOI: 10.1016/j.ymeth.2016.09.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/29/2016] [Accepted: 09/29/2016] [Indexed: 11/19/2022] Open
Abstract
The covalent coupling of cognate amino acid-tRNA pairs by corresponding aminoacyl-tRNA synthetases (aaRS) defines the genetic code and provides aminoacylated tRNAs for ribosomal protein synthesis. Besides the cognate substrate, some non-cognate amino acids may also compete for tRNA aminoacylation. However, their participation in protein synthesis is generally prevented by an aaRS proofreading activity located in the synthetic site and in a separate editing domain. These mechanisms, coupled with the ability of certain aaRSs to discriminate well against non-cognate amino acids in the synthetic reaction alone, define the accuracy of the aminoacylation reaction. aaRS quality control may also act as a gatekeeper for the standard genetic code and prevents infiltration by natural amino acids that are not normally coded for protein biosynthesis. This latter finding has reinforced interest in understanding the principles that govern discrimination against a range of potential non-cognate amino acids. This paper presents an overview of the kinetic assays that have been established for monitoring synthetic and editing reactions with cognate and non-cognate amino acid substrates. Taking into account the peculiarities of non-cognate reactions, the specific controls needed and the dedicated experimental designs are discussed in detail. Kinetic partitioning within the synthetic and editing sites controls the balance between editing and aminoacylation. We describe in detail steady-state and single-turnover approaches for the analysis of synthetic and editing reactions, which ultimately enable mechanisms of amino acid discrimination to be determined.
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Affiliation(s)
- Nevena Cvetesic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia.
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15
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Abstract
Aminoacyl-tRNA synthetases (aaRSs) are modular enzymes globally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation. Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g., in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show huge structural plasticity related to function and limited idiosyncrasies that are kingdom or even species specific (e.g., the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS). Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably between distant groups such as Gram-positive and Gram-negative Bacteria. The review focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation, and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulated in last two decades is reviewed, showing how the field moved from essentially reductionist biology towards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRS paralogs (e.g., during cell wall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointed throughout the review and distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Mathias Springer
- Université Paris Diderot, Sorbonne Cité, UPR9073 CNRS, IBPC, 75005 Paris, France
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16
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The evolution of Class II Aminoacyl-tRNA synthetases and the first code. FEBS Lett 2015; 589:3499-507. [DOI: 10.1016/j.febslet.2015.10.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/02/2015] [Accepted: 10/05/2015] [Indexed: 11/24/2022]
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17
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Cvetesic N, Bilus M, Gruic-Sovulj I. The tRNA A76 Hydroxyl Groups Control Partitioning of the tRNA-dependent Pre- and Post-transfer Editing Pathways in Class I tRNA Synthetase. J Biol Chem 2015; 290:13981-91. [PMID: 25873392 DOI: 10.1074/jbc.m115.648568] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 11/06/2022] Open
Abstract
Aminoacyl-tRNA synthetases catalyze ATP-dependent covalent coupling of cognate amino acids and tRNAs for ribosomal protein synthesis. Escherichia coli isoleucyl-tRNA synthetase (IleRS) exploits both the tRNA-dependent pre- and post-transfer editing pathways to minimize errors in translation. However, the molecular mechanisms by which tRNA(Ile) organizes the synthetic site to enhance pre-transfer editing, an idiosyncratic feature of IleRS, remains elusive. Here we show that tRNA(Ile) affects both the synthetic and editing reactions localized within the IleRS synthetic site. In a complex with cognate tRNA, IleRS exhibits a 10-fold faster aminoacyl-AMP hydrolysis and a 10-fold drop in amino acid affinity relative to the free enzyme. Remarkably, the specificity against non-cognate valine was not improved by the presence of tRNA in either of these processes. Instead, amino acid specificity is determined by the protein component per se, whereas the tRNA promotes catalytic performance of the synthetic site, bringing about less error-prone and kinetically optimized isoleucyl-tRNA(Ile) synthesis under cellular conditions. Finally, the extent to which tRNA(Ile) modulates activation and pre-transfer editing is independent of the intactness of its 3'-end. This finding decouples aminoacylation and pre-transfer editing within the IleRS synthetic site and further demonstrates that the A76 hydroxyl groups participate in post-transfer editing only. The data are consistent with a model whereby the 3'-end of the tRNA remains free to sample different positions within the IleRS·tRNA complex, whereas the fine-tuning of the synthetic site is attained via conformational rearrangement of the enzyme through the interactions with the remaining parts of the tRNA body.
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Affiliation(s)
- Nevena Cvetesic
- From the Department of Chemistry, University of Zagreb, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Mirna Bilus
- From the Department of Chemistry, University of Zagreb, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Ita Gruic-Sovulj
- From the Department of Chemistry, University of Zagreb, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia
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18
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Dulic M, Perona JJ, Gruic-Sovulj I. Determinants for tRNA-dependent pretransfer editing in the synthetic site of isoleucyl-tRNA synthetase. Biochemistry 2014; 53:6189-98. [PMID: 25207837 PMCID: PMC4188249 DOI: 10.1021/bi5007699] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The
accurate expression of genetic information relies on the fidelity
of amino acid–tRNA coupling by aminoacyl-tRNA synthetases (aaRS).
When the specificity against structurally similar noncognate amino
acids in the synthetic reaction does not support a threshold fidelity
level for translation, the aaRS employ intrinsic hydrolytic editing
to correct errors in aminoacylation. Escherichia coli isoleucyl-tRNA synthetase (EcIleRS) is a class I aaRS that is notable
for its use of tRNA-dependent pretransfer editing to hydrolyze noncognate
valyl-adenylate prior to aminoacyl-tRNA formation. On the basis of
the finding that IleRS possessing an inactivated post-transfer editing
domain is still capable of robust tRNA-dependent editing, we have
recently proposed that the pretransfer editing activity resides within
the synthetic site. Here we apply an improved methodology that allows
quantitation of the AMP fraction that arises particularly from tRNA-dependent
aa-AMP hydrolysis. By this approach, we demonstrate that tRNA-dependent
pretransfer editing accounts for nearly one-third of the total proofreading
by EcIleRS and that a highly conserved tyrosine within the synthetic
site modulates both editing and aminoacylation. Therefore, synthesis
of aminoacyl-tRNA and hydrolysis of aminoacyl-adenylates employ overlapping
amino acid determinants. We suggest that this overlap hindered the
evolution of synthetic site-based pretransfer editing as the predominant
proofreading pathway, because that activity is difficult to accommodate
in the context of efficient aminoacyl-tRNA synthesis. Instead, the
acquisition of a spatially separate domain dedicated to post-transfer
editing alone allowed for the development of a powerful deacylation
machinery that effectively competes with dissociation of misacylated
tRNAs.
