51
|
Jackman JE, Alfonzo JD. Transfer RNA modifications: nature's combinatorial chemistry playground. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 4:35-48. [PMID: 23139145 DOI: 10.1002/wrna.1144] [Citation(s) in RCA: 222] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Following synthesis, tRNAs are peppered by numerous chemical modifications which may differentially affect a tRNA's structure and function. Although modifications affecting the business ends of a tRNA are predictably important for cell viability, a majority of modifications play more subtle structural roles that can affect tRNA stability and folding. The current trend is that modifications act in concert and it is in the context of the specific sequence of a given tRNA that they impart their differing effects. Recent developments in the modification field have highlighted the diversity of modifications in tRNA. From these, the combinatorial nature of modifications in explaining previously described phenotypes derived from their absence has emerged as a growing theme.
Collapse
Affiliation(s)
- Jane E Jackman
- The Ohio State Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
| | | |
Collapse
|
52
|
Vilardo E, Nachbagauer C, Buzet A, Taschner A, Holzmann J, Rossmanith W. A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase--extensive moonlighting in mitochondrial tRNA biogenesis. Nucleic Acids Res 2012; 40:11583-93. [PMID: 23042678 PMCID: PMC3526285 DOI: 10.1093/nar/gks910] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Transfer RNAs (tRNAs) reach their mature functional form through several steps of processing and modification. Some nucleotide modifications affect the proper folding of tRNAs, and they are crucial in case of the non-canonically structured animal mitochondrial tRNAs, as exemplified by the apparently ubiquitous methylation of purines at position 9. Here, we show that a subcomplex of human mitochondrial RNase P, the endonuclease removing tRNA 5′ extensions, is the methyltransferase responsible for m1G9 and m1A9 formation. The ability of the mitochondrial tRNA:m1R9 methyltransferase to modify both purines is uncommon among nucleic acid modification enzymes. In contrast to all the related methyltransferases, the human mitochondrial enzyme, moreover, requires a short-chain dehydrogenase as a partner protein. Human mitochondrial RNase P, thus, constitutes a multifunctional complex, whose subunits moonlight in cascade: a fatty and amino acid degradation enzyme in tRNA methylation and the methyltransferase, in turn, in tRNA 5′ end processing.
Collapse
Affiliation(s)
- Elisa Vilardo
- Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | | | | | | | | | | |
Collapse
|
53
|
Bhaskaran H, Rodriguez-Hernandez A, Perona JJ. Kinetics of tRNA folding monitored by aminoacylation. RNA (NEW YORK, N.Y.) 2012; 18:569-80. [PMID: 22286971 PMCID: PMC3285943 DOI: 10.1261/rna.030080.111] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 11/23/2011] [Indexed: 05/20/2023]
Abstract
We describe a strategy for tracking Mg²⁺-initiated folding of ³²P-labeled tRNA molecules to their native structures based on the capacity for aminoacylation by the cognate aminoacyl-tRNA synthetase enzyme. The approach directly links folding to function, paralleling a common strategy used to study the folding of catalytic RNAs. Incubation of unfolded tRNA with magnesium ions, followed by the addition of aminoacyl-tRNA synthetase and further incubation, yields a rapid burst of aminoacyl-tRNA formation corresponding to the prefolded tRNA fraction. A subsequent slower increase in product formation monitors continued folding in the presence of the enzyme. Further analysis reveals the presence of a parallel fraction of tRNA that folds more rapidly than the majority of the population. The application of the approach to study the influence of post-transcriptional modifications in folding of Escherichia coli tRNA₁(Gln) reveals that the modified bases increase the folding rate but do not affect either the equilibrium between properly folded and misfolded states or the folding pathway. This assay allows the use of ³²P-labeled tRNA in integrated studies combining folding, post-transcriptional processing, and aminoacylation reactions.
