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Sabalette KB, Makarova L, Marcia M. G·U base pairing motifs in long non-coding RNAs. Biochimie 2023; 214:123-140. [PMID: 37353139 DOI: 10.1016/j.biochi.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/25/2023]
Abstract
Long non-coding RNAs (lncRNAs) are recently-discovered transcripts involved in gene expression regulation and associated with diseases. Despite the unprecedented molecular complexity of these transcripts, recent studies of the secondary and tertiary structure of lncRNAs are starting to reveal the principles of lncRNA structural organization, with important functional implications. It therefore starts to be possible to analyze lncRNA structures systematically. Here, using a set of prototypical and medically-relevant lncRNAs of known secondary structure, we specifically catalogue the distribution and structural environment of one of the first-identified and most frequently occurring non-canonical Watson-Crick interactions, the G·U base pair. We compare the properties of G·U base pairs in our set of lncRNAs to those of the G·U base pairs in other well-characterized transcripts, like rRNAs, tRNAs, ribozymes, and riboswitches. Furthermore, we discuss how G·U base pairs in these targets participate in establishing interactions with proteins or miRNAs, and how they enable lncRNA tertiary folding by forming intramolecular or metal-ion interactions. Finally, by identifying highly-G·U-enriched regions of yet unknown function in our target lncRNAs, we provide a new rationale for future experimental investigation of these motifs, which will help obtain a more comprehensive understanding of lncRNA functions and molecular mechanisms in the future.
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Affiliation(s)
- Karina Belen Sabalette
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France
| | - Liubov Makarova
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France.
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2
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Giegé R, Eriani G. The tRNA identity landscape for aminoacylation and beyond. Nucleic Acids Res 2023; 51:1528-1570. [PMID: 36744444 PMCID: PMC9976931 DOI: 10.1093/nar/gkad007] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
Abstract
tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.
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Affiliation(s)
- Richard Giegé
- Correspondence may also be addressed to Richard Giegé.
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3
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Warden MS, Tonelli M, Cornilescu G, Liu D, Hopersberger LJ, Ponniah K, Pascal SM. Structure of RNA Stem Loop B from the Picornavirus Replication Platform. Biochemistry 2017; 56:2549-2557. [PMID: 28459542 DOI: 10.1021/acs.biochem.7b00141] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The presumptive RNA cloverleaf at the start of the 5'-untranslated region of the picornavirus genome is an essential element in replication. Stem loop B (SLB) of the cloverleaf is a recognition site for the host polyC-binding protein, which initiates a switch from translation to replication. Here we present the solution structure of human rhinovirus isotype 14 SLB using nuclear magnetic resonance spectroscopy. SLB adopts a predominantly A-form helical structure. The stem contains five Watson-Crick base pairs and one wobble base pair and is capped by an eight-nucleotide loop. The wobble base pair introduces perturbations into the helical parameters but does not appear to introduce flexibility. However, the helix major groove appears to be accessible. Flexibility is seen throughout the loop and in the terminal nucleotides. The pyrimidine-rich region of the loop, the apparent recognition site for the polyC-binding protein, is the most disordered region of the structure.
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Affiliation(s)
- Meghan S Warden
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Dong Liu
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Lorelei J Hopersberger
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Komala Ponniah
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Steven M Pascal
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
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4
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Liu LC, Grundy FJ, Henkin TM. Non-Conserved Residues in Clostridium acetobutylicum tRNA(Ala) Contribute to tRNA Tuning for Efficient Antitermination of the alaS T Box Riboswitch. Life (Basel) 2015; 5:1567-82. [PMID: 26426057 PMCID: PMC4695836 DOI: 10.3390/life5041567] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 09/16/2015] [Accepted: 09/18/2015] [Indexed: 11/16/2022] Open
Abstract
The T box riboswitch regulates expression of amino acid-related genes in Gram-positive bacteria by monitoring the aminoacylation status of a specific tRNA, the binding of which affects the folding of the riboswitch into mutually exclusive terminator or antiterminator structures. Two main pairing interactions between the tRNA and the leader RNA have been demonstrated to be necessary, but not sufficient, for efficient antitermination. In this study, we used the Clostridium acetobutylicum alaS gene, which encodes alanyl-tRNA synthetase, to investigate the specificity of the tRNA response. We show that the homologous C. acetobutylicum tRNAAla directs antitermination of the C. acetobutylicum alaS gene in vitro, but the heterologous Bacillus subtilis tRNAAla (with the same anticodon and acceptor end) does not. Base substitutions at positions that vary between these two tRNAs revealed synergistic and antagonistic effects. Variation occurs primarily at positions that are not conserved in tRNAAla species, which indicates that these non-conserved residues contribute to optimal antitermination of the homologous alaS gene. This study suggests that elements in tRNAAla may have coevolved with the homologous alaS T box leader RNA for efficient antitermination.