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Affiliation(s)
- Morana Dulic
- Department of Chemistry, Faculty of Science, University of Zagreb , Horvatovac 102a, 10000 Zagreb, Croatia
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19
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Cvetesic N, Palencia A, Halasz I, Cusack S, Gruic-Sovulj I. The physiological target for LeuRS translational quality control is norvaline. EMBO J 2014; 33:1639-53. [PMID: 24935946 DOI: 10.15252/embj.201488199] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The fidelity of protein synthesis depends on the capacity of aminoacyl-tRNA synthetases (AARSs) to couple only cognate amino acid-tRNA pairs. If amino acid selectivity is compromised, fidelity can be ensured by an inherent AARS editing activity that hydrolyses mischarged tRNAs. Here, we show that the editing activity of Escherichia coli leucyl-tRNA synthetase (EcLeuRS) is not required to prevent incorrect isoleucine incorporation. Rather, as shown by kinetic, structural and in vivo approaches, the prime biological function of LeuRS editing is to prevent mis-incorporation of the non-standard amino acid norvaline. This conclusion follows from a reassessment of the discriminatory power of LeuRS against isoleucine and the demonstration that a LeuRS editing-deficient E. coli strain grows normally in high concentrations of isoleucine but not under oxygen deprivation conditions when norvaline accumulates to substantial levels. Thus, AARS-based translational quality control is a key feature for bacterial adaptive response to oxygen deprivation. The non-essential role for editing under normal bacterial growth has important implications for the development of resistance to antimicrobial agents targeting the LeuRS editing site.
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Affiliation(s)
- Nevena Cvetesic
- Department of Chemistry, Faculty of Science University of Zagreb, Zagreb, Croatia
| | - Andrés Palencia
- European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS UMI 3265, France
| | | | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS UMI 3265, France
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science University of Zagreb, Zagreb, Croatia
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20
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Boyarshin KS, Priss AE, Kriklivyi IA, Kovalenko OP, Yaremchuk AD, Tukalo MA. Role of tRNAPro in pretransfer editing of alanine by prolyl-tRNA synthetase. ACTA ACUST UNITED AC 2013. [DOI: 10.7124/bc.00082d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- K. S. Boyarshin
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - A. E. Priss
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - I. A. Kriklivyi
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - O. P. Kovalenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - A. D. Yaremchuk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - M. A. Tukalo
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
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21
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Zhou X, Wang E. Transfer RNA: a dancer between charging and mis-charging for protein biosynthesis. SCIENCE CHINA-LIFE SCIENCES 2013; 56:921-32. [PMID: 23982864 DOI: 10.1007/s11427-013-4542-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/13/2013] [Indexed: 01/17/2023]
Abstract
Transfer RNA plays a fundamental role in the protein biosynthesis as an adaptor molecule by functioning as a biological link between the genetic nucleotide sequence in the mRNA and the amino acid sequence in the protein. To perform its role in protein biosynthesis, it has to be accurately recognized by aminoacyl-tRNA synthetases (aaRSs) to generate aminoacyl-tRNAs (aa-tRNAs). The correct pairing between an amino acid with its cognate tRNA is crucial for translational quality control. Production and utilization of mis-charged tRNAs are usually detrimental for all the species, resulting in cellular dysfunctions. Correct aa-tRNAs formation is collectively controlled by aaRSs with distinct mechanisms and/or other trans-factors. However, in very limited instances, mis-charged tRNAs are intermediate for specific pathways or essential components for the translational machinery. Here, from the point of accuracy in tRNA charging, we review our understanding about the mechanism ensuring correct aa-tRNA generation. In addition, some unique mis-charged tRNA species necessary for the organism are also briefly described.
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Affiliation(s)
- Xiaolong Zhou
- Center for RNA Research, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
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22
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Caetano-Anollés G, Wang M, Caetano-Anollés D. Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility. PLoS One 2013; 8:e72225. [PMID: 23991065 PMCID: PMC3749098 DOI: 10.1371/journal.pone.0072225] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 07/07/2013] [Indexed: 11/18/2022] Open
Abstract
The genetic code shapes the genetic repository. Its origin has puzzled molecular scientists for over half a century and remains a long-standing mystery. Here we show that the origin of the genetic code is tightly coupled to the history of aminoacyl-tRNA synthetase enzymes and their interactions with tRNA. A timeline of evolutionary appearance of protein domain families derived from a structural census in hundreds of genomes reveals the early emergence of the 'operational' RNA code and the late implementation of the standard genetic code. The emergence of codon specificities and amino acid charging involved tight coevolution of aminoacyl-tRNA synthetases and tRNA structures as well as episodes of structural recruitment. Remarkably, amino acid and dipeptide compositions of single-domain proteins appearing before the standard code suggest archaic synthetases with structures homologous to catalytic domains of tyrosyl-tRNA and seryl-tRNA synthetases were capable of peptide bond formation and aminoacylation. Results reveal that genetics arose through coevolutionary interactions between polypeptides and nucleic acid cofactors as an exacting mechanism that favored flexibility and folding of the emergent proteins. These enhancements of phenotypic robustness were likely internalized into the emerging genetic system with the early rise of modern protein structure.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
| | - Minglei Wang
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Derek Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
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23
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Santra M, Bagchi B. Kinetic proofreading at single molecular level: aminoacylation of tRNA(Ile) and the role of water as an editor. PLoS One 2013; 8:e66112. [PMID: 23840412 PMCID: PMC3688713 DOI: 10.1371/journal.pone.0066112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Accepted: 05/02/2013] [Indexed: 11/25/2022] Open
Abstract
Proofreading/editing in protein synthesis is essential for accurate translation of information from the genetic code. In this article we present a theoretical investigation of efficiency of a kinetic proofreading mechanism that employs hydrolysis of the wrong substrate as the discriminatory step in enzyme catalytic reactions. We consider aminoacylation of tRNAIle which is a crucial step in protein synthesis and for which experimental results are now available. We present an augmented kinetic scheme and then employ methods of stochastic simulation algorithm to obtain time dependent concentrations of different substances involved in the reaction and their rates of formation. We obtain the rates of product formation and ATP hydrolysis for both correct and wrong substrates (isoleucine and valine in our case, respectively), in single molecular enzyme as well as ensemble enzyme kinetics. The present theoretical scheme correctly reproduces (i) the amplitude of the discrimination factor in the overall rates between isoleucine and valine which is obtained as (1.8×102).(4.33×102) = 7.8×104, (ii) the rates of ATP hydrolysis for both Ile and Val at different substrate concentrations in the aminoacylation of tRNAIle. The present study shows a non-michaelis type dependence of rate of reaction on tRNAIle concentration in case of valine. The overall editing in steady state is found to be independent of amino acid concentration. Interestingly, the computed ATP hydrolysis rate for valine at high substrate concentration is same as the rate of formation of Ile-tRNAIle whereas at intermediate substrate concentration the ATP hydrolysis rate is relatively low. We find that the presence of additional editing domain in class I editing enzyme makes the kinetic proofreading more efficient through enhanced hydrolysis of wrong product at the editing CP1 domain.
