1
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Cela M, Théobald-Dietrich A, Rudinger-Thirion J, Wolff P, Geslain R, Frugier M. Identification of host tRNAs preferentially recognized by the Plasmodium surface protein tRip. Nucleic Acids Res 2021; 49:10618-10629. [PMID: 34530443 PMCID: PMC8501954 DOI: 10.1093/nar/gkab769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/17/2021] [Accepted: 08/26/2021] [Indexed: 12/19/2022] Open
Abstract
Malaria is a life-threatening and devastating parasitic disease. Our previous work showed that parasite development requires the import of exogenous transfer RNAs (tRNAs), which represents a novel and unique form of host-pathogen interaction, as well as a potentially druggable target. This import is mediated by tRip (tRNA import protein), a membrane protein located on the parasite surface. tRip displays an extracellular domain homologous to the well-characterized OB-fold tRNA-binding domain, a structural motif known to indiscriminately interact with tRNAs. We used MIST (Microarray Identification of Shifted tRNAs), a previously established in vitro approach, to systematically assess the specificity of complexes between native Homo sapiens tRNAs and recombinant Plasmodium falciparum tRip. We demonstrate that tRip unexpectedly binds to host tRNAs with a wide range of affinities, suggesting that only a small subset of human tRNAs is preferentially imported into the parasite. In particular, we show with in vitro transcribed constructs that tRip does not bind specific tRNAs solely based on their primary sequence, hinting that post-transcriptional modifications modulate the formation of our host/parasite molecular complex. Finally, we discuss the potential utilization of the most efficient tRip ligands for the translation of the parasite's genetic information.
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Affiliation(s)
- Marta Cela
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, F-67000Strasbourg, France
| | - Anne Théobald-Dietrich
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, F-67000Strasbourg, France
| | - Joëlle Rudinger-Thirion
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, F-67000Strasbourg, France
| | - Philippe Wolff
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, F-67000Strasbourg, France
| | - Renaud Geslain
- Laboratory of tRNA Biology, Department of Biology, College of Charleston, Charleston, SC, USA
| | - Magali Frugier
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, F-67000Strasbourg, France
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2
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Krahn N, Fischer JT, Söll D. Naturally Occurring tRNAs With Non-canonical Structures. Front Microbiol 2020; 11:596914. [PMID: 33193279 PMCID: PMC7609411 DOI: 10.3389/fmicb.2020.596914] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/29/2020] [Indexed: 11/13/2022] Open
Abstract
Transfer RNA (tRNA) is the central molecule in genetically encoded protein synthesis. Most tRNA species were found to be very similar in structure: the well-known cloverleaf secondary structure and L-shaped tertiary structure. Furthermore, the length of the acceptor arm, T-arm, and anticodon arm were found to be closely conserved. Later research discovered naturally occurring, active tRNAs that did not fit the established 'canonical' tRNA structure. This review discusses the non-canonical structures of some well-characterized natural tRNA species and describes how these structures relate to their role in translation. Additionally, we highlight some newly discovered tRNAs in which the structure-function relationship is not yet fully understood.
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Affiliation(s)
- Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Jonathan T Fischer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States.,Department of Chemistry, Yale University, New Haven, CT, United States
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3
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Sakatani Y, Mizuuchi R, Ichihashi N. In vitro evolution of phi29 DNA polymerases through compartmentalized gene expression and rolling-circle replication. Protein Eng Des Sel 2020; 32:481-487. [PMID: 32533140 DOI: 10.1093/protein/gzaa011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/20/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022] Open
Abstract
Phi29 DNA polymerase is widely used for DNA amplification through rolling-circle replication or multiple displacement amplification. Here, we performed completely in vitro artificial evolution of phi29 DNA polymerase by combining the in vitro compartmentalization and the gene expression-coupled rolling-circle replication of a circular DNA encoding the polymerase. We conducted the experiments in six different conditions composed of three different levels of inhibitor concentrations with two different DNA labeling methods. One of the experiments was performed in our previous study and the other five experiments were newly conducted in this study. Under all conditions, we found several mutations that enhance the rolling-circle amplification by the polymerase when it was expressed in the reconstituted gene expression system. Especially, a combinatorial mutant polymerase (K555T/D570N) exhibits significantly higher rolling-circle activity than the wild type. These highly active mutant polymerases would be useful for various applications.
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Affiliation(s)
- Yoshihiro Sakatani
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ryo Mizuuchi
- Komaba Institute for Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan.,JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
| | - Norikazu Ichihashi
- Komaba Institute for Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan.,Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.,Universal Biology Institute, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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4
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Kellner S, DeMott MS, Cheng CP, Russell BS, Cao B, You D, Dedon PC. Oxidation of phosphorothioate DNA modifications leads to lethal genomic instability. Nat Chem Biol 2017; 13:888-894. [PMID: 28604692 PMCID: PMC5577368 DOI: 10.1038/nchembio.2407] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 03/30/2017] [Indexed: 12/12/2022]
Abstract
Genomic modification with sulfur as phosphorothioate (PT) is widespread among prokaryotes, including human pathogens. Apart from its physiological functions, the redox and nucleophilic properties of PT sulfur suggest effects on bacterial fitness in stressful environments. Here we show that PTs are dynamic and labile DNA modifications that cause genomic instability during oxidative stress. Using coupled isotopic labeling-mass spectrometry, we observed sulfur replacement in PTs at a rate of ~2%/h in unstressed Escherichia coli and Salmonella enterica. While PT levels were unaffected by exposure to hydrogen peroxide (H2O2) or hypochlorous acid (HOCl), PT turnover increased to 3.8–10%/h for HOCl and was unchanged for H2O2, consistent with repair of HOCl-induced sulfur damage. PT-dependent HOCl sensitivity extended to cytotoxicity and DNA strand-breaks, which occurred at orders-of-magnitude lower doses of HOCl than H2O2. The genotoxicity of HOCl in PT-containing bacteria suggests reduced fitness in competition with HOCl-producing organisms and during human infections.
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Affiliation(s)
- Stefanie Kellner
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ching Pin Cheng
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Brandon S Russell
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Bo Cao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Delin You
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Singapore-MIT Alliance for Research and Technology, Singapore
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5
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Lau MWL, Trachman RJ, Ferré-D'Amaré AR. A divalent cation-dependent variant of the glmS ribozyme with stringent Ca 2+ selectivity co-opts a preexisting nonspecific metal ion-binding site. RNA (NEW YORK, N.Y.) 2017; 23:355-364. [PMID: 27932587 PMCID: PMC5311495 DOI: 10.1261/rna.059824.116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 11/28/2016] [Indexed: 05/29/2023]
Abstract
Ribozymes use divalent cations for structural stabilization, as catalytic cofactors, or both. Because of the prominent role of Ca2+ in intracellular signaling, engineered ribozymes with stringent Ca2+ selectivity would be important in biotechnology. The wild-type glmS ribozyme (glmSWT) requires glucosamine-6-phosphate (GlcN6P) as a catalytic cofactor. Previously, a glmS ribozyme variant with three adenosine mutations (glmSAAA) was identified, which dispenses with GlcN6P and instead uses, with little selectivity, divalent cations as cofactors for site-specific RNA cleavage. We now report a Ca2+-specific ribozyme (glmSCa) evolved from glmSAAA that is >10,000 times more active in Ca2+ than Mg2+, is inactive in even 100 mM Mg2+, and is not responsive to GlcN6P. This stringent selectivity, reminiscent of the protein nuclease from Staphylococcus, allows rapid and selective ribozyme inactivation using a Ca2+ chelator such as EGTA. Because glmSCa functions in physiologically relevant Ca2+ concentrations, it can form the basis for intracellular sensors that couple Ca2+ levels to RNA cleavage. Biochemical analysis of glmSCa reveals that it has co-opted for selective Ca2+ binding a nonspecific cation-binding site responsible for structural stabilization in glmSWT and glmSAAA Fine-tuning of the selectivity of the cation site allows repurposing of this preexisting molecular feature.
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Affiliation(s)
- Matthew W L Lau
- National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA
| | - Robert J Trachman
- National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA
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6
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Ichihashi N, Usui K, Kazuta Y, Sunami T, Matsuura T, Yomo T. Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment. Nat Commun 2014; 4:2494. [PMID: 24088711 DOI: 10.1038/ncomms3494] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 08/22/2013] [Indexed: 11/09/2022] Open
Abstract
The ability to evolve is a key characteristic that distinguishes living things from non-living chemical compounds. The construction of an evolvable cell-like system entirely from non-living molecules has been a major challenge. Here we construct an evolvable artificial cell model from an assembly of biochemical molecules. The artificial cell model contains artificial genomic RNA that replicates through the translation of its encoded RNA replicase. We perform a long-term (600-generation) replication experiment using this system, in which mutations are spontaneously introduced into the RNA by replication error, and highly replicable mutants dominate the population according to Darwinian principles. During evolution, the genomic RNA gradually reinforces its interaction with the translated replicase, thereby acquiring competitiveness against selfish (parasitic) RNAs. This study provides the first experimental evidence that replicating systems can be developed through Darwinian evolution in a cell-like compartment, even in the presence of parasitic replicators.
