1
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Cruz E, Vargas-Rodriguez O. The role of tRNA identity elements in aminoacyl-tRNA editing. Front Microbiol 2024; 15:1437528. [PMID: 39101037 PMCID: PMC11295145 DOI: 10.3389/fmicb.2024.1437528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 06/18/2024] [Indexed: 08/06/2024] Open
Abstract
The rules of the genetic code are implemented by the unique features that define the amino acid identity of each transfer RNA (tRNA). These features, known as "identity elements," mark tRNAs for recognition by aminoacyl-tRNA synthetases (ARSs), the enzymes responsible for ligating amino acids to tRNAs. While tRNA identity elements enable stringent substrate selectivity of ARSs, these enzymes are prone to errors during amino acid selection, leading to the synthesis of incorrect aminoacyl-tRNAs that jeopardize the fidelity of protein synthesis. Many error-prone ARSs have evolved specialized domains that hydrolyze incorrectly synthesized aminoacyl-tRNAs. These domains, known as editing domains, also exist as free-standing enzymes and, together with ARSs, safeguard protein synthesis fidelity. Here, we discuss how the same identity elements that define tRNA aminoacylation play an integral role in aminoacyl-tRNA editing, synergistically ensuring the correct translation of genetic information into proteins. Moreover, we review the distinct strategies of tRNA selection used by editing enzymes and ARSs to avoid undesired hydrolysis of correctly aminoacylated tRNAs.
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Affiliation(s)
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biology and Biophysics, University of Connecticut School of Medicine, Farmington, CT, United States
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2
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Watkins RR, Vradi A, Shulgina I, Musier-Forsyth K. Trypanosoma brucei multi-aminoacyl-tRNA synthetase complex formation limits promiscuous tRNA proofreading. Front Microbiol 2024; 15:1445687. [PMID: 39081885 PMCID: PMC11286415 DOI: 10.3389/fmicb.2024.1445687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 07/03/2024] [Indexed: 08/02/2024] Open
Abstract
Faithful mRNA decoding depends on the accuracy of aminoacyl-tRNA synthetases (ARSs). Aminoacyl-tRNA proofreading mechanisms have been well-described in bacteria, humans, and plants. However, our knowledge of translational fidelity in protozoans is limited. Trypanosoma brucei (Tb) is a eukaryotic, protozoan pathogen that causes Human African Trypanosomiasis, a fatal disease if untreated. Tb undergoes many physiological changes that are dictated by nutrient availability throughout its insect-mammal lifecycle. In the glucose-deprived insect vector, the tsetse fly, Tb use proline to make ATP via mitochondrial respiration. Alanine is one of the major by-products of proline consumption. We hypothesize that the elevated alanine pool challenges Tb prolyl-tRNA synthetase (ProRS), an ARS known to misactivate alanine in all three domains of life, resulting in high levels of misaminoacylated Ala-tRNAPro. Tb encodes two domains that are members of the INS superfamily of aminoacyl-tRNA deacylases. One homolog is appended to the N-terminus of Tb ProRS, and a second is the major domain of multi-aminoacyl-tRNA synthetase complex (MSC)-associated protein 3 (MCP3). Both ProRS and MCP3 are housed in the Tb MSC. Here, we purified Tb ProRS and MCP3 and observed robust Ala-tRNAPro deacylation activity from both enzymes in vitro. Size-exclusion chromatography multi-angle light scattering used to probe the oligomerization state of MCP3 revealed that although its unique N-terminal extension confers homodimerization in the absence of tRNA, the protein binds to tRNA as a monomer. Kinetic assays showed MCP3 alone has relaxed tRNA specificity and promiscuously hydrolyzes cognate Ala-tRNAAla; this activity is significantly reduced in the presence of Tb alanyl-tRNA synthetase, also housed in the MSC. Taken together, our results provide insight into translational fidelity mechanisms in Tb and lay the foundation for exploring MSC-associated proteins as novel drug targets.