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Affiliation(s)
- Mantu Santra
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, India
- * E-mail:
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24
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Vargas-Rodriguez O, Musier-Forsyth K. Exclusive use of trans-editing domains prevents proline mistranslation. J Biol Chem 2013; 288:14391-14399. [PMID: 23564458 DOI: 10.1074/jbc.m113.467795] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) catalyze the attachment of specific amino acids to cognate tRNAs. Although the accuracy of this process is critical for overall translational fidelity, similar sizes of many amino acids provide a challenge to ARSs. For example, prolyl-tRNA synthetases (ProRSs) mischarge alanine and cysteine onto tRNA(Pro). Many bacterial ProRSs possess an alanine-specific proofreading domain (INS) but lack the capability to edit Cys-tRNA(Pro). Instead, Cys-tRNA(Pro) is cleared by a single-domain homolog of INS, the trans-editing YbaK protein. A global bioinformatics analysis revealed that there are six types of "INS-like" proteins. In addition to INS and YbaK, four additional single-domain homologs are widely distributed throughout bacteria: ProXp-ala (formerly named PrdX), ProXp-x (annotated as ProX), ProXp-y (annotated as YeaK), and ProXp-z (annotated as PA2301). The last three are domains of unknown function. Whereas many bacteria encode a ProRS containing an INS domain in addition to YbaK, many other combinations of INS-like proteins exist throughout the bacterial kingdom. Here, we focus on Caulobacter crescentus, which encodes a ProRS with a truncated INS domain that lacks catalytic activity, as well as YbaK and ProXp-ala. We show that C. crescentus ProRS can readily form Cys- and Ala-tRNA(Pro), and deacylation studies confirmed that these species are cleared by C. crescentus YbaK and ProXp-ala, respectively. Substrate specificity of C. crescentus ProXp-ala is determined, in part, by elements in the acceptor stem of tRNA(Pro) and further ensured through collaboration with elongation factor Tu. These results highlight the diversity of approaches used to prevent proline mistranslation and reveal a novel triple-sieve mechanism of editing that relies exclusively on trans-editing factors.
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Affiliation(s)
- Oscar Vargas-Rodriguez
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210.
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25
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Rokov-Plavec J, Lesjak S, Gruic-Sovulj I, Mocibob M, Dulic M, Weygand-Durasevic I. Substrate recognition and fidelity of maize seryl-tRNA synthetases. Arch Biochem Biophys 2013; 529:122-30. [DOI: 10.1016/j.abb.2012.11.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 11/28/2012] [Accepted: 11/29/2012] [Indexed: 12/27/2022]
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26
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Perona JJ, Gruic-Sovulj I. Synthetic and editing mechanisms of aminoacyl-tRNA synthetases. Top Curr Chem (Cham) 2013; 344:1-41. [PMID: 23852030 DOI: 10.1007/128_2013_456] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRS) ensure the faithful transmission of genetic information in all living cells. The 24 known aaRS families are divided into 2 structurally distinct classes (class I and class II), each featuring a catalytic domain with a common fold that binds ATP, amino acid, and the 3'-terminus of tRNA. In a common two-step reaction, each aaRS first uses the energy stored in ATP to synthesize an activated aminoacyl adenylate intermediate. In the second step, either the 2'- or 3'-hydroxyl oxygen atom of the 3'-A76 tRNA nucleotide functions as a nucleophile in synthesis of aminoacyl-tRNA. Ten of the 24 aaRS families are unable to distinguish cognate from noncognate amino acids in the synthetic reactions alone. These enzymes possess additional editing activities for hydrolysis of misactivated amino acids and misacylated tRNAs, with clearance of the latter species accomplished in spatially separate post-transfer editing domains. A distinct class of trans-acting proteins that are homologous to class II editing domains also perform hydrolytic editing of some misacylated tRNAs. Here we review essential themes in catalysis with a view toward integrating the kinetic, stereochemical, and structural mechanisms of the enzymes. Although the aaRS have now been the subject of investigation for many decades, it will be seen that a significant number of questions regarding fundamental catalytic functioning still remain unresolved.
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Affiliation(s)
- John J Perona
- Department of Chemistry, Portland State University, 751, Portland, OR, 97207, USA,
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27
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Abstract
Aminoacyl-tRNAsynthetases (aaRSs) are modular enzymesglobally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation.Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g.,in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show hugestructural plasticity related to function andlimited idiosyncrasies that are kingdom or even speciesspecific (e.g.,the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS).Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably betweendistant groups such as Gram-positive and Gram-negative Bacteria.Thereview focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation,and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulatedin last two decades is reviewed,showing how thefield moved from essentially reductionist biologytowards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRSparalogs (e.g., during cellwall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointedthroughout the reviewand distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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28
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Zhou XL, Ruan ZR, Huang Q, Tan M, Wang ED. Translational fidelity maintenance preventing Ser mis-incorporation at Thr codon in protein from eukaryote. Nucleic Acids Res 2012; 41:302-14. [PMID: 23093606 PMCID: PMC3592468 DOI: 10.1093/nar/gks982] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aminoacyl-tRNA synthetase (aaRS) catalyzes the first step of protein synthesis, producing aminoacyl-tRNAs as building blocks. Eukaryotic aaRS differs from its prokaryotic counterpart in terminal extension or insertion. Moreover, the editing function of aaRSs is an indispensable checkpoint excluding non-cognate amino acids at a given codon and ensuring overall translational fidelity. We found higher eukaryotes encode two cytoplasmic threonyl-tRNA synthetases (ThrRSs) with difference in N-terminus. The longer isoform is more closely related to the ThrRSs of higher eukaryotes than to those of lower eukaryotes. A yeast strain was generated to include deletion of the thrS gene encoding ThrRS. Combining in vitro biochemical and in vivo genetic data, ThrRSs from eukaryotic cytoplasm were systematically analyzed, and role of the eukaryotic cytoplasmic ThrRS-specific N-terminal extension was elucidated. Furthermore, the mechanisms of aminoacylation and editing activity mediated by Saccharomyces cerevisiae ThrRS (ScThrRS) were clarified. Interestingly, yeast cells were tolerant of variation at the editing active sites of ScThrRS without significant Thr-to-Ser conversion in the proteome even under significant environmental stress, implying checkpoints downstream of aminoacylation to provide a further quality control mechanism for the yeast translation system. This study has provided the first comprehensive elucidation of the translational fidelity control mechanism of eukaryotic ThrRS.
