1
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Fricke R, Knudson I, Swenson CV, Smaga S, Schepartz A. Direct and quantitative analysis of tRNA acylation using intact tRNA liquid chromatography-mass spectrometry. Nat Protoc 2025; 20:1246-1274. [PMID: 39762443 DOI: 10.1038/s41596-024-01086-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 10/04/2024] [Indexed: 05/14/2025]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) provide an essential functional link between an mRNA sequence and the protein it encodes. aaRS enzymes catalyze a two-step chemical reaction that acylates specific tRNAs with a cognate α-amino acid. In addition to their role in translation, acylated tRNAs contribute to non-ribosomal natural product biosynthesis and are implicated in multiple human diseases. In synthetic biology, the acylation of tRNAs with a non-canonical α-amino acid or, more recently, a non-α-amino acid monomer is a critical first step in the incorporation of these monomers into proteins, where they can be used for fundamental and applied science. These endeavors all demand an understanding of aaRS activity and specificity. Here, we describe a liquid chromatography-mass spectrometry assay that directly monitors aaRS activity by detecting the intact acyl-tRNA product. After a simple tRNA acylation reaction workup, acyl- and non-acyl-tRNA molecules are resolved by using ion-pairing reverse-phase chromatography, and their exact masses are determined by using high-resolution time-of-flight mass spectrometry. Our assay is fast and simple, quantifies reaction yields as low as 0.23% and can also be used on tRNAs acylated with flexizyme to detect products that are undetectable by using standard techniques. The protocol requires basic expertise in molecular biology, liquid chromatography-mass spectrometry and RNase-free techniques. This protocol takes ≥5 h to complete, depending on the number of samples.
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Affiliation(s)
- Riley Fricke
- Department of Chemistry, University of California, Berkeley, CA, USA
- NSF Center for Genetically Encoded Materials (C-GEM), Berkeley, CA, USA
| | - Isaac Knudson
- Department of Chemistry, University of California, Berkeley, CA, USA
- NSF Center for Genetically Encoded Materials (C-GEM), Berkeley, CA, USA
| | - Cameron Verdayne Swenson
- Department of Chemistry, University of California, Berkeley, CA, USA
- NSF Center for Genetically Encoded Materials (C-GEM), Berkeley, CA, USA
| | - Sarah Smaga
- Department of Chemistry, University of California, Berkeley, CA, USA
- NSF Center for Genetically Encoded Materials (C-GEM), Berkeley, CA, USA
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, CA, USA.
- NSF Center for Genetically Encoded Materials (C-GEM), Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- ARC Institute, Palo Alto, CA, USA.
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2
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Pressimone M, Schissel C, Goss I, Swenson C, Schepartz A. Monitoring monomer-specific acyl-tRNA levels in cells with PARTI. Nucleic Acids Res 2025; 53:gkaf327. [PMID: 40335069 PMCID: PMC12058263 DOI: 10.1093/nar/gkaf327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Revised: 04/02/2025] [Accepted: 04/29/2025] [Indexed: 05/09/2025] Open
Abstract
We describe a new assay that reports directly on the acylation state of a user-chosen transfer RNA (tRNA) in cells. We call this assay 3-Prime Adenosine-Retaining Aminoacyl-tRNA Isolation (PARTI). It relies on high-resolution mass spectrometry identification of the acyl-adenosine species released upon RNase A cleavage of isolated cellular tRNA. Here we develop the PARTI workflow and apply it to understand three recent observations related to the cellular incorporation of non-α-amino acid monomers into protein: (i) the origins of the apparent selectivity of translation with respect to β2-hydroxy acid enantiomers; (ii) the activity of PylRS variants for benzyl derivatives of malonic acid; and (iii) the apparent inability of N-Me amino acids to function as ribosome substrates in living cells. Using the PARTI assay, we also provide direct evidence for the cellular production of 2',3'-diacylated tRNA in certain cases. The ease and simplicity of the PARTI workflow should benefit ongoing efforts to study and improve the cellular incorporation of non-α-amino acid monomers into proteins.