Collapse
Affiliation(s)
| | | | - John J. Perona
- Department of Chemistry and Biochemistry
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106-9510, USA
- Corresponding author.E-mail .
| |
Collapse
|
54
|
KOBITSKI ANDREIYU, NIERTH ALEXANDER, HENGESBACH MARTIN, JÄSCHKE ANDRES, HELM MARK, NIENHAUS GULRICH. EXPLORING THE FOLDING FREE ENERGY LANDSCAPE OF SMALL RNA MOLECULES BY SINGLE-PAIR FÖRSTER RESONANCE ENERGY TRANSFER. ACTA ACUST UNITED AC 2011. [DOI: 10.1142/s1793048008000873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Proteins and RNA are biological macromolecules built from linear polymers. The process by which they fold into compact, well-defined, three-dimensional architectures to perform their functional tasks is still not well understood. It can be visualized by Brownian motion of an ensemble of molecules through a rugged energy landscape in search of an energy minimum corresponding to the native state. To explore the conformational energy landscape of small RNAs, single pair Förster resonance energy transfer (spFRET) experiments on solutions as well as on surface-immobilized samples have provided new insights. In this review, we focus on our recent work on two FRET-labeled small RNAs, the Diels-Alderase (DAse) ribozyme and the human mitochondrial tRNA Lys . For both RNAs, three different conformational states can be distinguished, and the associated mean FRET efficiencies provide clues about their structural properties. The systematic variation of their free energies with the concentration of Mg 2+ counterions was analyzed quantitatively by using a thermodynamic model that separates conformational changes from Mg 2+ binding. Furthermore, time-resolved spFRET studies on immobilized DAse reveal slow interconversions between intermediate and folded states on the time scale of ~ 100 ms. The quantitative data obtained from spFRET experiments may likely assist in the further development of theories and models addressing the folding dynamics and (counterion-dependent) energetics of RNA molecules.
Collapse
Affiliation(s)
- ANDREI YU. KOBITSKI
- Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - ALEXANDER NIERTH
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - MARTIN HENGESBACH
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - ANDRES JÄSCHKE
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - MARK HELM
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - G. ULRICH NIENHAUS
- Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
55
|
Giegé R, Jühling F, Pütz J, Stadler P, Sauter C, Florentz C. Structure of transfer RNAs: similarity and variability. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:37-61. [DOI: 10.1002/wrna.103] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
56
|
Carrillo R, Feher-Voelger A, Martín T. Enantioselective Cooperativity Between Intra-Receptor Interactions and Guest Binding: Quantification of Reinforced Chiral Recognition. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103970] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
57
|
Carrillo R, Feher-Voelger A, Martín T. Enantioselective Cooperativity Between Intra-Receptor Interactions and Guest Binding: Quantification of Reinforced Chiral Recognition. Angew Chem Int Ed Engl 2011; 50:10616-20. [DOI: 10.1002/anie.201103970] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 07/25/2011] [Indexed: 11/08/2022]
|
58
|
Kobitski A, Hengesbach M, Seidu-Larry S, Dammertz K, Chow C, van Aerschot A, Nienhaus GU, Helm M. Single-Molecule FRET Reveals a Cooperative Effect of Two Methyl Group Modifications in the Folding of Human Mitochondrial tRNALys. ACTA ACUST UNITED AC 2011; 18:928-36. [DOI: 10.1016/j.chembiol.2011.03.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 03/14/2011] [Accepted: 03/29/2011] [Indexed: 10/17/2022]
|
59
|
A post-labeling approach for the characterization and quantification of RNA modifications based on site-directed cleavage by DNAzymes. Methods Mol Biol 2011; 718:259-70. [PMID: 21370054 DOI: 10.1007/978-1-61779-018-8_16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Deoxyribozymes or DNAzymes are small DNA molecules with catalytic activity originating from in vitro selection experiments. Variants of the two most popular DNAzymes with RNase activity, the 10-23 DNAzyme and the 8-17 DNAzyme, promote efficient in vitro cleavage of the phosphodiester bond in at least 11 out of 16 possible dinucleotide permutations. Judicious choice of the sequences flanking the active core of the DNAzymes permits to direct cleavage activity with high sequence specificity. Here, the harnessing of these features for the analysis of RNA nucleotide modifications by a post-labeling approach is described in detail. DNAzymes are designed such that RNase cleavage is directed precisely to the 5' end of the nucleotide to be analyzed. Iterative complex formation of DNAzyme and RNA substrate and subsequent cleavage are performed by temperature cycling. The DNAzyme activity liberates the analyte nucleotide on the very 5'-end of an RNA fragment, whose hydroxyl group can be conveniently phosphorylated with (32)P. The labeled RNA is digested to mononucleotides, and analyzed by thin layer chromatography.