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Affiliation(s)
- Xiao-Long Zhou
- Center for RNA research, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
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29
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Larson ET, Kim JE, Napuli AJ, Verlinde CLMJ, Fan E, Zucker FH, Van Voorhis WC, Buckner FS, Hol WGJ, Merritt EA. Structure of the prolyl-tRNA synthetase from the eukaryotic pathogen Giardia lamblia. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1194-200. [PMID: 22948920 PMCID: PMC3489102 DOI: 10.1107/s0907444912024699] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 05/30/2012] [Indexed: 11/10/2022]
Abstract
The genome of the human intestinal parasite Giardia lamblia contains only a single aminoacyl-tRNA synthetase gene for each amino acid. The Giardia prolyl-tRNA synthetase gene product was originally misidentified as a dual-specificity Pro/Cys enzyme, in part owing to its unexpectedly high off-target activation of cysteine, but is now believed to be a normal representative of the class of archaeal/eukaryotic prolyl-tRNA synthetases. The 2.2 Å resolution crystal structure of the G. lamblia enzyme presented here is thus the first structure determination of a prolyl-tRNA synthetase from a eukaryote. The relative occupancies of substrate (proline) and product (prolyl-AMP) in the active site are consistent with half-of-the-sites reactivity, as is the observed biphasic thermal denaturation curve for the protein in the presence of proline and MgATP. However, no corresponding induced asymmetry is evident in the structure of the protein. No thermal stabilization is observed in the presence of cysteine and ATP. The implied low affinity for the off-target activation product cysteinyl-AMP suggests that translational fidelity in Giardia is aided by the rapid release of misactivated cysteine.
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Affiliation(s)
- Eric T. Larson
- Medical Structural Genomics of Pathogenic Protozoa, http://msgpp.org, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jessica E. Kim
- Medical Structural Genomics of Pathogenic Protozoa, http://msgpp.org, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alberto J. Napuli
- Medical Structural Genomics of Pathogenic Protozoa, http://msgpp.org, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Christophe L. M. J. Verlinde
- Medical Structural Genomics of Pathogenic Protozoa, http://msgpp.org, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Erkang Fan
- Medical Structural Genomics of Pathogenic Protozoa, http://msgpp.org, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Frank H. Zucker
- Medical Structural Genomics of Pathogenic Protozoa, http://msgpp.org, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Wesley C. Van Voorhis
- Medical Structural Genomics of Pathogenic Protozoa, http://msgpp.org, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Frederick S. Buckner
- Medical Structural Genomics of Pathogenic Protozoa, http://msgpp.org, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Wim G. J. Hol
- Medical Structural Genomics of Pathogenic Protozoa, http://msgpp.org, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Ethan A. Merritt
- Medical Structural Genomics of Pathogenic Protozoa, http://msgpp.org, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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30
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Ling J, Peterson KM, Simonovic I, Söll D, Simonovic M. The mechanism of pre-transfer editing in yeast mitochondrial threonyl-tRNA synthetase. J Biol Chem 2012; 287:28518-25. [PMID: 22773845 DOI: 10.1074/jbc.m112.372920] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Accurate translation of mRNA into protein is a fundamental biological process critical for maintaining normal cellular functions. To ensure translational fidelity, aminoacyl-tRNA synthetases (aaRSs) employ pre-transfer and post-transfer editing activities to hydrolyze misactivated and mischarged amino acids, respectively. Whereas post-transfer editing, which requires either a specialized domain in aaRS or a trans-protein factor, is well described, the mechanism of pre-transfer editing is less understood. Here, we show that yeast mitochondrial threonyl-tRNA synthetase (MST1), which lacks an editing domain, utilizes pre-transfer editing to discriminate against serine. MST1 misactivates serine and edits seryl adenylate (Ser-AMP) in a tRNA-independent manner. MST1 hydrolyzes 80% of misactivated Ser-AMP at a rate 4-fold higher than that for the cognate threonyl adenylate (Thr-AMP) while releasing 20% of Ser-AMP into the solution. To understand the mechanism of pre-transfer editing, we solved the crystal structure of MST1 complexed with an analog of Ser-AMP. The binding of the Ser-AMP analog to MST1 induces conformational changes in the aminoacylation active site, and it positions a potential hydrolytic water molecule more favorably for nucleophilic attack. In addition, inhibition results reveal that the Ser-AMP analog binds the active site 100-fold less tightly than the Thr-AMP analog. In conclusion, we propose that the plasticity of the aminoacylation site in MST1 allows binding of Ser-AMP and the appropriate positioning of the hydrolytic water molecule.
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Affiliation(s)
- Jiqiang Ling
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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31
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Guo LT, Helgadóttir S, Söll D, Ling J. Rational design and directed evolution of a bacterial-type glutaminyl-tRNA synthetase precursor. Nucleic Acids Res 2012; 40:7967-74. [PMID: 22661575 PMCID: PMC3439900 DOI: 10.1093/nar/gks507] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Protein biosynthesis requires aminoacyl-transfer RNA (tRNA) synthetases to provide aminoacyl-tRNA substrates for the ribosome. Most bacteria and all archaea lack a glutaminyl-tRNA synthetase (GlnRS); instead, Gln-tRNAGln is produced via an indirect pathway: a glutamyl-tRNA synthetase (GluRS) first attaches glutamate (Glu) to tRNAGln, and an amidotransferase converts Glu-tRNAGln to Gln-tRNAGln. The human pathogen Helicobacter pylori encodes two GluRS enzymes, with GluRS2 specifically aminoacylating Glu onto tRNAGln. It was proposed that GluRS2 is evolving into a bacterial-type GlnRS. Herein, we have combined rational design and directed evolution approaches to test this hypothesis. We show that, in contrast to wild-type (WT) GlnRS2, an engineered enzyme variant (M110) with seven amino acid changes is able to rescue growth of the temperature-sensitive Escherichia coli glnS strain UT172 at its non-permissive temperature. In vitro kinetic analyses reveal that WT GluRS2 selectively acylates Glu over Gln, whereas M110 acylates Gln 4-fold more efficiently than Glu. In addition, M110 hydrolyzes adenosine triphosphate 2.5-fold faster in the presence of Glu than Gln, suggesting that an editing activity has evolved in this variant to discriminate against Glu. These data imply that GluRS2 is a few steps away from evolving into a GlnRS and provides a paradigm for studying aminoacyl-tRNA synthetase evolution using directed engineering approaches.