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Affiliation(s)
| | | | | | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH, United States
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3
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Liebau J, Laatsch BF, Rusnak J, Gunderson K, Finke B, Bargender K, Narkiewicz-Jodko A, Weeks K, Williams MT, Shulgina I, Musier-Forsyth K, Bhattacharyya S, Hati S. Polyethylene Glycol Impacts Conformation and Dynamics of Escherichia coli Prolyl-tRNA Synthetase Via Crowding and Confinement Effects. Biochemistry 2024; 63:1621-1635. [PMID: 38607680 PMCID: PMC11223479 DOI: 10.1021/acs.biochem.3c00719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
Abstract
Polyethylene glycol (PEG) is a flexible, nontoxic polymer commonly used in biological and medical research, and it is generally regarded as biologically inert. PEG molecules of variable sizes are also used as crowding agents to mimic intracellular environments. A recent study with PEG crowders revealed decreased catalytic activity of Escherichia coli prolyl-tRNA synthetase (Ec ProRS), where the smaller molecular weight PEGs had the maximum impact. The molecular mechanism of the crowding effects of PEGs is not clearly understood. PEG may impact protein conformation and dynamics, thus its function. In the present study, the effects of PEG molecules of various molecular weights and concentrations on the conformation and dynamics of Ec ProRS were investigated using a combined experimental and computational approach including intrinsic tryptophan fluorescence spectroscopy, atomic force microscopy, and atomistic molecular dynamic simulations. Results of the present study suggest that lower molecular weight PEGs in the dilute regime have modest effects on the conformational dynamics of Ec ProRS but impact the catalytic function primarily via the excluded volume effect; they form large clusters blocking the active site pocket. In contrast, the larger molecular weight PEGs in dilute to semidilute regimes have a significant impact on the protein's conformational dynamics; they wrap on the protein surface through noncovalent interactions. Thus, lower-molecular-weight PEG molecules impact protein dynamics and function via crowding effects, whereas larger PEGs induce confinement effects. These results have implications for the development of inhibitors for protein targets in a crowded cellular environment.
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Affiliation(s)
- Jessica Liebau
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Bethany F. Laatsch
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Joshua Rusnak
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Keegan Gunderson
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Brianna Finke
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Kassandra Bargender
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Alex Narkiewicz-Jodko
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Katelyn Weeks
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Murphi T. Williams
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Irina Shulgina
- Department
of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Karin Musier-Forsyth
- Department
of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sudeep Bhattacharyya
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Sanchita Hati
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
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4
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Yuan C, Li Z, Luo X, Huang P, Guo L, Lu M, Xia J, Xiao Y, Zhou XL, Chen M. Mammalian trans-editing factor ProX is able to deacylate tRNA Thr mischarged with alanine. Int J Biol Macromol 2023; 253:127121. [PMID: 37778588 DOI: 10.1016/j.ijbiomac.2023.127121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/16/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
The precise coupling of tRNAs with their cognate amino acids, known as tRNA aminoacylation, is a stringently regulated process that governs translation fidelity. To ensure fidelity, organisms deploy multiple layers of editing mechanisms to correct mischarged tRNAs. Prior investigations have unveiled the propensity of eukaryotic AlaRS to erroneously attach alanine onto tRNACys and tRNAThr featuring the G4:U69 base pair. In light of this, and given ProXp-ala's capacity in deacylating Ala-tRNAPro, we embarked on exploring whether this trans-editing factor could extend its corrective function to encompass these mischarged tRNAs. Our in vitro deacylation assays demonstrate that murine ProXp-ala (mProXp-ala) is able to efficiently hydrolyze Ala-tRNAThr, while Ala-tRNACys remains unaffected. Subsequently, we determined the first structure of eukaryotic ProXp-ala, revealing a dynamic helix α2 involved in substrate binding. By integrating molecular dynamics simulations and biochemical assays, we pinpointed the pivotal interactions between mProXp-ala and Ala-tRNA, wherein the basic regions of mProXp-ala as well as the C3-G70 plays essential role in recognition. These observations collectively provide a cogent rationale for mProXp-ala's deacylation proficiency against Ala-tRNAThr. Our findings offer valuable insights into the translation quality control within higher eukaryotic organisms, where the fidelity of translation is safeguarded by the multi-functionality of extensively documented proteins.
