1
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Flemmich L, Bereiter R, Micura R. Chemical Synthesis of Modified RNA. Angew Chem Int Ed Engl 2024; 63:e202403063. [PMID: 38529723 DOI: 10.1002/anie.202403063] [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: 02/12/2024] [Revised: 03/16/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Ribonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA in a controlled manner-both in vitro and in vivo-are thus essential to evaluate and understand RNA biology at the molecular and mechanistic levels. The diversity of modifications, combined with the size and uniformity of RNA (made up of only 4 nucleotides) makes its site-specific modification a challenging task that needs to be addressed by complementary approaches. One such approach is solid-phase RNA synthesis. We discuss recent developments in this field, starting with new protection concepts in the ongoing effort to overcome current size limitations. We continue with selected modifications that have posed significant challenges for their incorporation into RNA. These include deazapurine bases required for atomic mutagenesis to elucidate mechanistic aspects of catalytic RNAs, and RNA containing xanthosine, N4-acetylcytidine, 5-hydroxymethylcytidine, 3-methylcytidine, 2'-OCF3, and 2'-N3 ribose modifications. We also discuss the all-chemical synthesis of 5'-capped mRNAs and the enzymatic ligation of chemically synthesized oligoribonucleotides to obtain long RNA with multiple distinct modifications, such as those needed for single-molecule FRET studies. Finally, we highlight promising developments in RNA-catalyzed RNA modification using cofactors that transfer bioorthogonal functionalities.
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Affiliation(s)
- Laurin Flemmich
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
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2
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Kompatscher M, Bartosik K, Erharter K, Plangger R, Juen F, Kreutz C, Micura R, Westhof E, Erlacher M. Contribution of tRNA sequence and modifications to the decoding preferences of E. coli and M. mycoides tRNAGlyUCC for synonymous glycine codons. Nucleic Acids Res 2024; 52:1374-1386. [PMID: 38050960 PMCID: PMC10853795 DOI: 10.1093/nar/gkad1136] [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: 09/13/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023] Open
Abstract
tRNA superwobbling, used by certain bacteria and organelles, is an intriguing decoding concept in which a single tRNA isoacceptor is used to decode all synonymous codons of a four-fold degenerate codon box. While Escherichia coli relies on three tRNAGly isoacceptors to decode the four glycine codons (GGN), Mycoplasma mycoides requires only a single tRNAGly. Both organisms express tRNAGly with the anticodon UCC, which are remarkably similar in sequence but different in their decoding ability. By systematically introducing mutations and altering the number and type of tRNA modifications using chemically synthesized tRNAs, we elucidated the contribution of individual nucleotides and chemical groups to decoding by the E. coli and M. mycoides tRNAGly. The tRNA sequence was identified as the key factor for superwobbling, revealing the T-arm sequence as a novel pivotal element. In addition, the presence of tRNA modifications, although not essential for providing superwobbling, was shown to delicately fine-tune and balance the decoding of synonymous codons. This emphasizes that the tRNA sequence and its modifications together form an intricate system of high complexity that is indispensable for accurate and efficient decoding.
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Affiliation(s)
- Maria Kompatscher
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Karolina Bartosik
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Kevin Erharter
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Raphael Plangger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Fabian Sebastian Juen
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Eric Westhof
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l’ARN, CNRS UPR 9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Matthias D Erlacher
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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Thaler J, Syroegin EA, Breuker K, Polikanov YS, Micura R. Practical Synthesis of N-Formylmethionylated Peptidyl-tRNA Mimics. ACS Chem Biol 2023; 18:2233-2239. [PMID: 37433044 PMCID: PMC10594587 DOI: 10.1021/acschembio.3c00237] [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: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023]
Abstract
Hydrolysis-resistant RNA-peptide conjugates that mimic peptidyl-tRNAs are frequently needed for structural and functional studies of protein synthesis in the ribosome. Such conjugates are accessible by chemical solid-phase synthesis, allowing for the utmost flexibility of both the peptide and the RNA sequence. Commonly used protection group strategies, however, have severe limitations with respect to generating the characteristic Nα-formylmethionyl terminus because the formyl group of the conjugate synthesized at the solid support is easily cleaved during the final basic deprotection/release step. In this study, we demonstrate a simple solution to the problem by coupling appropriately activated Nα-formyl methionine to the fully deprotected conjugate. The structural integrity of the obtained Nα-formylmethionyl conjugate─and hence the chemoselectivity of the reaction─were verified by Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry sequence analysis. Additionally, we confirmed the applicability of our procedure for structural studies by obtaining two structures of the ribosome in complex with either fMAI-nh-ACCA or fMFI-nh-ACCA in the P site and ACC-PMN in the A site of the bacterial ribosome at 2.65 and 2.60 Å resolution, respectively. In summary, our approach for hydrolysis-resistant Nα-formylated RNA-peptide conjugates is synthetically straightforward and opens up new avenues to explore ribosomal translation with high-precision substrate mimics.