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Affiliation(s)
- Li-Tao Guo
- Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Sunna Helgadóttir
- Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
- *To whom correspondence should be addressed. Tel: +1 203 432 6205; Fax: +1 203 432 6202;
| | - Jiqiang Ling
- Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
- Correspondence may also be addressed to Dieter Söll. Tel: +1 203 432 6200; Fax: +1 203 432 6202;
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32
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Cvetesic N, Perona JJ, Gruic-Sovulj I. Kinetic partitioning between synthetic and editing pathways in class I aminoacyl-tRNA synthetases occurs at both pre-transfer and post-transfer hydrolytic steps. J Biol Chem 2012; 287:25381-94. [PMID: 22648413 DOI: 10.1074/jbc.m112.372151] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Comprehensive steady-state and transient kinetic studies of the synthetic and editing activities of Escherichia coli leucyl-tRNA synthetase (LeuRS) demonstrate that the enzyme depends almost entirely on post-transfer editing to endow the cell with specificity against incorporation of norvaline into protein. Among the three class I tRNA synthetases possessing a dedicated post-transfer editing domain (connective peptide 1; CP1 domain), LeuRS resembles valyl-tRNA synthetase in its reliance on post-transfer editing, whereas isoleucyl-tRNA synthetase differs in retaining a distinct tRNA-dependent synthetic site pre-transfer editing activity to clear noncognate amino acids before misacylation. Further characterization of the post-transfer editing activity in LeuRS by single-turnover kinetics demonstrates that the rate-limiting step is dissociation of deacylated tRNA and/or amino acid product and highlights the critical role of a conserved aspartate residue in mediating the first-order hydrolytic steps on the enzyme. Parallel analyses of adenylate and aminoacyl-tRNA formation reactions by wild-type and mutant LeuRS demonstrate that the efficiency of post-transfer editing is controlled by kinetic partitioning between hydrolysis and dissociation of misacylated tRNA and shows that trans editing after rebinding is a competent kinetic pathway. Together with prior analyses of isoleucyl-tRNA synthetase and valyl-tRNA synthetase, these experiments provide the basis for a comprehensive model of editing by class I tRNA synthetases, in which kinetic partitioning plays an essential role at both pre-transfer and post-transfer steps.
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Affiliation(s)
- Nevena Cvetesic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
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33
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Keller TL, Zocco D, Sundrud MS, Hendrick M, Edenius M, Yum J, Kim YJ, Lee HK, Cortese JF, Wirth DF, Dignam JD, Rao A, Yeo CY, Mazitschek R, Whitman M. Halofuginone and other febrifugine derivatives inhibit prolyl-tRNA synthetase. Nat Chem Biol 2012; 8:311-7. [PMID: 22327401 PMCID: PMC3281520 DOI: 10.1038/nchembio.790] [Citation(s) in RCA: 276] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 11/22/2011] [Indexed: 01/01/2023]
Abstract
Febrifugine, one of the fifty fundamental herbs of traditional Chinese medicine, has been characterized for its therapeutic activity whilst its molecular target has remained unknown. Febrifugine derivatives have been used to treat malaria, cancer, fibrosis, and inflammatory disease. We recently demonstrated that halofuginone (HF), a widely studied derivative of febrifugine, inhibits the development of Th17-driven autoimmunity in a mouse model of multiple sclerosis by activating the amino acid response pathway (AAR). Here we show that HF binds glutamyl-prolyl-tRNA synthetase (EPRS) inhibiting prolyl-tRNA synthetase activity; this inhibition is reversed by the addition of exogenous proline or EPRS. We further show that inhibition of EPRS underlies the broad bioactivities of this family of natural products. This work both explains the molecular mechanism of a promising family of therapeutics, and highlights the AAR pathway as an important drug target for promoting inflammatory resolution.
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Affiliation(s)
- Tracy L Keller
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, Massachusetts, USA.
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34
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Yadavalli SS, Ibba M. Quality control in aminoacyl-tRNA synthesis its role in translational fidelity. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 86:1-43. [PMID: 22243580 DOI: 10.1016/b978-0-12-386497-0.00001-3] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Accurate translation of mRNA into protein is vital for maintenance of cellular integrity. Translational fidelity is achieved by two key events: synthesis of correctly paired aminoacyl-tRNAs by aminoacyl-tRNA synthetases (aaRSs) and stringent selection of aminoacyl-tRNAs (aa-tRNAs) by the ribosome. AaRSs define the genetic code by catalyzing the formation of precise aminoacyl ester-linked tRNAs via a two-step reaction. AaRSs ensure faithful aa-tRNA synthesis via high substrate selectivity and/or by proofreading (editing) of noncognate products. About half of the aaRSs rely on proofreading mechanisms to achieve high levels of accuracy in aminoacylation. Editing functions in aaRSs contribute to the overall low error rate in protein synthesis. Over 40 years of research on aaRSs using structural, biochemical, and kinetic approaches has expanded our knowledge of their cellular roles and quality control mechanisms. Here, we review aaRS editing with an emphasis on the mechanistic and kinetic details of the process.
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Affiliation(s)
- Srujana S Yadavalli
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
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35
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Guo M, Schimmel P. Structural analyses clarify the complex control of mistranslation by tRNA synthetases. Curr Opin Struct Biol 2011; 22:119-26. [PMID: 22155179 DOI: 10.1016/j.sbi.2011.11.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 11/13/2011] [Accepted: 11/15/2011] [Indexed: 12/24/2022]
Abstract
Proteins are precisely assembled with amino acids by matching the anticodons of charged transfer RNAs to nucleotide triplets in mRNA sequences. Accurate translation depends on the specific coupling of cognate amino acids and tRNAs - a step carried out by aminoacyl-tRNA synthetases (aaRSs) and that generates the genetic code. Owing to their intrinsic similarity, aaRSs developed highly differentiated structures to discriminate between amino acids at the active site for aminoacylation. Because this discrimination is not sufficient to prevent toxic mistranslation, aaRSs developed separate structures to further refine recognition by proofreading. From comprehensive structural studies on aaRSs, many of the molecular details have been elucidated for the recognition of cognate amino acids and for the misactivation and editing of noncognate amino acids, Here we review recent advances in the structural description of the binding, activation and editing of amino acids, which collectively reveal many aspects of the fine-tuned systems that resulted in a robust and universal genetic code.
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Affiliation(s)
- Min Guo
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, United States
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36
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Jakubowski H. Quality control in tRNA charging. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:295-310. [PMID: 22095844 DOI: 10.1002/wrna.122] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Faithful translation of the genetic code during protein synthesis is fundamental to the growth, development, and function of living organisms. Aminoacyl-tRNA synthetases (AARSs), which define the genetic code by correctly pairing amino acids with their cognate tRNAs, are responsible for 'quality control' in the flow of information from a gene to a protein. When differences in binding energies of amino acids to an AARS are inadequate, editing is used to achieve high selectivity. Editing occurs at the synthetic active site by hydrolysis of noncognate aminoacyl-adenylates (pretransfer editing) and at a dedicated editing site located in a separate domain by deacylation of mischarged aminoacyl-tRNA (posttransfer editing). Access of nonprotein amino acids, such as homocysteine or ornithine, to the genetic code is prevented by the editing function of AARSs, which functionally partitions amino acids present in living cells into protein and nonprotein amino acids. Continuous editing is part of the tRNA aminoacylation process in living organisms from bacteria to human beings. Preventing mistranslation by the clearance of misactivated amino acids is crucial to cellular homeostasis and has a role in etiology of disease. Although there is a strong selective pressure to minimize mistranslation, some organisms possess error-prone AARSs that cause mistranslation. Elevated levels of mistranslation and the synthesis of statistical proteins can be beneficial for pathogens by increasing phenotypic variation essential for the evasion of host defenses.