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Affiliation(s)
- Meghan A Pressimone
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, United States
| | - Carly K Schissel
- Department of Chemistry, University of California, Berkeley CA 94720, United States
| | - Isabella H Goss
- Department of Chemistry, University of California, Berkeley CA 94720, United States
| | - Cameron V Swenson
- Department of Chemistry, University of California, Berkeley CA 94720, United States
| | - Alanna Schepartz
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, United States
- Department of Chemistry, University of California, Berkeley CA 94720, United States
- Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, United States
- Chan Zuckerberg Biohub, San Francisco, CA 94158, United States
- ARC Institute, Palo Alto, CA 94304, United States
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3
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Dale HJA, Sutherland JD. Indirect Formation of Peptide Bonds as a Prelude to Ribosomal Transpeptidation. J Am Chem Soc 2025; 147:305-317. [PMID: 39693575 PMCID: PMC11726440 DOI: 10.1021/jacs.4c10326] [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: 07/29/2024] [Revised: 11/20/2024] [Accepted: 11/21/2024] [Indexed: 12/20/2024]
Abstract
The catalytic competency of the ribosome in extant protein biosynthesis is thought to arise primarily from two sources: an ability to precisely juxtapose the termini of two key substrates─3'-aminoacyl and N-acyl-aminoacyl tRNAs─and an ability to ease direct transpeptidation by their desolvation and encapsulation. In the absence of ribosomal, or enzymatic, protection, however, these activated alkyl esters undergo efficient hydrolysis, while significant entropic barriers serve to hamper their intermolecular cross-aminolysis in bulk water. Given that the spontaneous emergence of a catalyst of comparable size and sophistication to the ribosome in a prebiotic RNA world would appear implausible, it is thus natural to ask how appreciable peptide formation could have occurred with such substrates in bulk water without the aid of advanced ribozymatic catalysis. Using a combination of fluorine-tagged aminoacyl adenylate esters, in situ monitoring by 19F{1H} NMR spectroscopy, analytical deconvolution of kinetics, pH-rate profile analysis, and temperature-dependence studies, we here explore the mechanistic landscape of indirect amidation, via transesterification and O-to-N rearrangement, as a highly efficient, alternative manifold for transpeptidation that may have served as a prelude to ribosomal peptide synthesis. Our results suggest a potentially overlooked role for those amino acids implicated by the cyanosulfidic reaction network with hydroxyl side chains (Ser and Thr), and they also help to resolve some outstanding ambiguities in the broader literature regarding studies of similar systems (e.g., aminolyzes with Tris buffer). The evolutionary implications of this mode of peptide synthesis and the involvement of a very specific subset of amino acids are discussed.
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Affiliation(s)
- Harvey J. A. Dale
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K.
| | - John D. Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K.
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4
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Fricke R, Swenson CV, Roe LT, Hamlish NX, Shah B, Zhang Z, Ficaretta E, Ad O, Smaga S, Gee CL, Chatterjee A, Schepartz A. Expanding the substrate scope of pyrrolysyl-transfer RNA synthetase enzymes to include non-α-amino acids in vitro and in vivo. Nat Chem 2023; 15:960-971. [PMID: 37264106 PMCID: PMC10322718 DOI: 10.1038/s41557-023-01224-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/28/2023] [Indexed: 06/03/2023]
Abstract
The absence of orthogonal aminoacyl-transfer RNA (tRNA) synthetases that accept non-L-α-amino acids is a primary bottleneck hindering the in vivo translation of sequence-defined hetero-oligomers and biomaterials. Here we report that pyrrolysyl-tRNA synthetase (PylRS) and certain PylRS variants accept α-hydroxy, α-thio and N-formyl-L-α-amino acids, as well as α-carboxy acid monomers that are precursors to polyketide natural products. These monomers are accommodated and accepted by the translation apparatus in vitro; those with reactive nucleophiles are incorporated into proteins in vivo. High-resolution structural analysis of the complex formed between one PylRS enzyme and a m-substituted 2-benzylmalonic acid derivative revealed an active site that discriminates prochiral carboxylates and accommodates the large size and distinct electrostatics of an α-carboxy substituent. This work emphasizes the potential of PylRS-derived enzymes for acylating tRNA with monomers whose α-substituent diverges substantially from the α-amine of proteinogenic amino acids. These enzymes or derivatives thereof could synergize with natural or evolved ribosomes and/or translation factors to generate diverse sequence-defined non-protein heteropolymers.