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Affiliation(s)
- Chen Yuan
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Zihan Li
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinyu Luo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Pingping Huang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lijie Guo
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Meiling Lu
- Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yibei Xiao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China; Chongqing Innovation Institute of China Pharmaceutical University, Chongqing 401135, China.
| | - Xiao-Long Zhou
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Meirong Chen
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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5
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Polikanov YS, Etheve-Quelquejeu M, Micura R. Synthesis of Peptidyl-tRNA Mimics for Structural Biology Applications. Acc Chem Res 2023; 56:2713-2725. [PMID: 37728742 PMCID: PMC10552525 DOI: 10.1021/acs.accounts.3c00412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Indexed: 09/21/2023]
Abstract
Protein biosynthesis is a central process in all living cells that is catalyzed by a complex molecular machine─the ribosome. This process is termed translation because the language of nucleotides in mRNAs is translated into the language of amino acids in proteins. Transfer RNA (tRNA) molecules charged with amino acids serve as adaptors and recognize codons of mRNA in the decoding center while simultaneously the individual amino acids are assembled into a peptide chain in the peptidyl transferase center (PTC). As the nascent peptide emerges from the ribosome, it is threaded through a long tunnel referred to as a nascent peptide exit tunnel (NPET). The PTC and NPET are the sites targeted by many antibiotics and are thus of tremendous importance from a biomedical perspective and for drug development in the pharmaceutical industry.Researchers have achieved much progress in characterizing ribosomal translation at the molecular level; an impressive number of high-resolution structures of different functional and inhibited states of the ribosome are now available. These structures have significantly contributed to our understanding of how the ribosome interacts with its key substrates, namely, mRNA, tRNAs, and translation factors. In contrast, much less is known about the mechanisms of how small molecules, especially antibiotics, affect ribosomal protein synthesis. This mainly concerns the structural basis of small molecule-NPET interference with cotranslational protein folding and the regulation of protein synthesis. Growing biochemical evidence suggests that NPET plays an active role in the regulation of protein synthesis.Much-needed progress in this field is hampered by the fact that during the preparation of ribosome complexes for structural studies (i.e., X-ray crystallography, cryoelectron microscopy, and NMR spectroscopy) the aminoacyl- or peptidyl-tRNAs are unstable and become hydrolyzed. A solution to this problem is the application of hydrolysis-resistant mimics of aminoacyl- or peptidyl-tRNAs.In this Account, we present an overview of synthetic methods for the generation of peptidyl-tRNA analogs. Modular approaches have been developed that combine (i) RNA and peptide solid-phase synthesis on 3'-aminoacylamino-adenosine resins, (ii) native chemical ligations and Staudinger ligations, (iii) tailoring of tRNAs by the selective cleavage of natural native tRNAs with DNAzymes followed by reassembly with enzymatic ligation to synthetic peptidyl-RNA fragments, and (iv) enzymatic tailing and cysteine charging of the tRNA to obtain modified CCA termini of a tRNA that are chemically ligated to the peptide moiety of interest. With this arsenal of tools, in principle, any desired sequence of a stably linked peptidyl-tRNA mimic is accessible. To underline the significance of the synthetic conjugates, we briefly point to the most critical applications that have shed new light on the molecular mechanisms underlying the context-specific activity of ribosome-targeting antibiotics, ribosome-dependent incorporation of multiple consecutive proline residues, the incorporation of d-amino acids, and tRNA mischarging.Furthermore, we discuss new types of stably charged tRNA analogs, relying on triazole- and squarate (instead of amide)-linked conjugates. Those have pushed forward our mechanistic understanding of nonribosomal peptide synthesis, where aminoacyl-tRNA-dependent enzymes are critically involved in various cellular processes in primary and secondary metabolism and in bacterial cell wall synthesis.