Collapse
|
60
|
Dammertz K, Hengesbach M, Helm M, Nienhaus GU, Kobitski AY. Single-Molecule FRET Studies of Counterion Effects on the Free Energy Landscape of Human Mitochondrial Lysine tRNA. Biochemistry 2011; 50:3107-15. [DOI: 10.1021/bi101804t] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Martin Hengesbach
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Germany
| | - Mark Helm
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Germany
- Institute of Pharmacy and Biochemistry, University of Mainz, 55128 Mainz, Germany
| | - G. Ulrich Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), 76128 Karlsruhe, Germany
- Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Andrei Yu. Kobitski
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), 76128 Karlsruhe, Germany
| |
Collapse
|
61
|
Motorin Y, Helm M. RNA nucleotide methylation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:611-31. [PMID: 21823225 DOI: 10.1002/wrna.79] [Citation(s) in RCA: 334] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Methylation of RNA occurs at a variety of atoms, nucleotides, sequences and tertiary structures. Strongly related to other posttranscriptional modifications, methylation of different RNA species includes tRNA, rRNA, mRNA, tmRNA, snRNA, snoRNA, miRNA, and viral RNA. Different catalytic strategies are employed for RNA methylation by a variety of RNA-methyltransferases which fall into four superfamilies. This review outlines the different functions of methyl groups in RNA, including biophysical, biochemical and metabolic stabilization of RNA, quality control, resistance to antibiotics, mRNA reading frame maintenance, deciphering of normal and altered genetic code, selenocysteine incorporation, tRNA aminoacylation, ribotoxins, splicing, intracellular trafficking, immune response, and others. Connections to other fields including gene regulation, DNA repair, stress response, and possibly histone acetylation and exocytosis are pointed out. WIREs RNA 2011 2 611-631 DOI: 10.1002/wrna.79 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Yuri Motorin
- Laboratoire ARN-RNP Maturation-Structure-Fonction, Enzymologie Moléculaire et Structurale (AREMS), Université Henri Poincaré, Vandoeuvre-les-Nancy, France
| | | |
Collapse
|
62
|
Error compensation of tRNA misacylation by codon-anticodon mismatch prevents translational amino acid misinsertion. Comput Biol Chem 2011; 35:81-95. [PMID: 21470914 DOI: 10.1016/j.compbiolchem.2011.03.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 02/22/2011] [Accepted: 03/01/2011] [Indexed: 11/20/2022]
Abstract
Codon-anticodon mismatches and tRNA misloadings cause translational amino acid misinsertions, producing dysfunctional proteins. Here I explore the original hypothesis whether mismatches tend to compensate misacylation, so as to insert the amino acid coded by the codon. This error compensation is promoted by the fact that codon-anticodon mismatch stabilities increase with tRNA misacylation potentials (predicted by 'tfam') by non-cognate amino acids coded by the mismatched codons for most tRNAs examined. Error compensation is independent of preferential misacylation by non-cognate amino acids physico-chemically similar to cognate amino acids, a phenomenon that decreases misinsertion impacts. Error compensation correlates negatively with (a) codon/anticodon abundance (in human mitochondria and Escherichia coli); (b) developmental instability (estimated by fluctuating asymmetry in bilateral counts of subdigital lamellae, in each of two lizard genera, Anolis and Sceloporus); and (c) pathogenicity of human mitochondrial tRNA polymorphisms. Patterns described here suggest that tRNA misacylation is sometimes compensated by codon-anticodon mismatches. Hence translation inserts the amino acid coded by the mismatched codon, despite mismatch and misloading. Results suggest that this phenomenon is sufficiently important to affect whole organism phenotypes, as shown by correlations with pathologies and morphological estimates of developmental stability.
Collapse
|
63
|
Motorin Y, Burhenne J, Teimer R, Koynov K, Willnow S, Weinhold E, Helm M. Expanding the chemical scope of RNA:methyltransferases to site-specific alkynylation of RNA for click labeling. Nucleic Acids Res 2010; 39:1943-52. [PMID: 21037259 PMCID: PMC3061074 DOI: 10.1093/nar/gkq825] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
This work identifies the combination of enzymatic transfer and click labeling as an efficient method for the site-specific tagging of RNA molecules for biophysical studies. A double-activated analog of the ubiquitous co-substrate S-adenosyl-l-methionine was employed to enzymatically transfer a five carbon chain containing a terminal alkynyl moiety onto RNA. The tRNA:methyltransferase Trm1 transferred the extended alkynyl moiety to its natural target, the N2 of guanosine 26 in tRNAPhe. LC/MS and LC/MS/MS techniques were used to detect and characterize the modified nucleoside as well as its cycloaddition product with a fluorescent azide. The latter resulted from a labeling reaction via Cu(I)-catalyzed azide-alkyne 1,3-cycloaddition click chemistry, producing site-specifically labeled RNA whose suitability for single molecule fluorescence experiments was verified in fluorescence correlation spectroscopy experiments.