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Affiliation(s)
- Norikazu Ichihashi
- 1] Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka University, Suita, Osaka 565-0871, Japan [2] Graduate School of Information Science and Technology, Osaka University, Suita, Osaka 565-0871, Japan
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7
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Lau MWL, Ferré-D'Amaré AR. An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence. Nat Chem Biol 2013; 9:805-10. [PMID: 24096303 DOI: 10.1038/nchembio.1360] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 09/05/2013] [Indexed: 12/26/2022]
Abstract
Uniquely among known ribozymes, the glmS ribozyme-riboswitch requires a small-molecule coenzyme, glucosamine-6-phosphate (GlcN6P). Although consistent with its gene-regulatory function, the use of GlcN6P is unexpected because all of the other characterized self-cleaving ribozymes use RNA functional groups or divalent cations for catalysis. To determine what active site features make this ribozyme reliant on GlcN6P and to evaluate whether it might have evolved from a coenzyme-independent ancestor, we isolated a GlcN6P-independent variant through in vitro selection. Three active site mutations suffice to generate a highly reactive RNA that adopts the wild-type fold but uses divalent cations for catalysis and is insensitive to GlcN6P. Biochemical and crystallographic comparisons of wild-type and mutant ribozymes show that a handful of functional groups fine-tune the RNA to be either coenzyme or cation dependent. These results indicate that a few mutations can confer new biochemical activities on structured RNAs. Thus, families of structurally related ribozymes with divergent function may exist.
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Affiliation(s)
- Matthew W L Lau
- National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
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8
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Dalby AB, Goodrich KJ, Pfingsten JS, Cech TR. RNA recognition by the DNA end-binding Ku heterodimer. RNA (NEW YORK, N.Y.) 2013; 19:841-51. [PMID: 23610127 PMCID: PMC3683917 DOI: 10.1261/rna.038703.113] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Most nucleic acid-binding proteins selectively bind either DNA or RNA, but not both nucleic acids. The Saccharomyces cerevisiae Ku heterodimer is unusual in that it has two very different biologically relevant binding modes: (1) Ku is a sequence-nonspecific double-stranded DNA end-binding protein with prominent roles in nonhomologous end-joining and telomeric capping, and (2) Ku associates with a specific stem-loop of TLC1, the RNA subunit of budding yeast telomerase, and is necessary for proper nuclear localization of this ribonucleoprotein enzyme. TLC1 RNA-binding and dsDNA-binding are mutually exclusive, so they may be mediated by the same site on Ku. Although dsDNA binding by Ku is well studied, much less is known about what features of an RNA hairpin enable specific recognition by Ku. To address this question, we localized the Ku-binding site of the TLC1 hairpin with single-nucleotide resolution using phosphorothioate footprinting, used chemical modification to identify an unpredicted motif within the hairpin secondary structure, and carried out mutagenesis of the stem-loop to ascertain the critical elements within the RNA that permit Ku binding. Finally, we provide evidence that the Ku-binding site is present in additional budding yeast telomerase RNAs and discuss the possibility that RNA binding is a conserved function of the Ku heterodimer.
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9
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Abstract
Polyacrylamide gel electrophoresis is a widely used technique for RNA analysis and purification. The polyacrylamide matrix is highly versatile for chemical derivitization, enabling facile exploitation of thio-mercury chemistry without the need of tedious manipulations and/or expensive coupling reagents, which often give low yields and side products. Here, we describe the use of [(N-acryloylamino)phenyl]mercuric chloride in three-layered polyacrylamide gels to detect, separate, quantify, and analyze sulfur-containing RNAs.
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Affiliation(s)
- Elisa Biondi
- Department of Molecular Microbiology and Immunology and Department of Biochemistry, University of Missouri-School of Medicine, Columbia, MO, USA.
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10
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The Seryl-tRNA synthetase/tRNASer acceptor stem interface is mediated via a specific network of water molecules. Biochem Biophys Res Commun 2011; 412:532-6. [PMID: 21787751 DOI: 10.1016/j.bbrc.2011.07.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 07/12/2011] [Indexed: 11/23/2022]
Abstract
tRNAs are aminoacylated by the aminoacyl-tRNA synthetases. There are at least 20 natural amino acids, but due to the redundancy of the genetic code, 64 codons on the mRNA. Therefore, there exist tRNA isoacceptors that are aminoacylated with the same amino acid, but differ in their sequence and in the anticodon. tRNA identity elements, which are sequence or structure motifs, assure the amino acid specificity. The Seryl-tRNA synthetase is an enzyme that depends on rather few and simple identity elements in tRNA(Ser). The Seryl-tRNA-synthetase interacts with the tRNA(Ser) acceptor stem, which makes this part of the tRNA a valuable structural element for investigating motifs of the protein-RNA complex. We solved the high resolution crystal structures of two tRNA(Ser) acceptor stem microhelices and investigated their interaction with the Seryl-tRNA-synthetase by superposition experiments. The results presented here show that the amino acid side chains Ser151 and Ser156 of the synthetase are interacting in a very similar way with the RNA backbone of the microhelix and that the involved water molecules have almost identical positions within the tRNA/synthetase interface.
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11
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Scripture JB, Huber PW. Binding site for Xenopus ribosomal protein L5 and accompanying structural changes in 5S rRNA. Biochemistry 2011; 50:3827-39. [PMID: 21446704 DOI: 10.1021/bi200286e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure of the eukaryotic L5-5S rRNA complex was investigated in protection and interference experiments and is compared with the corresponding structure (L18-5S rRNA) in the Haloarcula marismortui 50S subunit. In close correspondence with the archaeal structure, the contact sites for the eukaryotic ribosomal protein are located primarily in helix III and loop C and secondarily in loop A and helix V. While the former is unique to L5, the latter is also a critical contact site for transcription factor IIIA (TFIIIA), accounting for the mutually exclusive binding of these two proteins to 5S RNA. The binding of L5 causes structural changes in loops B and C that expose nucleotides that contact the Xenopus L11 ortholog in H. marismortui. This induced change in the structure of the RNA reveals the origins of the cooperative binding to 5S rRNA that has been observed for the bacterial counterparts of these proteins. The native structure of helix IV and loop D antagonizes binding of L5, indicating that this region of the RNA is dynamic and also influenced by the protein. Examination of the crystal structures of Thermus thermophilus ribosomes in the pre- and post-translocation states identified changes in loop D and in the surrounding region of 23S rRNA that support the proposal that 5S rRNA acts to transmit information between different functional domains of the large subunit.
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Affiliation(s)
- J Benjamin Scripture
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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12
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Eichert A, Fürste JP, Ulrich A, Betzel C, Erdmann VA, Förster C. Superposition of two tRNASer acceptor stem crystal structures: Comparison of structure, ligands and hydration. Biochem Biophys Res Commun 2010; 395:291-5. [DOI: 10.1016/j.bbrc.2010.03.106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 03/17/2010] [Indexed: 10/19/2022]
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13
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Sekhon GS, Sen D. Unusual DNA-DNA cross-links between a photolyase deoxyribozyme, UV1C, and its bound oligonucleotide substrate. Biochemistry 2009; 48:6335-47. [PMID: 19514779 DOI: 10.1021/bi900531z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
UV1C is a photolyase deoxyribozyme that repairs thymine dimers in a DNA oligonucleotide substrate. We report that treatment with iodine generates specific DNA-DNA cross-links between UV1C and a bound substrate analogue, LDPs, in which a single phosphate at the photoreactivation site has been replaced with a phosphorothioate. Although iodine has been reported to generate lysine-cysteine cross-links within a protein, the formation of DNA-DNA cross-links is both unexpected and novel. We have used different mapping procedures to identify a number of bases located in loops of the G-quadruplex fold of UV1C as the sites for cross-linking with LDPs. Mutation of one cross-linking adenine, in particular, leads to a major reduction in UVIC's catalytic activity. A map of these contact cross-linking sites enables us to refine an earlier structural-topological model for the folded UV1C.LDPs complex. The surprising facility with which these novel contact cross-links can be generated between a nucleic acid enzyme and its substrate's reaction site opens up a powerful new approach to mapping the active sites of different ribozymes and deoxyribozymes as well as enabling the dissection of key contacts within RNA-protein complexes.
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Affiliation(s)
- Gurpreet S Sekhon
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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14
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The 1.2A crystal structure of an E. coli tRNASer)acceptor stem microhelix reveals two magnesium binding sites. Biochem Biophys Res Commun 2009; 386:368-73. [PMID: 19527687 DOI: 10.1016/j.bbrc.2009.06.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 06/09/2009] [Indexed: 11/22/2022]
Abstract
tRNA identity elements assure the correct aminoacylation of tRNAs by the cognate aminoacyl-tRNA synthetases. tRNA(Ser) belongs to the so-called class II system, in which the identity elements are rather simple and are mostly located in the acceptor stem region, in contrast to 'class I', where tRNA determinants are more complex and are located within different regions of the tRNA. The structure of an Escherichia coli tRNA(Ser) acceptor stem microhelix was solved by high resolution X-ray structure analysis. The RNA crystallizes in the space group C2, with one molecule per asymmetric unit and with the cell constants a=35.79, b=39.13, c=31.37A, and beta=111.1 degrees . A defined hydration pattern of 97 water molecules surrounds the tRNA(Ser) acceptor stem microhelix. Additionally, two magnesium binding sites were detected in the tRNA(Ser) aminoacyl stem.