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Affiliation(s)
- Riley Fricke
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Cameron V Swenson
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Leah Tang Roe
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Noah Xue Hamlish
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Bhavana Shah
- Process Development, Amgen, Thousand Oaks, CA, USA
| | | | - Elise Ficaretta
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Omer Ad
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Sarah Smaga
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Christine L Gee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Abhishek Chatterjee
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
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5
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Zhang C, Talukder P, Dedkova LM, Hecht SM. Facilitated synthesis of proteins containing modified dipeptides. Bioorg Med Chem 2021; 41:116210. [PMID: 34022527 DOI: 10.1016/j.bmc.2021.116210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 11/29/2022]
Abstract
The elaboration of peptides and proteins containing non-proteinogenic amino acids has been realized using several complementary strategies, including chemical synthesis, ribosome- or non-ribosome-mediated elaboration, intein-mediated polypeptide rearrangements, or some combination of these strategies. All of these have strengths and limitations, and significant efforts have been focused on minimizing the effects of limitations, to improve the overall utility of individual strategies. Our laboratory has studied ribosomally mediated peptide and protein synthesis involving a wide variety of non-proteinogenic amino acids, and in recent years we have described a novel strategy for the selection of modified bacterial ribosomes. These modified ribosomes have enabled the incorporation into peptides and proteins of numerous modified amino acids not accessible using wild-type ribosomes. This has included d-amino acids, β-amino acids, dipeptides and dipeptidomimetic species, as well as phosphorylated amino acids. Presently, we have considered novel strategies for incorporating non-proteinogenic amino acids in improved yields. This has included the incorporation of non-proteinogenic amino acids into contiguous positions, a transformation known to be challenging. We demonstrate the preparation of this type of protein modification by utilizing a suppressor tRNACUA activated with a dipeptide consisting of two identical non-proteinogenic amino acids, in the presence of modified ribosomes selected to recognize such dipeptides. Also, we demonstrate that the use of bis-aminoacylated suppressor tRNAs, shown previously to increase protein yields significantly in vitro, can be extended to the use of non-proteinogenic amino acids.
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Affiliation(s)
- Chao Zhang
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Poulami Talukder
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
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6
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Maini R, Chowdhury SR, Dedkova LM, Roy B, Daskalova SM, Paul R, Chen S, Hecht SM. Protein Synthesis with Ribosomes Selected for the Incorporation of β-Amino Acids. Biochemistry 2015; 54:3694-706. [PMID: 25982410 PMCID: PMC4472090 DOI: 10.1021/acs.biochem.5b00389] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/16/2015] [Indexed: 02/04/2023]
Abstract
In an earlier study, β³-puromycin was used for the selection of modified ribosomes, which were utilized for the incorporation of five different β-amino acids into Escherichia coli dihydrofolate reductase (DHFR). The selected ribosomes were able to incorporate structurally disparate β-amino acids into DHFR, in spite of the use of a single puromycin for the selection of the individual clones. In this study, we examine the extent to which the structure of the β³-puromycin employed for ribosome selection influences the regio- and stereochemical preferences of the modified ribosomes during protein synthesis; the mechanistic probe was a single suppressor tRNA(CUA) activated with each of four methyl-β-alanine isomers (1-4). The modified ribosomes were found to incorporate each of the four isomeric methyl-β-alanines into DHFR but exhibited a preference for incorporation of 3(S)-methyl-β-alanine (β-mAla; 4), i.e., the isomer having the same regio- and stereochemistry as the O-methylated β-tyrosine moiety of β³-puromycin. Also conducted were a selection of clones that are responsive to β²-puromycin and a demonstration of reversal of the regio- and stereochemical preferences of these clones during protein synthesis. These results were incorporated into a structural model of the modified regions of 23S rRNA, which included in silico prediction of a H-bonding network. Finally, it was demonstrated that incorporation of 3(S)-methyl-β-alanine (β-mAla; 4) into a short α-helical region of the nucleic acid binding domain of hnRNP LL significantly stabilized the helix without affecting its DNA binding properties.