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Affiliation(s)
- Julia Thaler
- Institute
of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Egor A. Syroegin
- Department
of Biological Sciences, University of Illinois
at Chicago, Chicago, Illinois 60607, United States
| | - Kathrin Breuker
- Institute
of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - 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
| | - Ronald Micura
- Institute
of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
- Center
for Biomolecular Sciences, University of
Illinois at Chicago, Chicago, Illinois 60607, United States
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4
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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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5
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Insights into the ribosome function from the structures of non-arrested ribosome-nascent chain complexes. Nat Chem 2023; 15:143-153. [PMID: 36316410 PMCID: PMC9840698 DOI: 10.1038/s41557-022-01073-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 09/23/2022] [Indexed: 12/24/2022]
Abstract
During protein synthesis, the growing polypeptide threads through the ribosomal exit tunnel and modulates ribosomal activity by itself or by sensing various small molecules, such as metabolites or antibiotics, appearing in the tunnel. While arrested ribosome-nascent chain complexes (RNCCs) have been extensively studied structurally, the lack of a simple procedure for the large-scale preparation of peptidyl-tRNAs, intermediates in polypeptide synthesis that carry the growing chain, means that little attention has been given to RNCCs representing functionally active states of the ribosome. Here we report the facile synthesis of stably linked peptidyl-tRNAs through a chemoenzymatic approach based on native chemical ligation and use them to determine several structures of RNCCs in the functional pre-attack state of the peptidyl transferase centre. These structures reveal that C-terminal parts of the growing peptides adopt the same uniform β-strand conformation stabilized by an intricate network of hydrogen bonds with the universally conserved 23S rRNA nucleotides, and explain how the ribosome synthesizes growing peptides containing various sequences with comparable efficiencies.
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6
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Bremer J, Richter C, Schwalbe H, Richert C. Synthesis of a Peptidoyl RNA Hairpin via a Combination of Solid-Phase and Template-Directed Chain Assembly. Chembiochem 2022; 23:e202200352. [PMID: 35867587 PMCID: PMC9542650 DOI: 10.1002/cbic.202200352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/21/2022] [Indexed: 12/02/2022]
Abstract
Peptidoyl RNAs are the products of ribosome‐free, single‐nucleotide translation. They contain a peptide in the backbone of the oligoribonucleotide and are interesting from a synthetic and a bioorganic point of view. A synthesis of a stabilized version of peptidoyl RNA, with an amide bond between the C‐terminus of a peptide and a 3′‐amino‐2′,3′‐dideoxynucleoside in the RNA chain was developed. The preferred synthetic route used an N‐Teoc‐protected aminonucleoside support and involved a solution‐phase coupling of the amino‐terminal oligonucleotide to a dipeptido dinucleotide. Exploratory UV‐melting and NMR analysis of the hairpin 5′‐UUGGCGAAAGCdC‐LeuLeu‐AA‐3′ indicated that the peptide‐linked RNA segments do not fold in a cooperative fashion. The synthetic access to doubly RNA‐linked peptides on a scale sufficient for structural biology opens the door to the exploration of their structural and biochemical properties.