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15
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Vasil'eva IA, Semenova EA, Moor NA. Interaction of human phenylalanyl-tRNA synthetase with specific tRNA according to thiophosphate footprinting. BIOCHEMISTRY (MOSCOW) 2009; 74:175-85. [PMID: 19267673 DOI: 10.1134/s0006297909020084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The interaction of human cytoplasmic phenylalanyl-tRNA synthetase (an enzyme with yet unknown 3D-structure) with homologous tRNA(Phe) under functional conditions was studied by footprinting based on iodine cleavage of thiophosphate-substituted tRNA transcripts. Most tRNA(Phe) nucleotides recognized by the enzyme in the anticodon (G34), anticodon stem (G30-C40, A31-U39), and D-loop (G20) have effectively or moderately protected phosphates. Other important specificity elements (A35 and A36) were found to form weak nonspecific contacts. The D-stem, T-arm, and acceptor stem are also among continuous contacts of the tRNA(Phe) backbone with the enzyme, thus suggesting the presence of additional recognition elements in these regions. The data indicate that mechanisms of interaction between phenylalanyl-tRNA synthetases and specific tRNAs are different in prokaryotes and eukaryotes.
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Affiliation(s)
- I A Vasil'eva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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16
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An S, Barany G, Musier-Forsyth K. Evolution of acceptor stem tRNA recognition by class II prolyl-tRNA synthetase. Nucleic Acids Res 2008; 36:2514-21. [PMID: 18310681 PMCID: PMC2377447 DOI: 10.1093/nar/gkn063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Aminoacyl-tRNA synthetases (AARS) are an essential family of enzymes that catalyze the attachment of amino acids to specific tRNAs during translation. Previously, we showed that base-specific recognition of the tRNA(Pro) acceptor stem is critical for recognition by Escherichia coli prolyl-tRNA synthetase (ProRS), but not for human ProRS. To further delineate species-specific differences in acceptor stem recognition, atomic group mutagenesis was used to probe the role of sugar-phosphate backbone interactions in recognition of human tRNA(Pro). Incorporation of site-specific 2'-deoxynucleotides, as well as phosphorothioate and methylphosphonate modifications within the tRNA acceptor stem revealed an extensive network of interactions with specific functional groups proximal to the first base pair and the discriminator base. Backbone functional groups located at the base of the acceptor stem, especially the 2'-hydroxyl of A66, are also critical for aminoacylation catalytic efficiency by human ProRS. Therefore, in contrast to the bacterial system, backbone-specific interactions contribute significantly more to tRNA recognition by the human enzyme than base-specific interactions. Taken together with previous studies, these data show that ProRS-tRNA acceptor stem interactions have co-adapted through evolution from a mechanism involving 'direct readout' of nucleotide bases to one relying primarily on backbone-specific 'indirect readout'.
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Affiliation(s)
- Songon An
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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17
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Ozlem Tastan Bishop A, Stelzl U, Pech M, Nierhaus KH. Characterization of RNA-protein interactions by phosphorothioate footprinting and its applications to the ribosome. Methods Mol Biol 2008; 488:129-151. [PMID: 18982288 DOI: 10.1007/978-1-60327-475-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Analogs of naturally occurring substances obtained by chemical modifications are powerful tools to study intra- and intermolecular interactions. We have used the phosphorothioate technique to analyze RNA-protein interactions, here the interactions of transfer RNAs (tRNAs) with the three ribosomal binding sites. We describe preparation and purification of thioated tRNAs, formation of functional complexes of programmed ribosomes with tRNAs, and the evaluation of the observed phosphorothioate footprints on the tRNAs.
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18
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Förster C, Brauer ABE, Fürste JP, Betzel C, Weber M, Cordes F, Erdmann VA. Superposition of a tRNASer acceptor stem microhelix into the seryl-tRNA synthetase complex. Biochem Biophys Res Commun 2007; 362:415-8. [PMID: 17719008 DOI: 10.1016/j.bbrc.2007.07.178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 07/31/2007] [Indexed: 11/18/2022]
Abstract
Aminoacyl-tRNA synthetases catalyze the formation of aminoacyl-tRNAs. Seryl-tRNA synthetase is a class II synthetase, which depends on rather few and simple identity elements in tRNA(Ser) to determine the amino acid specificity. tRNA(Ser) acceptor stem microhelices can be aminoacylated with serine, which makes this part of the tRNA a valuable tool for investigating the structural motifs in a tRNA(Ser)-seryl-tRNA synthetase complex. A 1.8A-resolution tRNA(Ser) acceptor stem crystal structure was superimposed to a 2.9A-resolution crystal structure of a tRNA(Ser)-seryl-tRNA synthetase complex for a visualization of the binding environment of the tRNA(Ser) microhelix.
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MESH Headings
- Anticodon/chemistry
- Anticodon/metabolism
- Crystallization
- Crystallography, X-Ray
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Ser/chemistry
- RNA, Transfer, Ser/metabolism
- Serine-tRNA Ligase/chemistry
- Serine-tRNA Ligase/metabolism
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Affiliation(s)
- C Förster
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
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19
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Vasil'eva IA, Moor NA. Interaction of aminoacyl-tRNA synthetases with tRNA: general principles and distinguishing characteristics of the high-molecular-weight substrate recognition. BIOCHEMISTRY (MOSCOW) 2007; 72:247-63. [PMID: 17447878 DOI: 10.1134/s0006297907030029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review summarizes results of numerous (mainly functional) studies that have been accumulated over recent years on the problem of tRNA recognition by aminoacyl-tRNA synthetases. Development and employment of approaches that use synthetic mutant and chimeric tRNAs have demonstrated general principles underlying highly specific interaction in different systems. The specificity of interaction is determined by a certain number of nucleotides and structural elements of tRNA (constituting the set of recognition elements or specificity determinants), which are characteristic of each pair. Crystallographic structures available for many systems provide the details of the molecular basis of selective interaction. Diversity and identity of biochemical functions of the recognition elements make substantial contribution to the specificity of such interactions.
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Affiliation(s)
- I A Vasil'eva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
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20
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Yang Z, Sismour AM, Benner SA. Nucleoside alpha-thiotriphosphates, polymerases and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkages. Nucleic Acids Res 2007; 35:3118-27. [PMID: 17452363 PMCID: PMC1888802 DOI: 10.1093/nar/gkm168] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The use of DNA polymerases to incorporate phosphorothioate linkages into DNA, and the use of exonuclease III to determine where those linkages have been incorporated, are re-examined in this work. The results presented here show that exonuclease III degrades single-stranded DNA as a substrate and digests through phosphorothioate linkages having one absolute stereochemistry, assigned (assuming inversion in the polymerase reaction) as S, but not the other absolute stereochemistry. This contrasts with a general view in the literature that exonuclease III favors double-stranded nucleic acid as a substrate and stops completely at phosphorothioate linkages. Furthermore, not all DNA polymerases appear to accept exclusively the (R) stereoisomer of nucleoside alpha-thiotriphosphates [and not the (S) diastereomer], a conclusion inferred two decades ago by examination of five Family-A polymerases and a reverse transcriptase. This suggests that caution is appropriate when extrapolating the detailed behavior of one polymerase from the behaviors of other polymerases. Furthermore, these results provide constraints on how exonuclease III–thiotriphosphate–polymerase combinations can be used to analyze the behavior of the components of a synthetic biology.