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MESH Headings
- Alanine/analogs & derivatives
- Alanine/chemistry
- Alanine/metabolism
- Escherichia coli/enzymology
- Escherichia coli/metabolism
- Escherichia coli Proteins/biosynthesis
- Escherichia coli Proteins/chemistry
- Heterogeneous-Nuclear Ribonucleoprotein L/biosynthesis
- Heterogeneous-Nuclear Ribonucleoprotein L/chemistry
- Heterogeneous-Nuclear Ribonucleoprotein L/genetics
- Humans
- Hydrogen Bonding
- Models, Molecular
- Molecular Dynamics Simulation
- Mutant Proteins/biosynthesis
- Mutant Proteins/chemistry
- Mutant Proteins/genetics
- Nucleotide Motifs
- Peptidyl Transferases/genetics
- Peptidyl Transferases/metabolism
- Protein Conformation
- Protein Stability
- Puromycin/analogs & derivatives
- Puromycin/chemistry
- Puromycin/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/chemistry
- Ribosomes/metabolism
- Stereoisomerism
- Substrate Specificity
- Tetrahydrofolate Dehydrogenase/biosynthesis
- Tetrahydrofolate Dehydrogenase/chemistry
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Affiliation(s)
- Rumit Maini
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Sandipan Roy Chowdhury
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M. Dedkova
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Basab Roy
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Sasha M. Daskalova
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Rakesh Paul
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M. Hecht
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
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7
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Nangreave RC, Dedkova LM, Chen S, Hecht SM. A New Strategy for the Synthesis of Bisaminoacylated tRNAs. Org Lett 2011; 13:4906-9. [DOI: 10.1021/ol201993c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ryan C. Nangreave
- Center for BioEnergetics, The Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85827, United States
| | - Larisa M. Dedkova
- Center for BioEnergetics, The Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85827, United States
| | - Shengxi Chen
- Center for BioEnergetics, The Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85827, United States
| | - Sidney M. Hecht
- Center for BioEnergetics, The Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85827, United States
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8
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Duca M, Trindle CO, Hecht SM. Structural basis for the exceptional stability of bisaminoacylated nucleotides and transfer RNAs. J Am Chem Soc 2011; 133:11368-77. [PMID: 21648486 DOI: 10.1021/ja203994e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
At least one bisaminoacyl-tRNA is synthesized in nature (by Thermus thermophilus phenylalanyl-tRNA synthetase), and many disubstituted tRNAs have been prepared in vitro. Such misacylated tRNAs are able to participate in protein synthesis, even though they lack the free 2'-OH group of the 3'-terminal adenosine moiety. Their ready participation in protein synthesis implies significant chemical reactivity. The basis for this reactivity has been documented previously. Surprisingly, the aminoacyl moieties of these tRNAs also exhibit exceptional chemical stability. In the present report, bisaminoacylated nucleotides are investigated computationally and experimentally to define the basis for the stability of such species. Molecular modeling of bisalanyl-AMP in the absence of solvent and in the presence of a limited number of water molecules revealed two common features among the low-energy structures. The first was the presence of H-bonding interactions between the two aminoacyl moieties. The second was the presence of a H-bonding interaction between the 2'-O-alanyl moiety and the N-3 atom of the adenine nucleobase, typically mediated through a water molecule. The prediction of an interaction between an aminoacyl moiety and the adenine nucleobase was confirmed experimentally by comparing the behavior of bisalanyl-AMP and bisalanyl-UMP in the presence of model nucleophiles. This study suggests a possible role for the adenosine moiety at the 3'-end of aminoanyl-tRNAs in controlling the stability and reactivity of the aminoacyl moiety and has important implications for the reactivity and stability of normal aminoacyl-tRNAs.