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Affiliation(s)
- Jennifer Bremer
- University of Stuttgart: Universitat Stuttgart, Chemistry, GERMANY
| | - Christian Richter
- Universität Frankfurt am Main: Goethe-Universitat Frankfurt am Main, Chemistry, GERMANY
| | - Harald Schwalbe
- Universität Frankfurt am Main: Goethe-Universitat Frankfurt am Main, Chemistry, GERMANY
| | - Clemens Richert
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, GERMANY
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7
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Räuchle M, Leveau G, Richert C. Synthesis of Peptido RNAs from Unprotected Peptides and Oligoribonucleotides via Coupling in Aqueous Solution. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Maximilian Räuchle
- Institute of Organic Chemistry University of Stuttgart 70569 Stuttgart Germany
| | - Gabrielle Leveau
- Institute of Organic Chemistry University of Stuttgart 70569 Stuttgart Germany
| | - Clemens Richert
- Institute of Organic Chemistry University of Stuttgart 70569 Stuttgart Germany
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8
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Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020; 49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
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Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University Innsbruck, Innsbruck, Austria.
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9
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Katoh T, Suga H. Flexizyme-catalyzed synthesis of 3'-aminoacyl-NH-tRNAs. Nucleic Acids Res 2019; 47:e54. [PMID: 30843032 PMCID: PMC6511858 DOI: 10.1093/nar/gkz143] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/08/2019] [Accepted: 03/02/2019] [Indexed: 11/15/2022] Open
Abstract
Structural analysis of ribosomes in complex with aminoacyl- and/or peptidyl-transfer RNA (tRNA) often suffers from rapid hydrolysis of the ester bond of aminoacyl-tRNAs. To avoid this issue, several methods to introduce an unhydrolyzable amide bond instead of the canonical ester bond have been developed to date. However, the existing methodologies require rather complex steps of synthesis and are often inapplicable to a variety of amino acids including those with noncanonical structures. Here, we report a new method to synthesize 3'-aminoacyl-NH-tRNAs by means of flexizymes-ribozymes capable of charging amino acids onto tRNAs. We show that two types of flexizymes, dFx and eFx, are able to charge various amino acids, including nonproteinogenic ones, onto tRNA or microhelix RNA bearing the 3'-deoxy-3'-amino-adenosine. Due to the versatility of the flexizymes toward any pair of nonproteinogenic amino acids and full-length or fragment tRNAs, this method provides researchers an opportunity to use a wide array of hydrolytically stable 3'-aminoacyl-NH-tRNAs and analogs for various studies.
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Affiliation(s)
- Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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10
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Dégut C, Schwarz V, Ponchon L, Barraud P, Micura R, Tisné C. Design of cross-linked RNA/protein complexes for structural studies. Biochimie 2019; 164:95-98. [DOI: 10.1016/j.biochi.2019.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/28/2019] [Indexed: 10/27/2022]
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11
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Kaiser S, Jurkowski TP, Kellner S, Schneider D, Jeltsch A, Helm M. The RNA methyltransferase Dnmt2 methylates DNA in the structural context of a tRNA. RNA Biol 2016; 14:1241-1251. [PMID: 27819523 PMCID: PMC5699543 DOI: 10.1080/15476286.2016.1236170] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The amino acid sequence of Dnmt2 is very similar to the catalytic domains of bacterial and eukaryotic DNA-(cytosine 5)-methyltransferases, but it efficiently catalyzes tRNA methylation, while its DNA methyltransferase activity is the subject of controversial reports with rates varying between zero and very weak. By using composite nucleic acid molecules as substrates, we surprisingly found that DNA fragments, when presented as covalent DNA-RNA hybrids in the structural context of a tRNA, can be more efficiently methylated than the corresponding natural tRNA substrate. Furthermore, by stepwise development of tRNAAsp, we showed that this natural Dnmt2 substrate could be engineered to employ RNAs that act like guide RNAs in vitro. The 5’-half of tRNAAsp was able to efficiently guide methylation toward a single stranded tRNA fragment as would result from tRNA cleavage by tRNA specific nucleases. In a more artificial setting, a composite system of guide RNAs could ultimately be engineered to enable the enzyme to perform cytidine methylation on single stranded DNA in vitro.