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Affiliation(s)
| | | | - Steven A. Benner
- *To whom correspondence should be addressed at Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville FL 32604-1174, USA +1 352 271 7005+1 352 271 7076
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21
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Gruic-Sovulj I, Jaric J, Dulic M, Cindric M, Weygand-Durasevic I. Shuffling of discrete tRNASer regions reveals differently utilized identity elements in yeast and methanogenic archaea. J Mol Biol 2006; 361:128-39. [PMID: 16822522 DOI: 10.1016/j.jmb.2006.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Revised: 06/05/2006] [Accepted: 06/06/2006] [Indexed: 10/24/2022]
Abstract
Seryl-tRNA synthetases (SerRSs) from methanogenic archaea possess distinct evolutionary origin and show minimal sequence similarity with counterparts from bacteria, eukaryotes and other archaea. Here we show that SerRS from yeast Saccharomyces cerevisiae and archaeon Methanococcus maripaludis (ScSerRS and MmSerRS, respectively) display significantly different ability to serylate heterologous tRNA(Ser). Recognition in yeast was shown to be more stringent than in archaeon. While cross-aminoacylation of M. maripaludis tRNA(Ser) (MmtRNA(Ser)) by yeast SerRS barely occurs, yeast tRNA(Ser) (SctRNA(Ser)) was shown to be a good substrate for heterologous MmSerRS. To investigate the contribution of different tRNA regions for the recognition by yeast and archaeal SerRS, chimeric tRNAs bearing separated domains of SctRNA(Ser) in MmtRNA(Ser) framework were produced by in vitro transcription and subjected to kinetic and gel mobility shift analysis with both enzymes. Generally, the recognition in M. maripaludis seems to be relatively relaxed toward tertiary elements of tRNA(Ser) structure and relies on the direct recognition of identity nucleotides. On the other hand, expression of tRNA(Ser) identity elements in yeast seems to be more sensitive toward surrounding sequence context. In both systems variable arm of tRNA was recognized as a major identity region with a strong influence on SerRS:tRNA binding. Acceptor domain of SctRNA(Ser) was also shown to be important for serylation in yeast. We propose that cognate interactions between N-terminal domain of yeast SerRS and variable region of SctRNA(Ser) place the acceptor stem into the enzyme's active site and lead to increased affinity toward serine and efficient serylation of tRNA. The same effect was not observed in M. maripaludis. Unlike its yeast counterpart, MmSerRS forms only one type of covalent complex with MmtRNA(Ser), regardless of the tRNA/SerRS molar ratio. Stoichiometry of the complex, one tRNA per dimeric SerRS, was revealed by mass spectrometry. Our studies indicate that different SerRS:tRNA recognition mode is utilized by these two systems.
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Affiliation(s)
- Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
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22
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Korencic D, Polycarpo C, Weygand-Durasevic I, Söll D. Differential modes of transfer RNASer recognition in Methanosarcina barkeri. J Biol Chem 2004; 279:48780-6. [PMID: 15364939 DOI: 10.1074/jbc.m408753200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two dissimilar seryl-transfer RNA (tRNA) synthetases (SerRSs) exist in Methanosarcina barkeri, one of bacterial type and the other resembling SerRSs present only in some methanogenic archaea. To investigate the requirements of these enzymes for tRNASer recognition, serylation of variant transcripts of M. barkeri tRNASer was kinetically analyzed in vitro with pure enzyme preparations. Characteristically for the serine system, the length of the variable arm was shown to be crucial for both enzymes, as was the identity of the discriminator base (G73). Moreover, a novel determinant for the specific tRNASer recognition was identified as the anticodon stem base pair G30:C40; its contribution to the efficiency of serylation was remarkable for both SerRSs. However, despite these similarities, the two SerRSs do not possess a uniform mode of tRNASer recognition, and additional determinants are necessary for serylation specificity by the methanogenic enzyme. In particular, the methanogenic SerRS relies on G1:C72 identity and on the number of unpaired nucleotides at the base of the variable stem for tRNASer recognition, unlike its bacterial type counterpart. We propose that such a distinction between the two enzymes in tRNASer identity determinants reflects their evolutionary pathways, hence attesting to their diversity.
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Affiliation(s)
- Dragana Korencic
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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23
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Bilokapic S, Korencic D, Söll D, Weygand-Durasevic I. The unusual methanogenic seryl-tRNA synthetase recognizes tRNASer species from all three kingdoms of life. ACTA ACUST UNITED AC 2004; 271:694-702. [PMID: 14764085 DOI: 10.1111/j.1432-1033.2003.03971.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The methanogenic archaea Methanococcus jannaschii and M. maripaludis contain an atypical seryl-tRNA synthetase (SerRS), which recognizes eukaryotic and bacterial tRNAsSer, in addition to the homologous tRNASer and tRNASec species. The relative flexibility in tRNA recognition displayed by methanogenic SerRSs, shown by aminoacylation and gel mobility shift assays, indicates the conservation of some serine determinants in all three domains. The complex of M. maripaludis SerRS with the homologues tRNASer was isolated by gel filtration chromatography. Complex formation strongly depends on the conformation of tRNA. Therefore, the renaturation conditions for in vitro transcribed tRNASer(GCU) isoacceptor were studied carefully. This tRNA, unlike many other tRNAs, is prone to dimerization, possibly due to several stretches of complementary oligonucleotides within its sequence. Dimerization is facilitated by increased tRNA concentration and can be diminished by fast renaturation in the presence of 5 mm magnesium chloride.
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MESH Headings
- Anticodon/genetics
- Base Sequence
- Chromatography, Gel
- Dimerization
- Electrophoretic Mobility Shift Assay
- Escherichia coli/enzymology
- Isoelectric Focusing
- Methanococcus/enzymology
- Methanococcus/genetics
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Binding
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Ser/chemistry
- RNA, Transfer, Ser/genetics
- RNA, Transfer, Ser/metabolism
- Serine/metabolism
- Serine-tRNA Ligase/chemistry
- Serine-tRNA Ligase/metabolism
- Substrate Specificity
- Transcription, Genetic
- Yeasts/enzymology
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Affiliation(s)
- Silvija Bilokapic
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
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24
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Li PTX, Gollnick P. Characterization of a trp RNA-binding Attenuation Protein (TRAP) Mutant with Tryptophan Independent RNA Binding Activity. J Mol Biol 2004; 335:707-22. [PMID: 14687568 DOI: 10.1016/j.jmb.2003.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
TRAP (trp RNA-binding attenuation protein) is an 11 subunit RNA-binding protein that regulates expression of genes involved in tryptophan metabolism (trp) in Bacillus subtilis in response to changes in intracellular tryptophan concentration. When activated by binding up to 11 tryptophan residues, TRAP binds to the mRNAs of several trp genes and down-regulates their expression. Recently, a TRAP mutant was found that binds RNA in the absence of tryptophan. In this mutant protein, Thr30, which is part of the tryptophan-binding site, is replaced with Val (T30V). We have compared the RNA-binding properties of T30V and wild-type (WT) TRAP, as well as of a series of hetero-11-mers containing mixtures of WT and T30V TRAP subunits. The most significant difference between the interaction of T30V and WT TRAP with RNA is that the affinity of T30V TRAP is more dependent on ionic strength. Analysis of the hetero-11-mers allowed us to examine how subunits interact within an 11-mer with regard to binding to tryptophan or RNA. Our data suggest that individual subunits retain properties similar to those observed when they are in homo-11-mers and that individual G/UAG triplets within the RNA can bind to TRAP differently.
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Affiliation(s)
- Pan T X Li
- Department of Biological Sciences, State University of New York, Buffalo, NY 14260, USA
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25
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Abstract
This review describes some of the contributions of chemistry to the RNA field with a personal bias towards the phosphorothioate modification and the derivatives at the ribose 2'-position. The usefulness of these modifications is discussed and documented with some examples.
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Affiliation(s)
- F Eckstein
- Max-Planck-Institut für experimentelle Medizin, Hermann-Rein-Str. 3, 37075 Göttingen, Germany.
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26
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Crary SM, Kurz JC, Fierke CA. Specific phosphorothioate substitutions probe the active site of Bacillus subtilis ribonuclease P. RNA (NEW YORK, N.Y.) 2002; 8:933-47. [PMID: 12166648 PMCID: PMC1370310 DOI: 10.1017/s1355838202025025] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Ribonuclease P (RNase P) is a ribonucleoprotein that requires magnesium ions to catalyze the 5' maturation of transfer RNA. To identify interactions essential for catalysis, the properties of RNase P containing single sulfur substitutions for nonbridging phosphodiester oxygens in helix P4 of Bacillus subtilis RNase P were analyzed using transient kinetic experiments. Sulfur substitution at the nonbridging oxygens of the phosphodiester bond of nucleotide U51 only modestly affects catalysis. However, phosphorothioate substitutions at A49 and G50 decrease the cleavage rate constant enormously (300-4,000-fold for P RNA and 500-15,000-fold for RNase P holoenzyme) in magnesium without affecting the affinity of pre-tRNA(Asp), highlighting the importance of this region for catalysis. Furthermore, addition of manganese enhances pre-tRNA cleavage catalyzed by B. subtilis RNase P RNA containing an Sp phosphorothioate modification at A49, as observed for Escherichia coli P RNA [Christian et al., RNA, 2000, 6:511-519], suggesting that an essential metal ion may be coordinated at this site. In contrast, no manganese rescue is observed for the A49 Sp phosphorothioate modification in RNase P holoenzyme. These differential manganese rescue effects, along with affinity cleavage, suggest that the protein component may interact with a metal ion bound near A49 in helix P4 of P RNA.