Collapse
Affiliation(s)
- Yuri Motorin
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | | | | | | | | | | | | |
Collapse
|
64
|
Abstract
Post-transcriptional ribonucleotide modification is a phenomenon best studied in tRNA, where it occurs most frequently and in great chemical diversity. This paper reviews the intrinsic network of modifications in the structural core of the tRNA, which governs structural flexibility and rigidity to fine-tune the molecule to peak performance and to regulate its steady-state level. Structural effects of RNA modifications range from nanometer-scale rearrangements to subtle restrictions of conformational space on the angstrom scale. Structural stabilization resulting from nucleotide modification results in increased thermal stability and translates into protection against unspecific degradation by bases and nucleases. Several mechanisms of specific degradation of hypomodified tRNA, which were only recently discovered, provide a link between structural and metabolic stability.
Collapse
Affiliation(s)
- Yuri Motorin
- Laboratoire ARN-RNP Maturation-Structure-Fonction, Enzymologie Moléculaire et Structurale (AREMS), UMR 7214 CNRS-UHP Faculté des Sciences et Techniques, Université Henri Poincaré, Nancy 1, Bld des Aiguillettes, BP 70239, 54506 Vandoeuvre-les-Nancy, France
| | | |
Collapse
|
65
|
Hengesbach M, Voigts-Hoffmann F, Hofmann B, Helm M. Formation of a stalled early intermediate of pseudouridine synthesis monitored by real-time FRET. RNA (NEW YORK, N.Y.) 2010; 16:610-620. [PMID: 20106954 PMCID: PMC2822925 DOI: 10.1261/rna.1832510] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Accepted: 12/03/2009] [Indexed: 05/28/2023]
Abstract
Pseudouridine is the most abundant of more than 100 chemically distinct natural ribonucleotide modifications. Its synthesis consists of an isomerization reaction of a uridine residue in the RNA chain and is catalyzed by pseudouridine synthases. The unusual reaction mechanism has become the object of renewed research effort, frequently involving replacement of the substrate uridines with 5-fluorouracil (f(5)U). f(5)U is known to be a potent inhibitor of pseudouridine synthase activity, but the effect varies among the target pseudouridine synthases. Derivatives of f(5)U have previously been detected, which are thought to be either hydrolysis products of covalent enzyme-RNA adducts, or isomerization intermediates. Here we describe the interaction of pseudouridine synthase 1 (Pus1p) with f(5)U-containing tRNA. The interaction described is specific to Pus1p and position 27 in the tRNA anticodon stem, but the enzyme neither forms a covalent adduct nor stalls at a previously identified reaction intermediate of f(5)U. The f(5)U27 residue, as analyzed by a DNAzyme-based assay using TLC and mass spectrometry, displayed physicochemical properties unaltered by the reversible interaction with Pus1p. Thus, Pus1p binds an f(5)U-containing substrate, but, in contrast to other pseudouridine synthases, leaves the chemical structure of f(5)U unchanged. The specific, but nonproductive, interaction demonstrated here thus constitutes an intermediate of Pus turnover, stalled by the presence of f(5)U in an early state of catalysis. Observation of the interaction of Pus1p with fluorescence-labeled tRNA by a real-time readout of fluorescence anisotropy and FRET revealed significant structural distortion of f(5)U-tRNA structure in the stalled intermediate state of pseudouridine catalysis.
Collapse
Affiliation(s)
- Martin Hengesbach
- Institute of Pharmacy and Molecular Biotechnology, Department of Chemistry, Heidelberg University, 69120 Heidelberg, Germany
| | | | | | | |
Collapse
|
66
|
Helm M, Kobitski AY, Nienhaus GU. Single-molecule Förster resonance energy transfer studies of RNA structure, dynamics and function. Biophys Rev 2009; 1:161. [PMID: 28510027 PMCID: PMC5418384 DOI: 10.1007/s12551-009-0018-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 10/09/2009] [Indexed: 11/24/2022] Open
Abstract
Single-molecule fluorescence microscopy experiments on RNA molecules brought to light the highly complex dynamics of key biological processes, including RNA folding, catalysis of ribozymes, ligand sensing of riboswitches and aptamers, and protein synthesis in the ribosome. By using highly advanced biophysical spectroscopy techniques in combination with sophisticated biochemical synthesis approaches, molecular dynamics of individual RNA molecules can be observed in real time and under physiological conditions in unprecedented detail that cannot be achieved with bulk experiments. Here, we review recent advances in RNA folding and functional studies of RNA and RNA-protein complexes addressed by using single-molecule Förster (fluorescence) resonance energy transfer (smFRET) technique.