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Affiliation(s)
- Maria Duca
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
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9
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Turk RM, Illangasekare M, Yarus M. Catalyzed and spontaneous reactions on ribozyme ribose. J Am Chem Soc 2011; 133:6044-50. [PMID: 21438575 DOI: 10.1021/ja200275h] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The RNA world hypothesis requires that early translation be catalyzed by RNA enzymes. Here we show that a five-nucleotide RNA enzyme, reacting with a tetranucleotide substrate and elevated PheAMP, forms aminoacyl- and peptidyl-RNAs RNA-Phe through RNA-Phe(5). A second series of products is formed from RNA-Phe diesters, after trans migration of phenylalanine from the 2'- to the 3'-hydroxyl group of the substrate RNA, followed by reaminoacylation of the 2'-OH. While the ribozyme is required for initial attachment of phenylalanine to an RNA substrate, as well as reacylation (and thus for formation of all products), further extension into RNA-peptides appears to be an uncatalyzed, but RNA-stimulated reaction. The ribozyme readily turns over at high PheAMP and GCCU concentrations. Thus, GUGGC/GCCU comprises a true RNA enzyme. We define Michaelis-Menten parameters plus and minus divalent magnesium and characterize ca. 20 molecular species of aminoacyl-, peptidyl-, dipeptidyl-, and mixed peptidyl/aminoacyl-RNAs.
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Affiliation(s)
- Rebecca M Turk
- Department of MCD Biology, University of Colorado, Boulder, Colorado 80309-0347, United States
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10
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Fonvielle M, Chemama M, Lecerf M, Villet R, Busca P, Bouhss A, Ethève-Quelquejeu M, Arthur M. Decoding the Logic of the tRNA Regiospecificity of Nonribosomal FemXWv Aminoacyl Transferase. Angew Chem Int Ed Engl 2010; 49:5115-9. [DOI: 10.1002/anie.201001473] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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Fonvielle M, Chemama M, Lecerf M, Villet R, Busca P, Bouhss A, Ethève-Quelquejeu M, Arthur M. Decoding the Logic of the tRNA Regiospecificity of Nonribosomal FemXWv Aminoacyl Transferase. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001473] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Ye S, Ann Berger A, Petzold D, Reimann O, Matt B, Koksch B. Chemical aminoacylation of tRNAs with fluorinated amino acids for in vitro protein mutagenesis. Beilstein J Org Chem 2010; 6:40. [PMID: 20502658 PMCID: PMC2874332 DOI: 10.3762/bjoc.6.40] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 03/23/2010] [Indexed: 01/11/2023] Open
Abstract
This article describes the chemical aminoacylation of the yeast phenylalanine suppressor tRNA with a series of amino acids bearing fluorinated side chains via the hybrid dinucleotide pdCpA and ligation to the corresponding truncated tRNA species. Aminoacyl-tRNAs can be used to synthesize biologically relevant proteins which contain fluorinated amino acids at specific sites by means of a cell-free translation system. Such engineered proteins are expected to contribute to our understanding of discrete fluorines' interaction with canonical amino acids in a native protein environment and to enable the design of fluorinated proteins with arbitrary desired properties.