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Affiliation(s)
- Steffen Kaiser
- a Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz , Mainz , Germany
| | - Tomasz P Jurkowski
- b Institute of Biochemistry, Faculty of Chemistry, University Stuttgart , Stuttgart , Germany
| | - Stefanie Kellner
- a Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz , Mainz , Germany
| | - Dirk Schneider
- a Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz , Mainz , Germany
| | - Albert Jeltsch
- b Institute of Biochemistry, Faculty of Chemistry, University Stuttgart , Stuttgart , Germany
| | - Mark Helm
- a Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz , Mainz , Germany
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12
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Sothiselvam S, Neuner S, Rigger L, Klepacki D, Micura R, Vázquez-Laslop N, Mankin AS. Binding of Macrolide Antibiotics Leads to Ribosomal Selection against Specific Substrates Based on Their Charge and Size. Cell Rep 2016; 16:1789-99. [PMID: 27498876 DOI: 10.1016/j.celrep.2016.07.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/06/2016] [Accepted: 07/04/2016] [Indexed: 11/25/2022] Open
Abstract
Macrolide antibiotic binding to the ribosome inhibits catalysis of peptide bond formation between specific donor and acceptor substrates. Why particular reactions are problematic for the macrolide-bound ribosome remains unclear. Using comprehensive mutational analysis and biochemical experiments with synthetic substrate analogs, we find that the positive charge of these specific residues and the length of their side chains underlie inefficient peptide bond formation in the macrolide-bound ribosome. Even in the absence of antibiotic, peptide bond formation between these particular donors and acceptors is rather inefficient, suggesting that macrolides magnify a problem present for intrinsically difficult substrates. Our findings emphasize the existence of functional interactions between the nascent protein and the catalytic site of the ribosomal peptidyl transferase center.
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Affiliation(s)
| | - Sandro Neuner
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold Franzens University, 6020 Innsbruck, Austria
| | - Lukas Rigger
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold Franzens University, 6020 Innsbruck, Austria
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold Franzens University, 6020 Innsbruck, Austria
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA.
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA.
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13
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Geiermann AS, Micura R. Native Chemical Ligation of Hydrolysis-Resistant 3'-NH-Cysteine-Modified RNA. ACTA ACUST UNITED AC 2015; 62:4.64.1-4.64.36. [PMID: 26380904 DOI: 10.1002/0471142700.nc0464s62] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Hydrolysis-resistant RNA-peptide conjugates that contain a 3'-NH linkage between the adenosine ribose and the C-terminal carboxyl group of a peptide moiety instead of the natural ester mimic acylated tRNA termini. Their detailed preparation that combines solid-phase oligonucleotide synthesis and bioconjugation is described here. The key step is native chemical ligation (NCL) of 3'-NH-cysteine-modified RNA to highly soluble peptide thioesters. These hydrolysis-resistant 3'-NH-peptide-modified RNAs, containing the universally conserved 3'-CCA end of tRNA, are biologically active and can bind to the ribosome. They can be used as valuable probes for structural and functional studies of the ribosomal elongation cycle.
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Affiliation(s)
- Anna-Skrollan Geiermann
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Chemistry and Biomedicine, Leopold Franzens University, Innsbruck, Austria
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14
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Synthesis of aminoacylated N(6),N(6)-dimethyladenosine solid support for efficient access to hydrolysis-resistant 3'-charged tRNA mimics. Bioorg Med Chem 2014; 22:6989-95. [PMID: 25457127 PMCID: PMC4270447 DOI: 10.1016/j.bmc.2014.09.054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 09/25/2014] [Indexed: 11/21/2022]
Abstract
RNA-amino acid and RNA-peptide conjugates that mimic charged tRNA 3'-ends are valuable substrates for structural and functional investigations of ribosomal complexes. To obtain such conjugates, most synthetic approaches that are found in the literature make use of puromycin. This well available aminonucleoside antibiotic contains a dimethylamino group at the nucleobase and a methylated tyrosine that is connected via an amide linkage to the ribose moiety. To increase structural diversity, we present the synthesis of a N(6),N(6)-dimethylated 3'-azido-3'-deoxyadenosine precursor that can be coupled to any amino acid. Further derivatization results in the solid support that is eligible for the preparation of stable 3'-aminoacyl- or 3'-peptidyl-tRNA termini with an amide instead of the natural ester linkage. The present work expands our previously established route that delivered a broad range of peptidyl-tRNA mimics to the corresponding counterparts with N(6),N(6)-dimethylation pattern of the terminal adenosine (A76). This aspect is of significance to modulate the binding preferences of the mimics for ribosomal A- versus P-site.