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Affiliation(s)
- Sharon M Crary
- Biochemistry Department, Duke University Medical Center, Durham, North Carolina 27710, USA
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27
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Guillier M, Allemand F, Raibaud S, Dardel F, Springer M, Chiaruttini C. Translational feedback regulation of the gene for L35 in Escherichia coli requires binding of ribosomal protein L20 to two sites in its leader mRNA: a possible case of ribosomal RNA-messenger RNA molecular mimicry. RNA (NEW YORK, N.Y.) 2002; 8:878-889. [PMID: 12166643 PMCID: PMC1370305 DOI: 10.1017/s1355838202029084] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In addition to being a component of the large ribosomal subunit, ribosomal protein L20 of Escherichia coli also acts as a translational repressor. L20 is synthesized from the IF3 operon that contains three cistrons coding for IF3, and ribosomal proteins L35 and L20. L20 directly represses the expression of the gene encoding L35 and the expression of its own gene by translational coupling. All of the cis-acting sequences required for repression by L20, called the operator, are found on an mRNA segment extending from the middle of the IF3 gene to the start of the L35 gene. L20-mediated repression requires a long-range base-pairing interaction between nucleotide residues within the IF3 gene and residues just upstream of the L35 gene. This interaction results in the formation of a pseudoknot. Here we show that L20 causes protection of nucleotide residues in two regions of the operator in vitro. The first region is the pseudoknot itself and the second lies in an irregular stem located upstream of the L35 gene. By primer extension analysis, we show that L20 specifically induces reverse transcriptase stops in both regions. Therefore, these two regions define two L20-binding sites in the operator. Using mutations and deletions of rpml'-'lacZ fusions, we show that both sites are essential for repression in vivo. However L20 can bind to each site independently in vitro. One site is similar to the L20-binding site on 23S rRNA. Here we propose that L20 recognizes its mRNA and its rRNA in similar way.
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MESH Headings
- 5' Untranslated Regions
- Arabidopsis Proteins
- Bacterial Proteins
- Base Sequence
- Binding Sites/genetics
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Feedback
- Genes, Bacterial
- Molecular Mimicry
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Mutation
- Nucleic Acid Conformation
- Operon
- Plant Proteins/genetics
- Protein Biosynthesis
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Sequence Deletion
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Affiliation(s)
- Maude Guillier
- Institut de Biologie Physico-Chimique, Unité Propre de Recherche 9073 du Centre National de la Recherche Scientifique, Paris, France
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28
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Ming X, Smith K, Suga H, Hou YM. Recognition of tRNA backbone for aminoacylation with cysteine: evolution from Escherichia coli to human. J Mol Biol 2002; 318:1207-20. [PMID: 12083512 DOI: 10.1016/s0022-2836(02)00232-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The underlying basis of the genetic code is specific aminoacylation of tRNAs by aminoacyl-tRNA synthetases. Although the code is conserved, bases in tRNA that establish aminoacylation are not necessarily conserved. Even when the bases are conserved, positions of backbone groups that contribute to aminoacylation may vary. We show here that, although the Escherichia coli and human cysteinyl-tRNA synthetases both recognize the same bases (U73 and the GCA anticodon) of tRNA for aminoacylation, they have different emphasis on the tRNA backbone. The E. coli enzyme recognizes two clusters of phosphate groups. One is at A36 in the anticodon and the other is in the core of the tRNA structure and includes phosphate groups at positions 9, 12, 14, and 60. Metal-ion rescue experiments show that those at positions 9, 12, and 60 are involved with binding divalent metal ions that are important for aminoacylation. The E. coli enzyme also recognizes 2'-hydroxyl groups within the same two clusters: at positions 33, 35, and 36 in the anticodon loop, and at positions 49, 55, and 61 in the core. The human enzyme, by contrast, recognizes few phosphate or 2'-hydroxy groups for aminoacylation. The evolution from the backbone-dependent recognition by the E. coli enzyme to the backbone-independent recognition by the human enzyme demonstrates a previously unrecognized shift that nonetheless has preserved the specificity for aminoacylation with cysteine.
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Affiliation(s)
- Xiaotian Ming
- Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, Philadelphia, PA 19107, USA
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29
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Shimada N, Suzuki T, Watanabe K. Dual mode recognition of two isoacceptor tRNAs by mammalian mitochondrial seryl-tRNA synthetase. J Biol Chem 2001; 276:46770-8. [PMID: 11577083 DOI: 10.1074/jbc.m105150200] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Animal mitochondrial translation systems contain two serine tRNAs, corresponding to the codons AGY (Y = U and C) and UCN (N = U, C, A, and G), each possessing an unusual secondary structure; tRNA(GCU)(Ser) (for AGY) lacks the entire D arm, whereas tRNA(UGA)(Ser) (for UCN) has an unusual cloverleaf configuration. We previously demonstrated that a single bovine mitochondrial seryl-tRNA synthetase (mt SerRS) recognizes these topologically distinct isoacceptors having no common sequence or structure. Recombinant mt SerRS clearly footprinted at the TPsiC loop of each isoacceptor, and kinetic studies revealed that mt SerRS specifically recognized the TPsiC loop sequence in each isoacceptor. However, in the case of tRNA(UGA)(Ser), TPsiC loop-D loop interaction was further required for recognition, suggesting that mt SerRS recognizes the two substrates by distinct mechanisms. mt SerRS could slightly but significantly misacylate mitochondrial tRNA(Gln), which has the same TPsiC loop sequence as tRNA(UGA)(Ser), implying that the fidelity of mitochondrial translation is maintained by kinetic discrimination of tRNAs in the network of aminoacyl-tRNA synthetases.
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Affiliation(s)
- N Shimada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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30
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Fechter P, Giegé R, Rudinger-Thirion J. Specific tyrosylation of the bulky tRNA-like structure of brome mosaic virus RNA relies solely on identity nucleotides present in its amino acid-accepting domain. J Mol Biol 2001; 309:387-99. [PMID: 11371160 DOI: 10.1006/jmbi.2001.4654] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Residues specifying aminoacylation by yeast tyrosyl-tRNA synthetase (TyrRS) of the tRNA-like structure present at the 3'-end of brome mosaic virus (BMV) RNA were determined by the in vitro approach using phage T7 transcripts. They correspond to nucleotides equivalent to base-pair C1-G72 and discriminator base A73 in the amino acid-acceptor branch of the molecule. No functional equivalents of the tyrosine anticodon residues, shown to be weakly involved in tyrosine identity of canonical tRNA(Tyr), were found in the BMV tRNA-like structure. This indicates a behaviour of this large and intricate molecule reminiscent of that of a minihelix derived from an amino acid-acceptor branch. Furthermore, iodine footprinting experiments performed on a tyrosylable BMV RNA transcript of 196 nt complexed to yeast TyrRS indicate that the amino acid-acceptor branch of the viral RNA is protected against cleavages as well as a hairpin domain, which is possibly located perpendicularly to its accepting branch. This domain without the canonical anticodon loop or the tyrosine anticodon acts as an anchor for TyrRS interaction leading to a better efficiency of tyrosylation.
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Affiliation(s)
- P Fechter
- Département "Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse", UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, Strasbourg Cedex F-67084, France
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31
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Stelzl U, Nierhaus KH. A short fragment of 23S rRNA containing the binding sites for two ribosomal proteins, L24 and L4, is a key element for rRNA folding during early assembly. RNA (NEW YORK, N.Y.) 2001; 7:598-609. [PMID: 11345438 PMCID: PMC1370113 DOI: 10.1017/s1355838201002059] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Previously we described an in vitro selection variant abbreviated SERF (in vitro selection from random rRNA fragments) that identifies protein binding sites within large RNAs. With this method, a small rRNA fragment derived from the 23S rRNA was isolated that binds simultaneously and independently the ribosomal proteins L4 and L24 from Escherichia coli. Until now the rRNA structure within the ternary complex L24-rRNA-L4 could not be studied due to the lack of an appropriate experimental strategy. Here we tackle the issue by separating the various complexes via native gel-electrophoresis and analyzing the rRNA structure by in-gel iodine cleavage of phosphorothioated RNA. The results demonstrate that during the transition from either the L4 or L24 binary complex to the ternary complex the structure of the rRNA fragment changes significantly. The identified protein binding sites are in excellent agreement with the recently reported crystal structure of the 50S subunit. Because both proteins play a prominent role in early assembly of the large subunit, the results suggest that the identified rRNA fragment is a key element for the folding of the 23S RNA during early assembly. The introduced in-gel cleavage method should be useful when an RNA structure within mixed populations of different but related complexes should be studied.
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Affiliation(s)
- U Stelzl
- Max-Planck-Institut for Molekulare Genetik, AG Ribosomen, Berlin, Germany
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32
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Dertinger D, Uhlenbeck OC. Evaluation of methylphosphonates as analogs for detecting phosphate contacts in RNA-protein complexes. RNA (NEW YORK, N.Y.) 2001; 7:622-631. [PMID: 11345440 PMCID: PMC1370115 DOI: 10.1017/s1355838201002217] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The well-studied interaction between the MS2 coat protein and its cognate hairpin was used to test the utility of the methylphosphonate linkage as a phosphate analog. A nitrocellulose filter binding assay was used to measure the change in binding affinity upon introduction of a single methylphosphonate stereoisomer at 13 different positions in the RNA hairpin. Comparing these data to the available crystal structure of the complex shows that all phosphates that are in proximity to the protein show a weaker binding affinity when substituted with a phosphorothioate and control positions show no change. However, in two cases, a methylphosphonate isomer either increased or decreased the binding affinity where no interaction can be detected in the crystal structure. It is possible that methylphosphonate substitutions at these positions affect the structure or flexibility of the hairpin. The utility of the methylphosphonate substitution is compared to phosphate ethylation and phosphorothioate substitution experiments previously performed on the same system.