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Affiliation(s)
- Yury S. Polikanov
- Department
of Biological Sciences, University of Illinois
at Chicago, Chicago, Illinois 60607, United States
- Department
of Pharmaceutical Sciences, University of
Illinois at Chicago, Chicago, Illinois 60607, United States
- Center for
Biomolecular Sciences, University of Illinois
at Chicago, Chicago, Illinois 60607, United States
| | - Mélanie Etheve-Quelquejeu
- Université
Paris Cité, CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques
et Toxicologiques, Paris F-75006, France
| | - Ronald Micura
- Institute
of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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6
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Ma X, Bakhtina M, Shulgina I, Cantara WA, Kuzmishin Nagy A, Goto Y, Suga H, Foster MP, Musier-Forsyth K. Structural basis of tRNAPro acceptor stem recognition by a bacterial trans-editing domain. Nucleic Acids Res 2023; 51:3988-3999. [PMID: 36951109 PMCID: PMC10164551 DOI: 10.1093/nar/gkad192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/24/2023] Open
Abstract
High fidelity tRNA aminoacylation by aminoacyl-tRNA synthetases is essential for cell viability. ProXp-ala is a trans-editing protein that is present in all three domains of life and is responsible for hydrolyzing mischarged Ala-tRNAPro and preventing mistranslation of proline codons. Previous studies have shown that, like bacterial prolyl-tRNA synthetase, Caulobacter crescentus ProXp-ala recognizes the unique C1:G72 terminal base pair of the tRNAPro acceptor stem, helping to ensure deacylation of Ala-tRNAPro but not Ala-tRNAAla. The structural basis for C1:G72 recognition by ProXp-ala is still unknown and was investigated here. NMR spectroscopy, binding, and activity assays revealed two conserved residues, K50 and R80, that likely interact with the first base pair, stabilizing the initial protein-RNA encounter complex. Modeling studies are consistent with direct interaction between R80 and the major groove of G72. A third key contact between A76 of tRNAPro and K45 of ProXp-ala was essential for binding and accommodating the CCA-3' end in the active site. We also demonstrated the essential role that the 2'OH of A76 plays in catalysis. Eukaryotic ProXp-ala proteins recognize the same acceptor stem positions as their bacterial counterparts, albeit with different nucleotide base identities. ProXp-ala is encoded in some human pathogens; thus, these results have the potential to inform new antibiotic drug design.
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Affiliation(s)
- Xiao Ma
- Department of Chemistry and Biochemistry and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Marina Bakhtina
- Department of Chemistry and Biochemistry and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Irina Shulgina
- Department of Chemistry and Biochemistry and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - William A Cantara
- Department of Chemistry and Biochemistry and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Alexandra B Kuzmishin Nagy
- Department of Chemistry and Biochemistry and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Mark P Foster
- Department of Chemistry and Biochemistry and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
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7
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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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8
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Jani J, Pappachan A. A review on quality control agents of protein translation - The role of Trans-editing proteins. Int J Biol Macromol 2022; 199:252-263. [PMID: 34995670 DOI: 10.1016/j.ijbiomac.2021.12.176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/18/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022]
Abstract
Translation of RNA to protein is a key feature of cellular life. The fidelity of this process mainly depends on the availability of correctly charged tRNAs. Different domains of tRNA synthetase (aaRS) maintain translation quality by ensuring the proper attachment of particular amino acid with respective tRNA, thus it establishes the rule of genetic code. However occasional errors by aaRS generate mischarged tRNAs, which can become lethal to the cells. Accurate protein synthesis necessitates hydrolysis of mischarged tRNAs. Various cis and trans-editing proteins are identified which recognize these mischarged products and correct them by hydrolysis. Trans-editing proteins are homologs of cis-editing domains of aaRS. The trans-editing proteins work in close association with aaRS, Ef-Tu, and ribosome to prevent global mistranslation and ensures correct charging of tRNA. In this review, we discuss the major trans-editing proteins and compared them with their cis-editing counterparts. We also discuss their structural features, biochemical activity and role in maintaining cellular protein homeostasis.
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Affiliation(s)
- Jaykumar Jani
- School of Life Sciences, Central University of Gujarat, Sector 30, Gandhinagar 382030, Gujarat, India
| | - Anju Pappachan
- School of Life Sciences, Central University of Gujarat, Sector 30, Gandhinagar 382030, Gujarat, India.
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9
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Krasheninina OA, Thaler J, Erlacher MD, Micura R. Amine-to-Azide Conversion on Native RNA via Metal-Free Diazotransfer Opens New Avenues for RNA Manipulations. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:7046-7050. [PMID: 38504956 PMCID: PMC10947191 DOI: 10.1002/ange.202015034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/19/2020] [Indexed: 03/21/2024]
Abstract
A major challenge in the field of RNA chemistry is the identification of selective and quantitative conversion reactions on RNA that can be used for tagging and any other RNA tool development. Here, we introduce metal-free diazotransfer on native RNA containing an aliphatic primary amino group using the diazotizing reagent fluorosulfuryl azide (FSO2N3). The reaction provides the corresponding azide-modified RNA in nearly quantitatively yields without affecting the nucleobase amino groups. The obtained azido-RNA can then be further processed utilizing well-established bioortho-gonal reactions, such as azide-alkyne cycloadditions (Click) or Staudinger ligations. We exemplify the robustness of this approach for the synthesis of peptidyl-tRNA mimics and for the pull-down of 3-(3-amino-3-carboxypropyl)uridine (acp3U)- and lysidine (k2C)-containing tRNAs of an Escherichia coli tRNA pool isolated from cellular extracts. Our approach therefore adds a new dimension to the targeted chemical manipulation of diverse RNA species.