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Affiliation(s)
- Liang-Chun Liu
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - Frank J Grundy
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - Tina M Henkin
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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5
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Le Chevalier Isaad A, Carrara P, Stano P, Krishnakumar KS, Lafont D, Zamboulis A, Buchet R, Bouchu D, Albrieux F, Strazewski P. A hydrophobic disordered peptide spontaneously anchors a covalently bound RNA hairpin to giant lipidic vesicles. Org Biomol Chem 2015; 12:6363-73. [PMID: 24915577 DOI: 10.1039/c4ob00721b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The attraction of nucleic acids to lipidic compartments is the first step for carriers of potentially inheritable information to self-organise in functionalised synthetic cells. Confocal fluorescence imaging shows that a synthetic amphiphilic peptidyl RNA molecule spontaneously accumulates at the outer bilayer membranes of phospho- and glycolipidic giant vesicles. Cooperatively attractive interactions of -3.4 to -4.0 kcal mol(-1) between a random coil hydrophobic peptide and lipid membranes can thus pilot lipophobic RNA to its compartmentation. The separation of mixed lipid phases in the membranes further enhances the local concentration of anchored RNA.
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Affiliation(s)
- Alexandra Le Chevalier Isaad
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (Unité Mixte de Recherche 5246), Université de Lyon, Claude Bernard Lyon 1, 69622 Villeurbanne Cedex, Lyon, France.
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6
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Naganuma M, Sekine SI, Chong YE, Guo M, Yang XL, Gamper H, Hou YM, Schimmel P, Yokoyama S. The selective tRNA aminoacylation mechanism based on a single G•U pair. Nature 2014; 510:507-11. [PMID: 24919148 DOI: 10.1038/nature13440] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/06/2014] [Indexed: 11/09/2022]
Abstract
Ligation of tRNAs with their cognate amino acids, by aminoacyl-tRNA synthetases, establishes the genetic code. Throughout evolution, tRNA(Ala) selection by alanyl-tRNA synthetase (AlaRS) has depended predominantly on a single wobble base pair in the acceptor stem, G3•U70, mainly on the kcat level. Here we report the crystal structures of an archaeal AlaRS in complex with tRNA(Ala) with G3•U70 and its A3•U70 variant. AlaRS interacts with both the minor- and the major-groove sides of G3•U70, widening the major groove. The geometry difference between G3•U70 and A3•U70 is transmitted along the acceptor stem to the 3'-CCA region. Thus, the 3'-CCA region of tRNA(Ala) with G3•U70 is oriented to the reactive route that reaches the active site, whereas that of the A3•U70 variant is folded back into the non-reactive route. This novel mechanism enables the single wobble pair to dominantly determine the specificity of tRNA selection, by an approximate 100-fold difference in kcat.
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Affiliation(s)
- Masahiro Naganuma
- 1] RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan [2] Department of Biophysics and Biochemistry and Laboratory of Structural Biology, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan [3] RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shun-ichi Sekine
- 1] RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan [2] Department of Biophysics and Biochemistry and Laboratory of Structural Biology, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan [3] Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yeeting Esther Chong
- 1] The Skaggs Institute for Chemical Biology and the Department of Cell and Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, California 92037, USA [2] aTyr Pharma, 3545 John Hopkins Court, San Diego, California 92121, USA (Y.E.C.); Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, USA (M.G.)
| | - Min Guo
- 1] The Skaggs Institute for Chemical Biology and the Department of Cell and Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, California 92037, USA [2] aTyr Pharma, 3545 John Hopkins Court, San Diego, California 92121, USA (Y.E.C.); Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, USA (M.G.)
| | - Xiang-Lei Yang
- The Skaggs Institute for Chemical Biology and the Department of Cell and Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
| | - Paul Schimmel
- 1] The Skaggs Institute for Chemical Biology and the Department of Cell and Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, California 92037, USA [2] The Scripps Florida Research Institute, 130 Scripps Way, 3B3 Jupiter, Florida 33458-5284, USA
| | - Shigeyuki Yokoyama
- 1] RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan [2] Department of Biophysics and Biochemistry and Laboratory of Structural Biology, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan [3] RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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7
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Das M, Vargas-Rodriguez O, Goto Y, Suga H, Musier-Forsyth K. Distinct tRNA recognition strategies used by a homologous family of editing domains prevent mistranslation. Nucleic Acids Res 2013; 42:3943-53. [PMID: 24371276 PMCID: PMC3973320 DOI: 10.1093/nar/gkt1332] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Errors in protein synthesis due to mispairing of amino acids with tRNAs jeopardize cell viability. Several checkpoints to prevent formation of Ala- and Cys-tRNAPro have been described, including the Ala-specific editing domain (INS) of most bacterial prolyl-tRNA synthetases (ProRSs) and an autonomous single-domain INS homolog, YbaK, which clears Cys-tRNAPro in trans. In many species where ProRS lacks an INS domain, ProXp-ala, another single-domain INS-like protein, is responsible for editing Ala-tRNAPro. Although the amino acid specificity of these editing domains has been established, the role of tRNA sequence elements in substrate selection has not been investigated in detail. Critical recognition elements for aminoacylation by bacterial ProRS include acceptor stem elements G72/A73 and anticodon bases G35/G36. Here, we show that ProXp-ala and INS require these same acceptor stem and anticodon elements, respectively, whereas YbaK lacks inherent tRNA specificity. Thus, these three related domains use divergent approaches to recognize tRNAs and prevent mistranslation. Whereas some editing domains have borrowed aspects of tRNA recognition from the parent aminoacyl-tRNA synthetase, relaxed tRNA specificity leading to semi-promiscuous editing may offer advantages to cells.