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Affiliation(s)
- D Dertinger
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA
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33
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Drygin D, Zimmermann RA. Magnesium ions mediate contacts between phosphoryl oxygens at positions 2122 and 2176 of the 23S rRNA and ribosomal protein L1. RNA (NEW YORK, N.Y.) 2000; 6:1714-1726. [PMID: 11142372 PMCID: PMC1370042 DOI: 10.1017/s1355838200001436] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The complex of ribosomal protein L1 with 23S rRNA from Escherichia coli is of great interest because of the unique structural and functional aspects of this ribonucleoprotein domain. We have minimized the binding site for protein L1 on the 23S rRNA to nt 2120-2129, 2159-2162, and 2167-2178. This RNA fragment consists of two helices as well as an interconnecting loop of unknown structure. RNA molecules corresponding to the minimized L1 binding site, in which G, A, U, or C were individually replaced by their deoxyribo- (dN) or alpha-thio- (rNaS) analogs have been synthesized by T7 transcription in vitro and analyzed for their ability to bind protein L1. It has been demonstrated that the substitution of rNaS at position 2122 or 2176 decreases the affinity of the RNA for the protein in the presence of magnesium five- to tenfold, whereas the same changes have little effect on binding in the presence of manganese. This suggests that Rp oxygens in the phosphates preceding positions 2122 and 2176 are coordinated with Mg2+ and may participate in L1-23S rRNA interaction via magnesium bridges. We have also shown that this interaction is impaired by the presence of dC at position 2122 coupled with the presence of deoxyribonucleotide(s) at other positions in the RNA. This study demonstrates that the ribose-phosphate backbone of the helix encompassing nt 2120-2124/2174-2178 is intimately involved in the interaction of protein L1 with the 23S rRNA. In particular, we suggest that this helix is positioned in the cleft between the two domains of protein L1.
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Affiliation(s)
- D Drygin
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst 01003-4505, USA
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34
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Yokogawa T, Shimada N, Takeuchi N, Benkowski L, Suzuki T, Omori A, Ueda T, Nishikawa K, Spremulli LL, Watanabe K. Characterization and tRNA recognition of mammalian mitochondrial seryl-tRNA synthetase. J Biol Chem 2000; 275:19913-20. [PMID: 10764807 DOI: 10.1074/jbc.m908473199] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Animal mitochondrial protein synthesis systems contain two serine tRNAs (tRNAs(Ser)) corresponding to the codons AGY and UCN, each possessing an unusual secondary structure; the former lacks the entire D arm, and the latter has a slightly different cloverleaf structure. To elucidate whether these two tRNAs(Ser) can be recognized by the single animal mitochondrial seryl-tRNA synthetase (mt SerRS), we purified mt SerRS from bovine liver 2400-fold and showed that it can aminoacylate both of them. Specific interaction between mt SerRS and either of the tRNAs(Ser) was also observed in a gel retardation assay. cDNA cloning of bovine mt SerRS revealed that the deduced amino acid sequence of the enzyme contains 518 amino acid residues. The cDNAs of human and mouse mt SerRS were obtained by reverse transcription-polymerase chain reaction and expressed sequence tag data base searches. Elaborate inspection of primary sequences of mammalian mt SerRSs revealed diversity in the N-terminal domain responsible for tRNA recognition, indicating that the recognition mechanism of mammalian mt SerRS differs considerably from that of its prokaryotic counterpart. In addition, the human mt SerRS gene was found to be located on chromosome 19q13.1, to which the autosomal deafness locus DFNA4 is mapped.
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Affiliation(s)
- T Yokogawa
- Department of Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagito, Gifu 501-1193, Japan
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35
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Lenhard B, Orellana O, Ibba M, Weygand-Durasević I. tRNA recognition and evolution of determinants in seryl-tRNA synthesis. Nucleic Acids Res 1999; 27:721-9. [PMID: 9889265 PMCID: PMC148239 DOI: 10.1093/nar/27.3.721] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have analyzed the evolution of recognition of tRNAsSerby seryl-tRNA synthetases, and compared it to other type 2 tRNAs, which contain a long extra arm. In Eubacteria and chloroplasts this type of tRNA is restricted to three families: tRNALeu, tRNASer and tRNATyr. tRNALeuand tRNASer also carry a long extra arm in Archaea, Eukarya and all organelles with the exception of animal mitochondria. In contrast, the long extra arm of tRNATyr is far less conserved: it was drastically shortened after the separation of Archaea and Eukarya from Eubacteria, and it is also truncated in animal mitochondria. The high degree of phylo-genetic divergence in the length of tRNA variable arms, which are recognized by both class I and class II aminoacyl-tRNA synthetases, makes type 2 tRNA recognition an ideal system with which to study how tRNA discrimination may have evolved in tandem with the evolution of other components of the translation machinery.
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Affiliation(s)
- B Lenhard
- Department of Chemistry, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
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36
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Hartmuth K, Raker VA, Huber J, Branlant C, Lührmann R. An unusual chemical reactivity of Sm site adenosines strongly correlates with proper assembly of core U snRNP particles. J Mol Biol 1999; 285:133-47. [PMID: 9878394 DOI: 10.1006/jmbi.1998.2300] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The small nuclear ribonucleoprotein particles (snRNP) U1, U2, U4, and U5 contain a common set of eight Sm proteins that bind to the conserved single-stranded 5'-PuAU3-6GPu-3' (Sm binding site) region of their constituent U snRNA (small nuclear RNA), forming the Sm core RNP. Using native and in vitro reconstituted U1 snRNPs, accessibility of the RNA within the Sm core RNP to chemical structure probes was analyzed. Hydroxyl radical footprinting of in vitro reconstituted U1 snRNP demonstrated that riboses within a large continuous RNA region, including the Sm binding site, were protected. This protection was dependent on the binding of the Sm proteins. In contrast with the riboses, the phosphate groups within the Sm core site were accessible to modifying reagents. The invariant adenosine residue at the 5' end, as well as an adenosine two nucleotides downstream of the Sm binding site, showed an unexpected reactivity with dimethyl sulfate. This novel reactivity could be attributed to N7-methylation of the adenosine and was not observed in naked RNA, indicating that it is an intrinsic property of the RNA- protein interactions within the Sm core RNP. Further, this reactivity was observed concomitantly with formation of the Sm subcore intermediate during Sm core RNP assembly. As the Sm subcore can be viewed as the commitment complex in this assembly pathway, these results suggest that the peculiar reactivity of the Sm site adenosine bases may be diagnostic for proper assembly of the Sm core RNP. Consistent with this idea, a strong correlation was found between the unusual N7-A methylation sensitivity of the Sm core RNP and its ability to be imported into the nucleus of Xenopus laevis oocytes.
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Affiliation(s)
- K Hartmuth
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität, Emil-Mankopff-Strasse 2, Marburg, D-35037, Germany
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37
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Dabrowski M, Spahn CM, Schäfer MA, Patzke S, Nierhaus KH. Protection patterns of tRNAs do not change during ribosomal translocation. J Biol Chem 1998; 273:32793-800. [PMID: 9830024 DOI: 10.1074/jbc.273.49.32793] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The translocation reaction of two tRNAs on the ribosome during elongation of the nascent peptide chain is one of the most puzzling reactions of protein biosynthesis. We show here that the ribosomal contact patterns of the two tRNAs at A and P sites, although strikingly different from each other, hardly change during the translocation reaction to the P and E sites, respectively. The results imply that the ribosomal micro-environment of the tRNAs remains the same before and after translocation and thus suggest that a movable ribosomal domain exists that tightly binds two tRNAs and carries them together with the mRNA during the translocation reaction from the A-P region to the P-E region. These findings lead to a new explanation for the translocation reaction.