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Affiliation(s)
- Olga A. Krasheninina
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Julia Thaler
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Matthias D. Erlacher
- Institute of Genomics and RNomicsBiocenterMedical University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
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10
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Krasheninina OA, Thaler J, Erlacher MD, Micura R. Amine-to-Azide Conversion on Native RNA via Metal-Free Diazotransfer Opens New Avenues for RNA Manipulations. Angew Chem Int Ed Engl 2021; 60:6970-6974. [PMID: 33400347 PMCID: PMC8048507 DOI: 10.1002/anie.202015034] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/19/2020] [Indexed: 12/12/2022]
Abstract
A major challenge in the field of RNA chemistry is the identification of selective and quantitative conversion reactions on RNA that can be used for tagging and any other RNA tool development. Here, we introduce metal-free diazotransfer on native RNA containing an aliphatic primary amino group using the diazotizing reagent fluorosulfuryl azide (FSO2 N3 ). The reaction provides the corresponding azide-modified RNA in nearly quantitatively yields without affecting the nucleobase amino groups. The obtained azido-RNA can then be further processed utilizing well-established bioortho-gonal reactions, such as azide-alkyne cycloadditions (Click) or Staudinger ligations. We exemplify the robustness of this approach for the synthesis of peptidyl-tRNA mimics and for the pull-down of 3-(3-amino-3-carboxypropyl)uridine (acp3 U)- and lysidine (k2 C)-containing tRNAs of an Escherichia coli tRNA pool isolated from cellular extracts. Our approach therefore adds a new dimension to the targeted chemical manipulation of diverse RNA species.
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Affiliation(s)
- Olga A. Krasheninina
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Julia Thaler
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Matthias D. Erlacher
- Institute of Genomics and RNomicsBiocenterMedical University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
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11
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Vargas-Rodriguez O, Bakhtina M, McGowan D, Abid J, Goto Y, Suga H, Musier-Forsyth K. Human trans-editing enzyme displays tRNA acceptor-stem specificity and relaxed amino acid selectivity. J Biol Chem 2020; 295:16180-16190. [PMID: 33051185 PMCID: PMC7705315 DOI: 10.1074/jbc.ra120.015981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/06/2020] [Indexed: 01/20/2023] Open
Abstract
Accurate translation of genetic information into proteins is vital for cell sustainability. ProXp-ala prevents proteome-wide Pro-to-Ala mutations by hydrolyzing misacylated Ala-tRNAPro, which is synthesized by prolyl-tRNA synthetase. Bacterial ProXp-ala was previously shown to combine a size-based exclusion mechanism with conformational and chemical selection for the recognition of the alanyl moiety, whereas tRNAPro is selected via recognition of tRNA acceptor-stem elements G72 and A73. The identity of these critical bases changed during evolution with eukaryotic cytosolic tRNAPro possessing a cytosine at the corresponding positions. The mechanism by which eukaryotic ProXp-ala adapted to these changes remains unknown. In this work, recognition of the aminoacyl moiety and tRNA acceptor stem by human (Homo sapiens, or Hs) ProXp-ala was examined. Enzymatic assays revealed that Hs ProXp-ala requires C72 and C73 in the context of Hs cytosolic tRNAPro for efficient deacylation of mischarged Ala-tRNAPro The strong dependence on these bases prevents cross-species deacylation of bacterial Ala-tRNAPro or of Hs mitochondrial Ala-tRNAPro by the human enzyme. Similar to the bacterial enzyme, Hs ProXp-ala showed strong tRNA acceptor-stem recognition but differed in its amino acid specificity profile relative to bacterial ProXp-ala. Changes at conserved residues in both the Hs and bacterial ProXp-ala substrate-binding pockets modulated this specificity. These results illustrate how the mechanism of substrate selection diverged during the evolution of the ProXp-ala family, providing the first example of a trans-editing domain whose specificity evolved to adapt to changes in its tRNA substrate.
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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, USA
| | - Marina Bakhtina
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Daniel McGowan
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Jawad Abid
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA.