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Affiliation(s)
- Hieronim Jakubowski
- Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, International Center for Public Health, Newark, NJ, USA.
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37
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Sarkar J, Martinis SA. Amino-acid-dependent shift in tRNA synthetase editing mechanisms. J Am Chem Soc 2011; 133:18510-3. [PMID: 22017352 DOI: 10.1021/ja2048122] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many aminoacyl-tRNA synthetases prevent mistranslation by relying upon proofreading activities at multiple stages of the aminoacylation reaction. In leucyl-tRNA synthetase (LeuRS), editing activities that precede or are subsequent to tRNA charging have been identified. Although both are operational, either the pre- or post-transfer editing activity can predominate. Yeast cytoplasmic LeuRS (ycLeuRS) misactivates structurally similar noncognate amino acids including isoleucine and methionine. We show that ycLeuRS has a robust post-transfer editing activity that efficiently clears tRNA(Leu) mischarged with isoleucine. In comparison, the enzyme's post-transfer hydrolytic activity against tRNA(Leu) mischarged with methionine is weak. Rather, methionyl-adenylate is cleared robustly via an enzyme-mediated pre-transfer editing activity. We hypothesize that, similar to E. coli LeuRS, ycLeuRS has coexisting functional pre- and post-transfer editing activities. In the case of ycLeuRS, a shift between the two editing pathways is triggered by the identity of the noncognate amino acid.
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Affiliation(s)
- Jaya Sarkar
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 419 Roger Adams Laboratory, Box B-4, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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38
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Zhou XL, Du DH, Tan M, Lei HY, Ruan LL, Eriani G, Wang ED. Role of tRNA amino acid-accepting end in aminoacylation and its quality control. Nucleic Acids Res 2011; 39:8857-68. [PMID: 21775341 PMCID: PMC3203616 DOI: 10.1093/nar/gkr595] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Aminoacyl–tRNA synthetases (aaRSs) are remarkable enzymes that are in charge of the accurate recognition and ligation of amino acids and tRNA molecules. The greatest difficulty in accurate aminoacylation appears to be in discriminating between highly similar amino acids. To reduce mischarging of tRNAs by non-cognate amino acids, aaRSs have evolved an editing activity in a second active site to cleave the incorrect aminoacyl–tRNAs. Editing occurs after translocation of the aminoacyl–CCA76 end to the editing site, switching between a hairpin and a helical conformation for aminoacylation and editing. Here, we studied the consequence of nucleotide changes in the CCA76 accepting end of tRNALeu during the aminoacylation and editing reactions. The analysis showed that the terminal A76 is essential for both reactions, suggesting that critical interactions occur in the two catalytic sites. Substitutions of C74 and C75 selectively decreased aminoacylation keeping nearly unaffected editing. These mutations might favor the regular helical conformation required to reach the editing site. Mutating the editing domain residues that contribute to CCA76 binding reduced the aminoacylation fidelity leading to cell-toxicity in the presence of non-cognate amino acids. Collectively, the data show how protein synthesis quality is controlled by the CCA76 homogeneity of tRNAs.
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Affiliation(s)
- Xiao-Long Zhou
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, Shanghai 200031, China
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39
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So BR, An S, Kumar S, Das M, Turner DA, Hadad CM, Musier-Forsyth K. Substrate-mediated fidelity mechanism ensures accurate decoding of proline codons. J Biol Chem 2011; 286:31810-20. [PMID: 21768119 DOI: 10.1074/jbc.m111.232611] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aminoacyl-tRNA synthetases attach specific amino acids to cognate tRNAs. Prolyl-tRNA synthetases are known to mischarge tRNA(Pro) with the smaller amino acid alanine and with cysteine, which is the same size as proline. Quality control in proline codon translation is partly ensured by an editing domain (INS) present in most bacterial prolyl-tRNA synthetases that hydrolyzes smaller Ala-tRNA(Pro) and excludes Pro-tRNA(Pro). In contrast, Cys-tRNA(Pro) is cleared by a freestanding INS domain homolog, YbaK. Here, we have investigated the molecular mechanism of catalysis and substrate recognition by Hemophilus influenzae YbaK using site-directed mutagenesis, enzymatic assays of isosteric substrates and functional group analogs, and computational modeling. These studies together with mass spectrometric characterization of the YbaK-catalyzed reaction products support a novel substrate-assisted mechanism of Cys-tRNA(Pro) deacylation that prevents nonspecific Pro-tRNA(Pro) hydrolysis. Collectively, we propose that the INS and YbaK domains co-evolved distinct mechanisms involving steric exclusion and thiol-specific chemistry, respectively, to ensure accurate decoding of proline codons.
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Affiliation(s)
- Byung Ran So
- Department of Chemistry, Ohio State University, Columbus, Ohio 43210, USA
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40
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Error compensation of tRNA misacylation by codon-anticodon mismatch prevents translational amino acid misinsertion. Comput Biol Chem 2011; 35:81-95. [PMID: 21470914 DOI: 10.1016/j.compbiolchem.2011.03.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 02/22/2011] [Accepted: 03/01/2011] [Indexed: 11/20/2022]
Abstract
Codon-anticodon mismatches and tRNA misloadings cause translational amino acid misinsertions, producing dysfunctional proteins. Here I explore the original hypothesis whether mismatches tend to compensate misacylation, so as to insert the amino acid coded by the codon. This error compensation is promoted by the fact that codon-anticodon mismatch stabilities increase with tRNA misacylation potentials (predicted by 'tfam') by non-cognate amino acids coded by the mismatched codons for most tRNAs examined. Error compensation is independent of preferential misacylation by non-cognate amino acids physico-chemically similar to cognate amino acids, a phenomenon that decreases misinsertion impacts. Error compensation correlates negatively with (a) codon/anticodon abundance (in human mitochondria and Escherichia coli); (b) developmental instability (estimated by fluctuating asymmetry in bilateral counts of subdigital lamellae, in each of two lizard genera, Anolis and Sceloporus); and (c) pathogenicity of human mitochondrial tRNA polymorphisms. Patterns described here suggest that tRNA misacylation is sometimes compensated by codon-anticodon mismatches. Hence translation inserts the amino acid coded by the mismatched codon, despite mismatch and misloading. Results suggest that this phenomenon is sufficiently important to affect whole organism phenotypes, as shown by correlations with pathologies and morphological estimates of developmental stability.
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41
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Reynolds NM, Lazazzera BA, Ibba M. Cellular mechanisms that control mistranslation. Nat Rev Microbiol 2010; 8:849-56. [PMID: 21079633 DOI: 10.1038/nrmicro2472] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Mistranslation broadly encompasses the introduction of errors during any step of protein synthesis, leading to the incorporation of an amino acid that is different from the one encoded by the gene. Recent research has vastly enhanced our understanding of the mechanisms that control mistranslation at the molecular level and has led to the discovery that the rates of mistranslation in vivo are not fixed but instead are variable. In this Review we describe the different steps in translation quality control and their variations under different growth conditions and between species though a comparison of in vitro and in vivo findings. This provides new insights as to why mistranslation can have both positive and negative effects on growth and viability.