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Affiliation(s)
- Shijie Ye
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry – Organic Chemistry, Takustrasse 3, 14195 Berlin, Germany; Tel.: 0049-30-83855344; Fax: 0049-30-83855644
| | - Allison Ann Berger
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry – Organic Chemistry, Takustrasse 3, 14195 Berlin, Germany; Tel.: 0049-30-83855344; Fax: 0049-30-83855644
| | - Dominique Petzold
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry – Organic Chemistry, Takustrasse 3, 14195 Berlin, Germany; Tel.: 0049-30-83855344; Fax: 0049-30-83855644
| | - Oliver Reimann
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry – Organic Chemistry, Takustrasse 3, 14195 Berlin, Germany; Tel.: 0049-30-83855344; Fax: 0049-30-83855644
| | - Benjamin Matt
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry – Organic Chemistry, Takustrasse 3, 14195 Berlin, Germany; Tel.: 0049-30-83855344; Fax: 0049-30-83855644
| | - Beate Koksch
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry – Organic Chemistry, Takustrasse 3, 14195 Berlin, Germany; Tel.: 0049-30-83855344; Fax: 0049-30-83855644
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13
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Duca M, Chen S, Hecht SM. Aminoacylation of transfer RNAs with one and two amino acids. Methods 2008; 44:87-99. [PMID: 18241791 DOI: 10.1016/j.ymeth.2007.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Revised: 10/20/2007] [Accepted: 10/22/2007] [Indexed: 11/18/2022] Open
Abstract
The detailed synthesis of (bis)aminoacyl-pdCpAs and the corresponding singly and tandemly activated tRNAs is reported. The synthetic pathway leading to these compounds has been validated for simple amino acid residues as well as for amino acids bearing more complex side chains. Protection/deprotection strategies are described. For the bisaminoacylated tRNAs, both the synthesis of tRNAs bearing the same amino acid residue at the 2' and 3' positions and tRNAs bearing two different aminoacyl moieties are reported. Further, it is shown that the tandemly activated tRNAs are able to participate in protein synthesis.
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Affiliation(s)
- Maria Duca
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, USA.
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14
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Duca M, Chen S, Hecht SM. Modeling the reactive properties of tandemly activated tRNAs. Org Biomol Chem 2008; 6:3292-9. [DOI: 10.1039/b806790b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Rodriguez EA, Lester HA, Dougherty DA. Improved amber and opal suppressor tRNAs for incorporation of unnatural amino acids in vivo. Part 1: minimizing misacylation. RNA (NEW YORK, N.Y.) 2007; 13:1703-14. [PMID: 17698638 PMCID: PMC1986802 DOI: 10.1261/rna.666807] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The incorporation of unnatural amino acids site-specifically is a valuable technique for structure-function studies, incorporation of biophysical probes, and determining protein-protein interactions. THG73 is an amber suppressor tRNA used extensively for the incorporation of >100 different residues in over 20 proteins, but under certain conditions THG73 is aminoacylated in vivo by endogenous aminoacyl-tRNA synthetase. Similar aminoacylation is seen with the Escherichia coli Asn amber suppressor tRNA, which has also been used to incorporate UAAs in many studies. We now find that the natural amino acid placed on THG73 is Gln. Since the E. coli GlnRS recognizes positions in the acceptor stem, we made several acceptor stem mutations in the second to fourth positions on THG73. All mutations reduce aminoacylation in vivo and allow for the selection of highly orthogonal tRNAs. To show the generality of these mutations, we created opal suppressor tRNAs that show less aminoacylation in Xenopus oocytes relative to THG73. We have created a library of Tetrahymena thermophila Gln amber suppressor tRNAs that will be useful for determining optimal suppressor tRNAs for use in other eukaryotic cells.