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12
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Osmer PS, Singh G, Boris-Lawrie K. A New Approach to 3D Modeling of Inhomogeneous Populations of Viral Regulatory RNA. Viruses 2020; 12:v12101108. [PMID: 33003639 PMCID: PMC7650772 DOI: 10.3390/v12101108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 12/17/2022] Open
Abstract
Tertiary structure (3D) is the physical context of RNA regulatory activity. Retroviruses are RNA viruses that replicate through the proviral DNA intermediate transcribed by hosts. Proviral transcripts form inhomogeneous populations due to variable structural ensembles of overlapping regulatory RNA motifs in the 5′-untranslated region (UTR), which drive RNAs to be spliced or translated, and/or dimerized and packaged into virions. Genetic studies and structural techniques have provided fundamental input constraints to begin predicting HIV 3D conformations in silico. Using SimRNA and sets of experimentally-determined input constraints of HIVNL4-3 trans-activation responsive sequence (TAR) and pairings of unique-5′ (U5) with dimerization (DIS) or AUG motifs, we calculated a series of 3D models that differ in proximity of 5′-Cap and the junction of TAR and PolyA helices; configuration of primer binding site (PBS)-segment; and two host cofactors binding sites. Input constraints on U5-AUG pairings were most compatible with intramolecular folding of 5′-UTR motifs in energetic minima. Introducing theoretical constraints predicted metastable PolyA region drives orientation of 5′-Cap with TAR, U5 and PBS-segment helices. SimRNA and the workflow developed herein provides viable options to predict 3D conformations of inhomogeneous populations of large RNAs that have been intractable to conventional ensemble methods.
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Affiliation(s)
- Patrick S. Osmer
- Department of Astronomy, The Ohio State University, Columbus, OH 43210, USA;
| | - Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA;
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA;
- Correspondence: ; Tel.: +1-612-625-2100
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13
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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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14
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Waudby CA, Ouvry M, Davis B, Christodoulou J. Two-dimensional NMR lineshape analysis of single, multiple, zero and double quantum correlation experiments. JOURNAL OF BIOMOLECULAR NMR 2020; 74:95-109. [PMID: 31915980 PMCID: PMC7015968 DOI: 10.1007/s10858-019-00297-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 12/31/2019] [Indexed: 05/05/2023]
Abstract
NMR spectroscopy provides a powerful approach for the characterisation of chemical exchange and molecular interactions by analysis of series of experiments acquired over the course of a titration measurement. The appearance of NMR resonances undergoing chemical exchange depends on the frequency difference relative to the rate of exchange, and in the case of one-dimensional experiments chemical exchange regimes are well established and well known. However, two-dimensional experiments present additional complexity, as at least one additional frequency difference must be considered. Here we provide a systematic classification of chemical exchange regimes in two-dimensional NMR spectra. We highlight important differences between exchange in HSQC and HMQC experiments, that on a practical level result in more severe exchange broadening in HMQC spectra, but show that complementary alternatives to the HMQC are available in the form of HZQC and HDQC experiments. We present the longitudinal relaxation optimised SOFAST-H(Z/D)QC experiment for the simultaneous acquisition of sensitivity-enhanced HZQC and HDQC spectra, and the longitudinal and transverse relaxation optimised BEST-ZQ-TROSY for analysis of large molecular weight systems. We describe the application of these experiments to the characterisation of the interaction between the Hsp90 N-terminal domain and a small molecule ligand, and show that the independent analysis of HSQC, HMQC, HZQC and HDQC experiments provides improved confidence in the fitted dissociation constant and dissociation rate. Joint analysis of such data may provide improved sensitivity to detect and analyse more complex multi-state interaction mechanisms such as induced fit or conformational selection.
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Affiliation(s)
- Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, UK.