Collapse
Affiliation(s)
- Mark Helm
- Institute of Pharmacy, University of Mainz, Staudinger Weg 5, 55128, Mainz, Germany.
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany.
| | - Andrei Yu Kobitski
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), 76128, Karlsruhe, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), 76128, Karlsruhe, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| |
Collapse
|
67
|
Messmer M, Pütz J, Suzuki T, Suzuki T, Sauter C, Sissler M, Catherine F. Tertiary network in mammalian mitochondrial tRNAAsp revealed by solution probing and phylogeny. Nucleic Acids Res 2009; 37:6881-95. [PMID: 19767615 PMCID: PMC2777451 DOI: 10.1093/nar/gkp697] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Primary and secondary structures of mammalian mitochondrial (mt) tRNAs are divergent from canonical tRNA structures due to highly skewed nucleotide content and large size variability of D- and T-loops. The nonconservation of nucleotides involved in the expected network of tertiary interactions calls into question the rules governing a functional L-shaped three-dimensional (3D) structure. Here, we report the solution structure of human mt-tRNAAsp in its native post-transcriptionally modified form and as an in vitro transcript. Probing performed with nuclease S1, ribonuclease V1, dimethylsulfate, diethylpyrocarbonate and lead, revealed several secondary structures for the in vitro transcribed mt-tRNAAsp including predominantly the cloverleaf. On the contrary, the native tRNAAsp folds into a single cloverleaf structure, highlighting the contribution of the four newly identified post-transcriptional modifications to correct folding. Reactivities of nucleotides and phosphodiester bonds in the native tRNA favor existence of a full set of six classical tertiary interactions between the D-domain and the variable region, forming the core of the 3D structure. Reactivities of D- and T-loop nucleotides support an absence of interactions between these domains. According to multiple sequence alignments and search for conservation of Leontis–Westhof interactions, the tertiary network core building rules apply to all tRNAAsp from mammalian mitochondria.
Collapse
Affiliation(s)
- Marie Messmer
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC 15 rue René Descartes, 67084 Strasbourg, France
| | | | | | | | | | | | | |
Collapse
|
68
|
Messmer M, Gaudry A, Sissler M, Florentz C. Pathology-related mutation A7526G (A9G) helps in the understanding of the 3D structural core of human mitochondrial tRNA(Asp). RNA (NEW YORK, N.Y.) 2009; 15:1462-1468. [PMID: 19535463 PMCID: PMC2714750 DOI: 10.1261/rna.1626109] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Accepted: 05/08/2009] [Indexed: 05/27/2023]
Abstract
More than 130 mutations in human mitochondrial tRNA (mt-tRNA) genes have been correlated with a variety of neurodegenerative and neuromuscular disorders. Their molecular impacts are of mosaic type, affecting various stages of tRNA biogenesis, structure, and/or functions in mt-translation. Knowledge of mammalian mt-tRNA structures per se remains scarce however. Primary and secondary structures deviate from classical tRNAs, while rules for three-dimensional (3D) folding are almost unknown. Here, we take advantage of a myopathy-related mutation A7526G (A9G) in mt-tRNA(Asp) to investigate both the primary molecular impact underlying the pathology and the role of nucleotide 9 in the network of 3D tertiary interactions. Experimental evidence is presented for existence of a 9-12-23 triple in human mt-tRNA(Asp) with a strongly conserved interaction scheme in mammalian mt-tRNAs. Mutation A7526G disrupts the triple interaction and in turn reduces aspartylation efficiency.
Collapse
|
69
|
Kobitski A, Hengesbach M, Helm M, Nienhaus G. Sculpting an RNA Conformational Energy Landscape by a Methyl Group Modification—A Single-Molecule FRET Study. Angew Chem Int Ed Engl 2008; 47:4326-30. [DOI: 10.1002/anie.200705675] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
70
|
Kobitski A, Hengesbach M, Helm M, Nienhaus G. Ausformung einer RNA-Konformationsenergielandschaft durch eine Methylgruppenmodifikation – eine Einzelmolekül-FRET-Studie. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705675] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|