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Affiliation(s)
- Noah M Reynolds
- Department of Microbiology, Ohio State University, Columbus, Ohio 43210, USA
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42
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Chen X, Ma JJ, Tan M, Yao P, Hu QH, Eriani G, Wang ED. Modular pathways for editing non-cognate amino acids by human cytoplasmic leucyl-tRNA synthetase. Nucleic Acids Res 2010; 39:235-47. [PMID: 20805241 PMCID: PMC3017609 DOI: 10.1093/nar/gkq763] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
To prevent potential errors in protein synthesis, some aminoacyl-transfer RNA (tRNA) synthetases have evolved editing mechanisms to hydrolyze misactivated amino acids (pre-transfer editing) or misacylated tRNAs (post-transfer editing). Class Ia leucyl-tRNA synthetase (LeuRS) may misactivate various natural and non-protein amino acids and then mischarge tRNA(Leu). It is known that the fidelity of prokaryotic LeuRS depends on multiple editing pathways to clear the incorrect intermediates and products in the every step of aminoacylation reaction. Here, we obtained human cytoplasmic LeuRS (hcLeuRS) and tRNA(Leu) (hctRNA(Leu)) with high activity from Escherichia coli overproducing strains to study the synthetic and editing properties of the enzyme. We revealed that hcLeuRS could adjust its editing strategy against different non-cognate amino acids. HcLeuRS edits norvaline predominantly by post-transfer editing; however, it uses mainly pre-transfer editing to edit α-amino butyrate, although both amino acids can be charged to tRNA(Leu). Post-transfer editing as a final checkpoint of the reaction was very important to prevent mis-incorporation in vitro. These results provide insight into the modular editing pathways created to prevent genetic code ambiguity by evolution.
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Affiliation(s)
- Xin Chen
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, The Chinese Academy of Sciences, Shanghai 200031, China
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43
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Structure of human cytosolic phenylalanyl-tRNA synthetase: evidence for kingdom-specific design of the active sites and tRNA binding patterns. Structure 2010; 18:343-53. [PMID: 20223217 DOI: 10.1016/j.str.2010.01.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 01/10/2010] [Accepted: 01/19/2010] [Indexed: 11/23/2022]
Abstract
The existence of three types of phenylalanyl-tRNA synthetase (PheRS), bacterial (alphabeta)(2), eukaryotic/archaeal cytosolic (alphabeta)(2), and mitochondrial alpha, is a prominent example of structural diversity within the aaRS family. PheRSs have considerably diverged in primary sequences, domain compositions, and subunit organizations. Loss of the anticodon-binding domain B8 in human cytosolic PheRS (hcPheRS) is indicative of variations in the tRNA(Phe) binding and recognition as compared to bacterial PheRSs. We report herein the crystal structure of hcPheRS in complex with phenylalanine at 3.3 A resolution. A novel structural module has been revealed at the N terminus of the alpha subunit. It stretches out into the solvent of approximately 80 A and is made up of three structural domains (DBDs) possessing DNA-binding fold. The dramatic reduction of aminoacylation activity for truncated N terminus variants coupled with structural data and tRNA-docking model testify that DBDs play crucial role in hcPheRS activity.
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44
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Seligmann H. Do anticodons of misacylated tRNAs preferentially mismatch codons coding for the misloaded amino acid? BMC Mol Biol 2010; 11:41. [PMID: 20509917 PMCID: PMC2887445 DOI: 10.1186/1471-2199-11-41] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 05/28/2010] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Accurate amino acid insertion during peptide elongation requires tRNAs loaded by cognate amino acids and that anticodons match codons. However, tRNA misloading does not necessarily cause misinsertions: misinsertion is avoided when anticodons mismatch codons coding for misloaded amino acids. PRESENTATION OF THE HYPOTHESIS Occasional compensation of misacylation by codon-anticodon mismatch necessarily occurs. Putatively, occasional error compensation may be enhanced beyond the random combination of independent errors in tRNA loading and codon-anticodon interactions: tRNA misacylation might alter potentials for codon-anticodon mismatches, perhaps specifically increasing potentials for mismatching those codons coding for the misacylated non-cognate amino acid. This hypothetical phenomenon is called 'error coordination', in distinction from 'error compensation' that assumes independence between misacylation and mismatch. TESTING THE HYPOTHESIS Eventually, the hypothesis should be tested for each combination of amino acid misacylation and codon-anticodon mismatch, by comparing stabilities or frequencies of mismatched codon-anticodon duplexes formed by tRNAs loaded by their cognate amino acid with stabilities formed by that tRNA when misloaded with the amino acid coded by the mismatched codon. Competitive mismatching experiments between misloaded and correctly loaded tRNAs could also be useful, yet more sophisticated experiments. IMPLICATIONS OF THE HYPOTHESIS Detecting error coordination implies estimating error compensation, which also promotes protein synthesis accuracy. Hence even in the absence of evidence for error coordination, experiments would yield very useful insights into misacylation and mismatch processes. In case experiments consider post-transcriptional RNA modifications (especially at wobble positions), results on codon-anticodon mismatches would enable significant improvements and sophistications of secondary structure prediction softwares. Positive results would show that protein translation enhances accuracies of products, not of single steps in the production. Ancient translational machineries putatively optimized error coordination, especially before tRNA editing by tRNA synthetases evolved: few primitive, but functionally versatile tRNA species perhaps executed low accuracy translation. Systems artificially designed/selected for low complexity and high efficiency could make use of this property for anticodons with high levels of error compensation and coordination.
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Affiliation(s)
- Hervé Seligmann
- Department of Evolution, Systematics & Ecology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel.
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Minajigi A, Francklyn CS. Aminoacyl transfer rate dictates choice of editing pathway in threonyl-tRNA synthetase. J Biol Chem 2010; 285:23810-7. [PMID: 20504770 DOI: 10.1074/jbc.m110.105320] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aminoacyl-tRNA synthetases hydrolyze aminoacyl adenylates and aminoacyl-tRNAs formed from near-cognate amino acids, thereby increasing translational fidelity. The contributions of pre- and post-transfer editing pathways to the fidelity of Escherichia coli threonyl-tRNA synthetase (ThrRS) were investigated by rapid kinetics. In the pre-steady state, asymmetric activation of cognate threonine and noncognate serine was observed in the active sites of dimeric ThrRS, with similar rates of activation. In the absence of tRNA, seryl-adenylate was hydrolyzed 29-fold faster by the ThrRS catalytic domain than threonyl-adenylate. The rate of seryl transfer to cognate tRNA was only 2-fold slower than threonine. Experiments comparing the rate of ATP consumption to the rate of aminoacyl-tRNA(AA) formation demonstrated that pre-transfer hydrolysis contributes to proofreading only when the rate of transfer is slowed significantly. Thus, the relative contributions of pre- and post-transfer editing in ThrRS are subject to modulation by the rate of aminoacyl transfer.