| | - Margaux Ouvry
- Biotechnologie, Sanofi, Route d'Avignon, 30390, Aramon, France
| | - Ben Davis
- Vernalis (R&D) Limited, Granta Park, Great Abington, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, UK
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15
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Waudby CA, Frenkiel T, Christodoulou J. Cross-Peaks in Simple Two-Dimensional NMR Experiments from Chemical Exchange of Transverse Magnetisation. Angew Chem Int Ed Engl 2019; 58:8784-8788. [PMID: 30997945 PMCID: PMC6771647 DOI: 10.1002/anie.201903245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/17/2019] [Indexed: 01/16/2023]
Abstract
Two-dimensional correlation measurements such as COSY, NOESY, HMQC, and HSQC experiments are central to small-molecule and biomolecular NMR spectroscopy, and commonly form the basis of more complex experiments designed to study chemical exchange occurring during additional mixing periods. However, exchange occurring during chemical shift evolution periods can also influence the appearance of such spectra. While this is often exploited through one-dimensional lineshape analysis ("dynamic NMR"), the analysis of exchange across multiple chemical shift evolution periods has received less attention. Here we report that chemical exchange-induced cross-peaks can arise in even the simplest two-dimensional NMR experiments. These cross-peaks can have highly distorted phases that contain rich information about the underlying exchange process. The quantitative analysis of such peaks, from a single 2D spectrum, can provide a highly accurate characterisation of underlying exchange processes.
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Affiliation(s)
- Christopher A. Waudby
- Institute of Structural and Molecular BiologyUniversity College LondonGower StreetLondonWC1E 6BTUK
| | - Tom Frenkiel
- MRC Biomedical NMR CentreFrancis Crick InstituteMidland RoadLondonNW1 1ATUK
| | - John Christodoulou
- Institute of Structural and Molecular BiologyUniversity College LondonGower StreetLondonWC1E 6BTUK
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16
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Waudby CA, Frenkiel T, Christodoulou J. Cross‐Peaks in Simple Two‐Dimensional NMR Experiments from Chemical Exchange of Transverse Magnetisation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Christopher A. Waudby
- Institute of Structural and Molecular BiologyUniversity College London Gower Street London WC1E 6BT UK
| | - Tom Frenkiel
- MRC Biomedical NMR CentreFrancis Crick Institute Midland Road London NW1 1AT UK
| | - John Christodoulou
- Institute of Structural and Molecular BiologyUniversity College London Gower Street London WC1E 6BT UK
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17
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Routh SB, Sankaranarayanan R. Enzyme action at RNA–protein interface in DTD-like fold. Curr Opin Struct Biol 2018; 53:107-114. [DOI: 10.1016/j.sbi.2018.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 07/24/2018] [Accepted: 07/30/2018] [Indexed: 02/08/2023]
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18
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Wang W, Qin B, Wojdyla JA, Wang M, Gao X, Cui S. Structural characterization of free-state and product-state Mycobacterium tuberculosis methionyl-tRNA synthetase reveals an induced-fit ligand-recognition mechanism. IUCRJ 2018; 5:478-490. [PMID: 30002848 PMCID: PMC6038951 DOI: 10.1107/s2052252518008217] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
Mycobacterium tuberculosis (MTB) caused 10.4 million cases of tuberculosis and 1.7 million deaths in 2016. The incidence of multidrug-resistant and extensively drug-resistant MTB is becoming an increasing threat to public health and the development of novel anti-MTB drugs is urgently needed. Methionyl-tRNA synthetase (MetRS) is considered to be a valuable drug target. However, structural characterization of M. tuberculosis MetRS (MtMetRS) was lacking for decades, thus hampering drug design. Here, two high-resolution crystal structures of MtMetRS are reported: the free-state structure (apo form; 1.9 Å resolution) and a structure with the intermediate product methionyl-adenylate (Met-AMP) bound (2.4 Å resolution). It was found that free-state MtMetRS adopts a previously unseen conformation that has never been observed in other MetRS homologues. The pockets for methionine and AMP are not formed in free-state MtMetRS, suggesting that it is in a nonproductive conformation. Combining these findings suggests that MtMetRS employs an induced-fit mechanism in ligand binding. By comparison with the structure of human cytosolic MetRS, additional pockets specific to MtMetRS that could be used for anti-MTB drug design were located.
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Affiliation(s)
- Wei Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Science, No. 9 Dong Dan San Tiao, Dong Cheng Qu, Beijing 100730, People’s Republic of China
| | - Bo Qin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Science, No. 9 Dong Dan San Tiao, Dong Cheng Qu, Beijing 100730, People’s Republic of China
| | | | - Meitian Wang
- Paul Scherrer Institute, Swiss Light Source, CH-5232 Villigen, Switzerland
| | - Xiaopan Gao
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Science, No. 9 Dong Dan San Tiao, Dong Cheng Qu, Beijing 100730, People’s Republic of China
| | - Sheng Cui
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Science, No. 9 Dong Dan San Tiao, Dong Cheng Qu, Beijing 100730, People’s Republic of China
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19
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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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