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Affiliation(s)
- M Dabrowski
- Max-Planck-Institut für Molekulare Genetik, AG Ribosomen, Ihnestrasse 73, D-14195 Berlin, Germany
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38
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Vörtler CS, Fedorova O, Persson T, Kutzke U, Eckstein F. Determination of 2'-hydroxyl and phosphate groups important for aminoacylation of Escherichia coli tRNAAsp: a nucleotide analogue interference study. RNA (NEW YORK, N.Y.) 1998; 4:1444-1454. [PMID: 9814764 PMCID: PMC1369716 DOI: 10.1017/s1355838298980967] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
2'-Deoxynucleoside 5'-a-thiotriphosphates have been incorporated randomly, replacing any of the four nucleotides separately and at a low level in Escherichia colitRNA(AsP)transcripts. After some tRNAs were charged with the cognate aminoacyl-tRNA synthetase and biotinylated, charged and uncharged tRNAs were separated by binding to Streptavidin. A comparison of the iodine cleavage pattern of charged and uncharged tRNAs indicated positions of 2'-deoxyphosphorothioate interference with charging. To separate the 2'-deoxy from the phosphorothioate effect, the same sequence of reactions was performed with the corresponding NTPalphaS. Several positions were identified with a 2'-deoxy or a phosphorothioate effect. tRNAs with single deoxy substitutions at the identified positions were prepared by enzymatic ligation of chemically synthesized halves. The kinetics of charging these tRNAs were determined. The 2'-deoxy effects identified by the interference assay were confirmed, showing a reduction in charging efficiency of between 2.5-6-fold, except for the terminal A76 with a 25-fold reduction. Inspection of the X-ray structure of the tRNA-synthetase complex showed consistency of most of these findings. Critical 2'-deoxy groups are localized mainly on the proposed contact surface with the synthetase or at the interface of the two tRNA domains. The same overall picture emerged for critical phosphorothioates. With the exception of 2'-deoxy-adenosine-containing tRNAs, multiple 2'-deoxy-substituted tRNAs, prepared by ligation of halves, showed a much larger reduction in charging efficiency than the mono-substituted tRNAs, indicating an additive effect.
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Affiliation(s)
- C S Vörtler
- Max-Planck-Institut für experimentelle Medizin, Göttingen, Germany
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39
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Abstract
Synthetic oligonucleotide analogs have greatly aided our understanding of several biochemical processes. Efficient solid-phase and enzyme-assisted synthetic methods and the availability of modified base analogs have added to the utility of such oligonucleotides. In this review, we discuss the applications of synthetic oligonucleotides that contain backbone, base, and sugar modifications to investigate the mechanism and stereochemical aspects of biochemical reactions. We also discuss interference mapping of nucleic acid-protein interactions; spectroscopic analysis of biochemical reactions and nucleic acid structures; and nucleic acid cross-linking studies. The automation of oligonucleotide synthesis, the development of versatile phosphoramidite reagents, and efficient scale-up have expanded the application of modified oligonucleotides to diverse areas of fundamental and applied biological research. Numerous reports have covered oligonucleotides for which modifications have been made of the phosphodiester backbone, of the purine and pyrimidine heterocyclic bases, and of the sugar moiety; these modifications serve as structural and mechanistic probes. In this chapter, we review the range, scope, and practical utility of such chemically modified oligonucleotides. Because of space limitations, we discuss only those oligonucleotides that contain phosphate and phosphate analogs as internucleotidic linkages.
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Affiliation(s)
- S Verma
- Max-Planck-Institut für Experimentelle Medizin, Göttingen, Germany
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40
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Sood VD, Beattie TL, Collins RA. Identification of phosphate groups involved in metal binding and tertiary interactions in the core of the Neurospora VS ribozyme. J Mol Biol 1998; 282:741-50. [PMID: 9743623 DOI: 10.1006/jmbi.1998.2049] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have used ethylation protection experiments and modification interference using phosphorothioate nucleosides to identify phosphate groups involved in the magnesium-dependent tertiary structure and function of the VS ribozyme, a small, self-cleaving RNA. Phosphorothioate interference-rescue experiments in the presence of the thiophilic manganese ion implicate four phosphate groups in direct metal ion binding. Phosphorothioate substitution also creates a new manganese binding site that increases the cis cleavage rate of the ribozyme, possibly by disrupting an inhibitory structure. Interpreting these data in the context of a recently developed structural model shows that almost all of the important phosphate groups are located in the central core of the ribozyme. The model suggests roles for certain phosphate groups in particular steps of RNA folding and identifies a candidate region for the active site of the ribozyme.
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Affiliation(s)
- V D Sood
- Department of Molecular and Medical Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
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41
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Pleiss JA, Derrick ML, Uhlenbeck OC. T7 RNA polymerase produces 5' end heterogeneity during in vitro transcription from certain templates. RNA (NEW YORK, N.Y.) 1998; 4:1313-7. [PMID: 9769105 PMCID: PMC1369703 DOI: 10.1017/s135583829800106x] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The use of T7 RNA polymerase to prepare large quantities of RNA of a particular sequence has greatly facilitated the study of both the structure and function of RNA. Generally, it has been believed that the products of this technique are highly homogeneous in sequence, with only a few noted exceptions. We have carefully examined the transcriptional products of several tRNAs that vary in their 5' end sequence and found that, for those molecules that begin with multiple, consecutive guanosines, the transcriptional products are far from homogenous. Although a template beginning with GCG showed no detectable 5' end heterogeneity, two tRNA templates designed to have either four or five consecutive guanosines at their 5' ends had more than 30% of their total transcriptional products extended by at least one untemplated nucleotide at their 5' end. By simply reducing the number of consecutive guanosines, the heterogeneity was reduced significantly. The presence of this 5' end heterogeneity in combination with the 3' end heterogeneity common to T7 transcriptions results in a mixture of RNA molecules even after rigorous size purification.
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Affiliation(s)
- J A Pleiss
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA
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42
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Hoch I, Berens C, Westhof E, Schroeder R. Antibiotic inhibition of RNA catalysis: neomycin B binds to the catalytic core of the td group I intron displacing essential metal ions. J Mol Biol 1998; 282:557-69. [PMID: 9737922 DOI: 10.1006/jmbi.1998.2035] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The aminoglycoside antibiotic neomycin B induces misreading of the genetic code during translation and inhibits several ribozymes. The self-splicing group I intron derived from the T4 phage thymidylate synthase (td) gene is one of these. Here we report how neomycin B binds to the intron RNA inhibiting splicing in vitro. Footprinting experiments identified two major regions of protection by neomycin B: one in the internal loop between the stems P4 and P5 and the other in the catalytic core close to the G-binding site. Mutational analyses defined the latter as the inhibitory site. Splicing inhibition is strongly dependent on pH and Mg2+ concentration, suggesting electrostatic interactions and competition with divalent metal ions. Fe2+-induced hydroxyl radical (Fe-OH.) cleavage of the RNA backbone was used to monitor neomycin-mediated changes in the proximity of the metal ions. Neomycin B protected several positions in the catalytic core from Fe-OH. cleavage, suggesting that metal ions are displaced in the presence of the antibiotic. Mutation of the bulged nucleotide in the P7 stem, a position which is strongly protected by neomycin B from Fe-OH. cleavage and which has been proposed to be involved in binding an essential metal ion, renders splicing resistant to neomycin. These results allowed the docking of neomycin to the core of the group I intron in the 3D model.
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Affiliation(s)
- I Hoch
- Vienna Biocenter, Dr Bohrgasse 9, Vienna, A-1030, Austria
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43
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Shpanchenko OV, Dontsova OA, Bogdanov AA, Nierhaus KH. Structure of 5S rRNA within the Escherichia coli ribosome: iodine-induced cleavage patterns of phosphorothioate derivatives. RNA (NEW YORK, N.Y.) 1998; 4:1154-1164. [PMID: 9740132 PMCID: PMC1369689 DOI: 10.1017/s1355838298980359] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The protection patterns of 5S rRNA in solution, within the ribosomal 50S subunit, 70S ribosomes, and functional complexes, were assessed with the phosphorothioate method. About 20% of the analyzed positions (G9-G107) showed strong assembly defects: A phosphorothioate at one of these positions significantly impaired the incorporation of 5S rRNA into 50S particles. The reverse has also been observed: A phosphorothioate is preferred over a phosphate residue in the assembly process at a few positions. The results further demonstrate that 5S rRNA undergoes conformational changes during the assembly in the central protuberance of the 50S subunit and upon association with the small ribosomal subunit forming a 70S ribosome. In striking contrast, when the 70S ribosomes are once formed, the contact pattern of the 5S rRNA is the same in various functional states such as initiation-like complexes and pre- and posttranslocational states.
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Affiliation(s)
- O V Shpanchenko
- Department of Chemistry, Moscow State University, Moscow, Russia
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44
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Abstract
The central process for the transfer of the genetic information from the nucleic acid world into the structure of proteins is the ribosomal elongation cycle, where the sequence of codons is translated into the sequence of amino acids. The nascent polypeptide chain is elongated by one amino acid during the reactions of one cycle. Essentially, three models for the elongation cycle have been proposed. The allosteric three-site model and the hybrid-site model describe different aspects of tRNA binding and do not necessarily contradict each other. However, the alpha-epsilon model is not compatible with both models. The three models are evaluated in the light of recent results on the tRNA localization within the ribosome: the tRNAs of the elongating ribosome could be localized by two different techniques, viz. an advanced method of small-angle neutron scattering and cryo-electron microscopy. The best fit with the biochemical and structural data is obtained with the alpha-epsilon model.