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Affiliation(s)
- Erik A Rodriguez
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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16
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Hauryliuk V. Evolution of translational machinery: Could translation termination come into being before elongation? J Theor Biol 2007; 248:574-8. [PMID: 17624369 DOI: 10.1016/j.jtbi.2007.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 05/03/2007] [Accepted: 06/01/2007] [Indexed: 11/30/2022]
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Spiegel PC, Ermolenko DN, Noller HF. Elongation factor G stabilizes the hybrid-state conformation of the 70S ribosome. RNA (NEW YORK, N.Y.) 2007; 13:1473-82. [PMID: 17630323 PMCID: PMC1950763 DOI: 10.1261/rna.601507] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Following peptide bond formation, transfer RNAs (tRNAs) and messenger RNA (mRNA) are translocated through the ribosome, a process catalyzed by elongation factor EF-G. Here, we have used a combination of chemical footprinting, peptidyl transferase activity assays, and mRNA toeprinting to monitor the effects of EF-G on the positions of tRNA and mRNA relative to the A, P, and E sites of the ribosome in the presence of GTP, GDP, GDPNP, and fusidic acid. Chemical footprinting experiments show that binding of EF-G in the presence of the non-hydrolyzable GTP analog GDPNP or GDP.fusidic acid induces movement of a deacylated tRNA from the classical P/P state to the hybrid P/E state. Furthermore, stabilization of the hybrid P/E state by EF-G compromises P-site codon-anticodon interaction, causing frame-shifting. A deacylated tRNA bound to the P site and a peptidyl-tRNA in the A site are completely translocated to the E and P sites, respectively, in the presence of EF-G with GTP or GDPNP but not with EF-G.GDP. Unexpectedly, translocation with EF-G.GTP leads to dissociation of deacylated tRNA from the E site, while tRNA remains bound in the presence of EF-G.GDPNP, suggesting that dissociation of tRNA from the E site is promoted by GTP hydrolysis and/or EF-G release. Our results show that binding of EF-G in the presence of GDPNP or GDP.fusidic acid stabilizes the ribosomal intermediate hybrid state, but that complete translocation is supported only by EF-G.GTP or EF-G.GDPNP.
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Affiliation(s)
- P Clint Spiegel
- Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, University of California-Santa Cruz 95064, USA
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Duca M, Maloney DJ, Lodder M, Wang B, Hecht SM. Synthesis of bisaminoacylated pdCpAs and tandemly activated transfer RNAs. Bioorg Med Chem 2007; 15:4629-42. [PMID: 17490885 DOI: 10.1016/j.bmc.2007.03.088] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 03/28/2007] [Accepted: 03/29/2007] [Indexed: 10/23/2022]
Abstract
Described herein is the preparation of new bisacylated tRNAs and their participation in protein synthesis. It has been reported that Thermus thermophilus phenylalanyl-tRNA synthetase can introduce two phenylalanine moieties onto the 3'-terminal adenosine of its cognate tRNA. It is also possible to prepare bisactivated tRNAs in vitro; these participate in protein synthesis [Wang, B.; Zhou, J.; Lodder, M.; Anderson, R. D.; Hecht, S. M. J. Biol. Chem.2006, 281, 13865]. Presently, the chemical strategy used for the synthesis of the key intermediate bisacylated pdCpAs is described. Bis-S-alanyl- and bis-S-methionyl-pdCpAs were prepared initially. Further, S-threonine, S-allo-threonine, S-homoserine, and (S)-(+)-2-amino-3-hydroxy-3-methylbutyric acid were coupled with the dinucleotide to define preparative methods applicable to more complex amino acids bearing additional functionality in the form of an OH group.
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Affiliation(s)
- Maria Duca
- Department of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, USA
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Maloney DJ, Ghanem N, Zhou J, Hecht SM. Positional assignment of differentially substituted bisaminoacylated pdCpAs. Org Biomol Chem 2007; 5:3135-8. [PMID: 17878972 DOI: 10.1039/b708786a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The synthesis and NMR analysis of a 2'-O-alanyl, 3'-O-[1-(13)C]valyl-pdCpA derivative has permitted the definitive assignment of the positions of acylation of tandemly activated pdCpAs, and the bisaminoacylated transfer RNAs derived therefrom.
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Affiliation(s)
- David J Maloney
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
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