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15
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Rigger L, Schmidt RL, Holman KM, Simonović M, Micura R. The synthesis of methylated, phosphorylated, and phosphonated 3'-aminoacyl-tRNA(Sec) mimics. Chemistry 2013; 19:15872-8. [PMID: 24127424 DOI: 10.1002/chem.201302188] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Indexed: 11/12/2022]
Abstract
The twenty first amino acid, selenocysteine (Sec), is the only amino acid that is synthesized on its cognate transfer RNA (tRNA(Sec)) in all domains of life. The multistep pathway involves O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS), an enzyme that catalyzes the terminal chemical reaction during which the phosphoseryl-tRNA(Sec) intermediate is converted into selenocysteinyl-tRNA(Sec). The SepSecS architecture and the mode of tRNA(Sec) recognition have been recently determined at atomic resolution. The crystal structure provided valuable insights that gave rise to mechanistic proposals that could not be validated because of the lack of appropriate molecular probes. To further improve our understanding of the mechanism of the biosynthesis of selenocysteine in general and the mechanism of SepSecS in particular, stable tRNA(Sec) substrates carrying aminoacyl moieties that mimic particular reaction intermediates are needed. Here, we report on the accurate synthesis of methylated, phosphorylated, and phosphonated serinyl-derived tRNA(Sec) mimics that contain a hydrolysis-resistant ribose 3'-amide linkage instead of the natural ester bond. The procedures introduced allow for efficient site-specific methylation and/or phosphorylation directly on the solid support utilized in the automated RNA synthesis. For the preparation of (S)-2-amino-4-phosphonobutyric acid-oligoribonucleotide conjugates, a separate solid support was generated. Furthermore, we developed a three-strand enzymatic ligation protocol to obtain the corresponding full-length tRNA(Sec) derivatives. Finally, we developed an electrophoretic mobility shift assay (EMSA) for rapid, qualitative characterization of the SepSecS-tRNA interactions. The novel tRNA(Sec) mimics are promising candidates for further elucidation of the biosynthesis of selenocysteine by X-ray crystallography and other biochemical approaches, and could be attractive for similar studies on other tRNA-dependent enzymes.
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Affiliation(s)
- Lukas Rigger
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University, Center for Chemistry and Biomedicine, Innrain 80-82, 6020 Innsbruck (Austria), Fax: (+43) 512 507 57799
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16
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Fonvielle M, Li de La Sierra-Gallay I, El-Sagheer AH, Lecerf M, Patin D, Mellal D, Mayer C, Blanot D, Gale N, Brown T, van Tilbeurgh H, Ethève-Quelquejeu M, Arthur M. The structure of FemX(Wv) in complex with a peptidyl-RNA conjugate: mechanism of aminoacyl transfer from Ala-tRNA(Ala) to peptidoglycan precursors. Angew Chem Int Ed Engl 2013; 52:7278-81. [PMID: 23744707 DOI: 10.1002/anie.201301411] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Matthieu Fonvielle
- Laboratoire de Recherche Moléculaire sur les Antibiotiques, Centre de Recherche des Cordeliers, Equipe 12, INSERM, U872, 75006 Paris, France
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17
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Fonvielle M, Li de La Sierra-Gallay I, El-Sagheer AH, Lecerf M, Patin D, Mellal D, Mayer C, Blanot D, Gale N, Brown T, van Tilbeurgh H, Ethève-Quelquejeu M, Arthur M. The Structure of FemXWvin Complex with a Peptidyl-RNA Conjugate: Mechanism of Aminoacyl Transfer from Ala-tRNAAlato Peptidoglycan Precursors. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301411] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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Geiermann AS, Micura R. Selective desulfurization significantly expands sequence variety of 3'-peptidyl-tRNA mimics obtained by native chemical ligation. Chembiochem 2012; 13:1742-5. [PMID: 22786696 PMCID: PMC3430856 DOI: 10.1002/cbic.201200368] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Indexed: 12/30/2022]