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Affiliation(s)
- C M Spahn
- Max-Planck-Institut für Molekulare Genetik, AG Ribosomen, Berlin, Germany
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45
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Burkhardt N, Jünemann R, Spahn CM, Nierhaus KH. Ribosomal tRNA binding sites: three-site models of translation. Crit Rev Biochem Mol Biol 1998; 33:95-149. [PMID: 9598294 DOI: 10.1080/10409239891204189] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The first models of translation described protein synthesis in terms of two operationally defined tRNA binding sites, the P-site for the donor substrate, the peptidyl-tRNA, and the A-site for the acceptor substrates, the aminoacyl-tRNAs. The discovery and analysis of the third tRNA binding site, the E-site specific for deacylated tRNAs, resulted in the allosteric three-site model, the two major features of which are (1) the reciprocal relationship of A-site and E-site occupation, and (2) simultaneous codon-anticodon interactions of both tRNAs present at the elongating ribosome. However, structural studies do not support the three operationally defined sites in a simple fashion as three topographically fixed entities, thus leading to new concepts of tRNA binding and movement: (1) the hybrid-site model describes the tRNAs' movement through the ribosome in terms of changing binding sites on the 30S and 50S subunits in an alternating fashion. The tRNAs thereby pass through hybrid binding states. (2) The alpha-epsilon model introduces the concept of a movable tRNA-binding domain comprising two binding sites, termed alpha and epsilon. The translocation movement is seen as a result of a conformational change of the ribosome rather than as a diffusion process between fixed binding sites. The alpha-epsilon model reconciles most of the experimental data currently available.
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MESH Headings
- Allosteric Site/genetics
- Animals
- Base Sequence
- Escherichia coli
- Humans
- Models, Biological
- Models, Molecular
- Molecular Sequence Data
- Peptide Chain Elongation, Translational/genetics
- Protein Biosynthesis
- RNA, Transfer, Amino Acid-Specific/chemistry
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Amino Acid-Specific/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
- Structure-Activity Relationship
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Affiliation(s)
- N Burkhardt
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
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46
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Nierhaus KH, Stuhrmann HB, Svergun D. The ribosomal elongation cycle and the movement of tRNAs across the ribosome. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1998; 59:177-204. [PMID: 9427843 DOI: 10.1016/s0079-6603(08)61032-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ribosome research has reached an exciting state, where two lines of experimental research have considerably improved our understanding of the ribosomal functions. On one hand, functional analysis has elucidated principles of both the decoding process and the tRNA movement on the ribosome during translocation. Experimental data leading to current competing models of the ribosomal elongation cycle can be reconciled by a new model, the alpha-epsilon model, according to which both tRNAs are tightly bound to a movable ribosomal domain. This alpha-epsilon domain carries the tRNA2.mRNA complex from the A and P sites to the P and E sites in the course of translocation maintaining the binding of both tRNAs. On the other hand, the location of tRNAs within the elongating ribosome can be directly determined for the first time by neutron scattering and electron microscopy. Both lines of evidence complement each other and define a frame for the first experimentally sound functional model of the elongating ribosome.
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Affiliation(s)
- K H Nierhaus
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
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47
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Reardon JT, Thompson LH, Sancar A. Rodent UV-sensitive mutant cell lines in complementation groups 6-10 have normal general excision repair activity. Nucleic Acids Res 1997; 25:1015-21. [PMID: 9023113 PMCID: PMC146541 DOI: 10.1093/nar/25.5.1015] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Mammalian nucleotide excision repair is the primary enzymatic pathway for removing bulky lesions from DNA. The repair reaction involves three main steps: (i) dual incisions on both sides of the lesion; (ii) excision of the damaged base in an oligonucleotide 24-31 nt in length; (iii) filling in of the post-excision gap and ligation. We have developed assays that probe the individual steps of the reaction. Using these methods (assays for incision, excision and repair patch synthesis), we demonstrate that the mammalian excision nuclease system removes bulky lesions by incising mainly at the 22nd-25th phosphodiester bonds 5'and the 3rd-5th phosphodiester bonds 3'of the lesion, thus releasing oligonucleotides primarily 26-29 nt in length. The resulting excision gap is filled in by DNA polymerases delta and epsilon as revealed by the 'phosphorothioate repair patch assay'. When these assays were employed with cell-free extracts from the moderately UV-sensitive rodent mutants in complementation groups 6-10, we found that these mutants are essentially normal in all three steps of the repair reaction. This leads us to conclude that these cell lines have normal in vitro repair activities and that the defects in these mutants are most likely in genes controlling cellular functions not directly involved in general excision repair.
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Affiliation(s)
- J T Reardon
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7260, USA
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48
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Shpanchenko OV, Zvereva MI, Dontsova OA, Nierhaus KH, Bogdanov AA. 5S rRNA sugar-phosphate backbone protection in complexes with specific ribosomal proteins. FEBS Lett 1996; 394:71-5. [PMID: 8925931 DOI: 10.1016/0014-5793(96)00872-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
5S ribosomal RNA forms stable specific complexes with ribosomal proteins L18, L25 and L5. In this work, interaction of phosphate residues of E. coli 5S rRNA within 5S rRNA-protein complexes has been studied. For this purpose 5S rRNA with statistically distributed phosphorothioate residues has been used for complex formation and the accessibility of phosphorothioates to iodine cleavage in the complex and in the free state has been studied. In free 5S rRNA, the phosphate residue at A73 was partially protected, probably due to being involved in the organization of the spatial structure of 5S rRNA. This protection is stronger in the complex with three proteins when the 5S rRNA structure is stabilized. In the 5S rRNA-L18 complex only two phosphate groups, G7 and A34, were protected. L25 in a complex with 5S rRNA protects large numbers of phosphorothioate groups concentrating in two clusters, indicating the possibility of two binding sites for this protein on 5S rRNA. The protection pattern differs from that for individual proteins because of the possible rearrangement of the structure.
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Affiliation(s)
- O V Shpanchenko
- Department of Chemistry, Moscow State University, Russian Federation
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49
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Alexeeva EV, Shpanchenko OV, Dontsova OA, Bogdanov AA, Nierhaus KH. Interaction of mRNA with the Escherichia coli ribosome: accessibility of phosphorothioate-containing mRNA bound to ribosomes for iodine cleavage. Nucleic Acids Res 1996; 24:2228-35. [PMID: 8710490 PMCID: PMC145942 DOI: 10.1093/nar/24.12.2228] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The contacts of phosphate groups in mRNAs with ribosomes were studied. Two mRNAs were used: one mRNA contained in the middle two defined codons to construct the pre- and the post-translocational states, the other was a sequence around the initiation site of the natural cro-mRNA. Phosphorothioate nucleotides were randomly incorporated at a few A, G, U or C positions during in vitro transcription. Iodine can cleave the thioated positions if they are not shielded by ribosomal components. Only a few minor differences in iodine cleavage of ribosome bound and non-bound mRNA were observed: the nucleotide two positions upstream of the decoding codons (i.e. those codons involved in codon-anticodon interactions) showed a reduced accessibility for iodine and the nucleotide immediately following the decoding codons an enhanced accessibility in both elongating states. In initiating ribosomes where the mRNA contained a strong Shine-Dalgarno sequence, at least five phosphates were additionally slightly protected covering the Shine-Dalgarno sequence and nucleotides downstream including the initiator AUG in the P site (Al, G3, G-2, G-5 and A-7). The low contact levels of the phosphates in the mRNA with the elongating ribosome strikingly contrast with the pronounced contact patterns previously described for tRNAs. The data obtained in this study, as well as results of previous studies, suggest that mRNA regions downstream and upstream of decoding codons form only weak contacts with ribosomal components and that the mRNA thus is mainly fixed by codon-anticodon interaction on the elongating ribosome.
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Affiliation(s)
- E V Alexeeva
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
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50
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Saks ME, Sampson JR. Variant minihelix RNAs reveal sequence-specific recognition of the helical tRNA(Ser) acceptor stem by E.coli seryl-tRNA synthetase. EMBO J 1996; 15:2843-9. [PMID: 8654382 PMCID: PMC450222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Aminoacylation rate determinations for a series of variant RNA minihelix substrates revealed that Escherichia coli seryl-tRNA synthetase (SerRS) recognizes the 1--72 through 5--68 base pairs of the E.coli tRNA(Ser) acceptor stem with the major recognition elements clustered between positions 2--71 and 4--69. The rank order of effects of canonical base pair substitutions at each position on kcat/Km was used to assess the involvement of major groove functional groups in recognition. Conclusions based on the biochemical data are largely consistent with the interactions revealed by the refined structure of the homologous Thermus thermophilus tRNA(Ser)-SerRS complex that Cusack and colleagues report in the accompanying paper. Disruption of an end-on hydrophobic interaction between the major groove C5(H) of pyrimidine 69 and an aromatic side chain of SerRS is shown to significantly decrease kcat/Km of a minihelix substrate. This type of interaction provides a means by which proteins can recognize the binary information of 'degenerate' sequences, such as the purine-pyrimidine base pairs of tRNA(Ser). The 3--70 base pair is shown to contribute to recognition by SerRS even though it is not contacted specifically by the protein. The latter effect derives from the organization of the specific contacts that SerRS makes with the neighboring 2--71 and 4--69 acceptor stem base pairs.
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Affiliation(s)
- M E Saks
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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