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Affiliation(s)
- Anand Minajigi
- Cell and Molecular Biology Program, University of Vermont, Burlington, VT 05405, USA
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46
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Dulic M, Cvetesic N, Perona JJ, Gruic-Sovulj I. Partitioning of tRNA-dependent editing between pre- and post-transfer pathways in class I aminoacyl-tRNA synthetases. J Biol Chem 2010; 285:23799-809. [PMID: 20498377 DOI: 10.1074/jbc.m110.133553] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hydrolytic editing activities are present in aminoacyl-tRNA synthetases possessing reduced amino acid discrimination in the synthetic reactions. Post-transfer hydrolysis of misacylated tRNA in class I editing enzymes occurs in a spatially separate domain inserted into the catalytic Rossmann fold, but the location and mechanisms of pre-transfer hydrolysis of misactivated amino acids have been uncertain. Here, we use novel kinetic approaches to distinguish among three models for pre-transfer editing by Escherichia coli isoleucyl-tRNA synthetase (IleRS). We demonstrate that tRNA-dependent hydrolysis of noncognate valyl-adenylate by IleRS is largely insensitive to mutations in the editing domain of the enzyme and that noncatalytic hydrolysis after release is too slow to account for the observed rate of clearing. Measurements of the microscopic rate constants for amino acid transfer to tRNA in IleRS and the related valyl-tRNA synthetase (ValRS) further suggest that pre-transfer editing in IleRS is an enzyme-catalyzed activity residing in the synthetic active site. In this model, the balance between pre-transfer and post-transfer editing pathways is controlled by kinetic partitioning of the noncognate aminoacyl-adenylate. Rate constants for hydrolysis and transfer of a noncognate intermediate are roughly equal in IleRS, whereas in ValRS transfer to tRNA is 200-fold faster than hydrolysis. In consequence, editing by ValRS occurs nearly exclusively by post-transfer hydrolysis in the editing domain, whereas in IleRS both pre- and post-transfer editing are important. In both enzymes, the rates of amino acid transfer to tRNA are similar for cognate and noncognate aminoacyl-adenylates, providing a significant contrast with editing DNA polymerases.
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Affiliation(s)
- Morana Dulic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
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47
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Martinis SA, Boniecki MT. The balance between pre- and post-transfer editing in tRNA synthetases. FEBS Lett 2009; 584:455-9. [PMID: 19941860 DOI: 10.1016/j.febslet.2009.11.071] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 11/18/2009] [Accepted: 11/19/2009] [Indexed: 10/20/2022]
Abstract
The fidelity of tRNA aminoacylation is dependent in part on amino acid editing mechanisms. A hydrolytic activity that clears mischarged tRNAs typically resides in an active site on the tRNA synthetase that is distinct from its synthetic aminoacylation active site. A second pre-transfer editing pathway that hydrolyzes the tRNA synthetase aminoacyl adenylate intermediate can also be activated. Pre- and post-transfer editing activities can co-exist within a single tRNA synthetase resulting in a redundancy of fidelity mechanisms. However, in most cases one pathway appears to dominate, but when compromised, the secondary pathway can be activated to suppress tRNA synthetase infidelities.
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Affiliation(s)
- Susan A Martinis
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 419 Roger Adams Laboratory, Box B-4, 600 S. Mathews Ave., Urbana, IL 61801, United States.
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48
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tRNAs: cellular barcodes for amino acids. FEBS Lett 2009; 584:387-95. [PMID: 19903480 DOI: 10.1016/j.febslet.2009.11.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 10/29/2009] [Accepted: 11/05/2009] [Indexed: 01/06/2023]
Abstract
The role of tRNA in translating the genetic code has received considerable attention over the last 50 years, and we now know in great detail how particular amino acids are specifically selected and brought to the ribosome in response to the corresponding mRNA codon. Over the same period, it has also become increasingly clear that the ribosome is not the only destination to which tRNAs deliver amino acids, with processes ranging from lipid modification to antibiotic biosynthesis all using aminoacyl-tRNAs as substrates. Here we review examples of alternative functions for tRNA beyond translation, which together suggest that the role of tRNA is to deliver amino acids for a variety of processes that includes, but is not limited to, protein synthesis.
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49
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Abstract
Translating the 4-letter code of RNA into the 22-letter alphabet of proteins is a central feature of cellular life. The fidelity with which mRNA is translated during protein synthesis is determined by two factors: the availability of aminoacyl-tRNAs composed of cognate amino acid:tRNA pairs and the accurate selection of aminoacyl-tRNAs on the ribosome. The role of aminoacyl-tRNA synthetases in translation is to define the genetic code by accurately pairing cognate tRNAs with their corresponding amino acids. Synthetases achieve the amino acid substrate specificity necessary to keep errors in translation to an acceptable level in two ways: preferential binding of the cognate amino acid and selective editing of near-cognate amino acids. Editing significantly decreases the frequency of errors and is important for translational quality control, and many details of the various editing mechanisms and their effect on different cellular systems are now starting to emerge.
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Affiliation(s)
- Jiqiang Ling
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
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50
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Wen D, Vecchi MM, Gu S, Su L, Dolnikova J, Huang YM, Foley SF, Garber E, Pederson N, Meier W. Discovery and investigation of misincorporation of serine at asparagine positions in recombinant proteins expressed in Chinese hamster ovary cells. J Biol Chem 2009; 284:32686-94. [PMID: 19783658 DOI: 10.1074/jbc.m109.059360] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Misincorporation of amino acids in proteins expressed in Escherichia coli has been well documented but not in proteins expressed in mammalian cells under normal recombinant protein production conditions. Here we report for the first time that Ser can be incorporated at Asn positions in proteins expressed in Chinese hamster ovary cells. This misincorporation was discovered as a result of intact mass measurement, peptide mapping analysis, and tandem mass spectroscopy sequencing. Our analyses showed that the substitution was not related to specific protein molecules or DNA codons and was not site-specific. We believe that the incorporation of Ser at sites coded for Asn was due to mischarging of tRNA(Asn) rather than to codon misreading. The rationale for substitution of Asn by Ser and not by other amino acids is also discussed. Further investigation indicated that the substitution was due to the starvation for Asn in the cell culture medium and that the substitution could be limited by using the Asn-rich feed. These observations demonstrate that the quality of expressed proteins should be closely monitored when altering cell culture conditions.
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Affiliation(s)
- Dingyi Wen
- Biogen Idec Inc., 14 Cambridge Center, Cambridge, Massachusetts 02412, USA.
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