Affiliation(s)
- Anna-Skrollan Geiermann
- Institute of Organic Chemistry, CCB: Center for Chemistry and Biomedicine, University of Innsbruck6020 Innsbruck (Austria) E-mail:
| | - Ronald Micura
- Institute of Organic Chemistry, CCB: Center for Chemistry and Biomedicine, University of Innsbruck6020 Innsbruck (Austria) E-mail:
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19
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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20
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Graber D, Trappl K, Steger J, Geiermann AS, Rigger L, Moroder H, Polacek N, Micura R. Deoxyribozyme-based, semisynthetic access to stable peptidyl-tRNAs exemplified by tRNAVal carrying a macrolide antibiotic resistance peptide. Methods Mol Biol 2012; 848:201-213. [PMID: 22315071 DOI: 10.1007/978-1-61779-545-9_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present a protocol for the reliable synthesis of non-hydrolyzable 3'-peptidyl-tRNAs that contain all the respective genuine nucleoside modifications. The approach is exemplified by tRNA(Val)-3'-NH-VFLVM-NH(2) and relies on commercially available Escherichia coli tRNA(Val). This tRNA was cleaved site-specifically within the TΨC loop using a 10-23 type DNA enzyme to obtain a 58 nt tRNA 5'-fragment which contained the modifications. After cleavage of the 2',3'-cyclophosphate moiety from the 5'-fragment, it was ligated to the 18 nt RNA-pentapeptide conjugate which had been chemically synthesized. By this methodology, tRNA(Val)-3'-NH-VFLVM-NH(2) is accessible in efficient manner. Furthermore, we point out that the approach is applicable to other types of tRNA.
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MESH Headings
- Anti-Bacterial Agents/pharmacology
- Base Sequence
- DNA, Catalytic/metabolism
- Drug Resistance, Bacterial
- Escherichia coli
- Macrolides/pharmacology
- Mass Spectrometry
- Models, Molecular
- Nucleic Acid Conformation
- Peptides
- Phenol/chemistry
- Phosphorylation
- RNA Stability
- RNA, Bacterial/metabolism
- RNA, Transfer, Amino Acyl/chemical synthesis
- RNA, Transfer, Val/chemical synthesis
- RNA, Transfer, Val/chemistry
- RNA, Transfer, Val/isolation & purification
- RNA, Transfer, Val/metabolism
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Affiliation(s)
- Dagmar Graber
- Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), University of Innsbruck, Innsbruck, Austria
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21
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Geiermann AS, Polacek N, Micura R. Native Chemical Ligation of Hydrolysis-Resistant 3′-Peptidyl–tRNA Mimics. J Am Chem Soc 2011; 133:19068-71. [DOI: 10.1021/ja209053b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Anna-Skrollan Geiermann
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Austria
| | - Norbert Polacek
- Innsbruck Biocenter, Division of Genomics and RNomics, Medical University of Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Austria
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22
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Steger J, Micura R. Functionalized polystyrene supports for solid-phase synthesis of glycyl-, alanyl-, and isoleucyl-RNA conjugates as hydrolysis-resistant mimics of peptidyl-tRNAs. Bioorg Med Chem 2011; 19:5167-74. [PMID: 21807524 PMCID: PMC3162138 DOI: 10.1016/j.bmc.2011.07.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 07/08/2011] [Accepted: 07/10/2011] [Indexed: 12/20/2022]
Abstract
RNA-peptide conjugates that mimic amino acid-charged tRNAs and peptidyl-tRNAs are of high importance for structural and functional investigations of ribosomal complexes. Here, we present the synthesis of glycyl-, alanyl-, and isoleucyladenosine modified solid supports that are eligible for the synthesis of stable 3′-aminoacyl- and 3′-peptidyl-tRNA termini with an amide instead of the natural ester linkage. The present work significantly expands the range of accessible peptidyl-tRNA mimics for ribosomal studies.
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Affiliation(s)
- Jessica Steger
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, University of Innsbruck, Innsbruck, Austria
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