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Affiliation(s)
- Mom Das
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA and Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
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8
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Halder S, Bhattacharyya D. RNA structure and dynamics: a base pairing perspective. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 113:264-83. [PMID: 23891726 DOI: 10.1016/j.pbiomolbio.2013.07.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 06/25/2013] [Accepted: 07/16/2013] [Indexed: 12/12/2022]
Abstract
RNA is now known to possess various structural, regulatory and enzymatic functions for survival of cellular organisms. Functional RNA structures are generally created by three-dimensional organization of small structural motifs, formed by base pairing between self-complementary sequences from different parts of the RNA chain. In addition to the canonical Watson-Crick or wobble base pairs, several non-canonical base pairs are found to be crucial to the structural organization of RNA molecules. They appear within different structural motifs and are found to stabilize the molecule through long-range intra-molecular interactions between basic structural motifs like double helices and loops. These base pairs also impart functional variation to the minor groove of A-form RNA helices, thus forming anchoring site for metabolites and ligands. Non-canonical base pairs are formed by edge-to-edge hydrogen bonding interactions between the bases. A large number of theoretical studies have been done to detect and analyze these non-canonical base pairs within crystal or NMR derived structures of different functional RNA. Theoretical studies of these isolated base pairs using ab initio quantum chemical methods as well as molecular dynamics simulations of larger fragments have also established that many of these non-canonical base pairs are as stable as the canonical Watson-Crick base pairs. This review focuses on the various structural aspects of non-canonical base pairs in the organization of RNA molecules and the possible applications of these base pairs in predicting RNA structures with more accuracy.
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Affiliation(s)
- Sukanya Halder
- Biophysics division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700 064, India
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9
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Réblová K, Šponer J, Lankaš F. Structure and mechanical properties of the ribosomal L1 stalk three-way junction. Nucleic Acids Res 2012; 40:6290-303. [PMID: 22451682 PMCID: PMC3401443 DOI: 10.1093/nar/gks258] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 03/07/2012] [Accepted: 03/07/2012] [Indexed: 01/06/2023] Open
Abstract
The L1 stalk is a key mobile element of the large ribosomal subunit which interacts with tRNA during translocation. Here, we investigate the structure and mechanical properties of the rRNA H76/H75/H79 three-way junction at the base of the L1 stalk from four different prokaryotic organisms. We propose a coarse-grained elastic model and parameterize it using large-scale atomistic molecular dynamics simulations. Global properties of the junction are well described by a model in which the H76 helix is represented by a straight, isotropically flexible elastic rod, while the junction core is represented by an isotropically flexible spherical hinge. Both the core and the helix contribute substantially to the overall H76 bending fluctuations. The presence of wobble pairs in H76 does not induce any increased flexibility or anisotropy to the helix. The half-closed conformation of the L1 stalk seems to be accessible by thermal fluctuations of the junction itself, without any long-range allosteric effects. Bending fluctuations of H76 with a bulge introduced in it suggest a rationale for the precise position of the bulge in eukaryotes. Our elastic model can be generalized to other RNA junctions found in biological systems or in nanotechnology.
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Affiliation(s)
- Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, CEITEC—Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, CEITEC—Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Filip Lankaš
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, CEITEC—Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
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10
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The origin of the tRNA molecule: Independent data favor a specific model of its evolution. Biochimie 2012; 94:1464-6. [DOI: 10.1016/j.biochi.2012.01.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 01/18/2012] [Indexed: 10/14/2022]
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11
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šponer J, Cang X, Cheatham TE. Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. Methods 2012; 57:25-39. [PMID: 22525788 PMCID: PMC3775459 DOI: 10.1016/j.ymeth.2012.04.005] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 04/04/2012] [Accepted: 04/06/2012] [Indexed: 11/29/2022] Open
Abstract
The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids.
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Affiliation(s)
- Jiří šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC – Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Xiaohui Cang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, Skaggs Hall 201, 2000 East 30 South, University of Utah, Salt Lake City, UT 84112, United States
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12
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Oberthür D, Eichert A, Erdmann VA, Fürste JP, Betzel C, Förster C. The crystal structure of a Thermus thermophilus tRNA(Gly) acceptor stem microhelix at 1.6 Å resolution. Biochem Biophys Res Commun 2011; 404:245-249. [PMID: 21114959 DOI: 10.1016/j.bbrc.2010.11.101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 11/23/2010] [Indexed: 05/30/2023]
Abstract
tRNAs are aminoacylated with the correct amino acid by the cognate aminoacyl-tRNA synthetase. The tRNA/synthetase systems can be divided into two classes: class I and class II. Within class I, the tRNA identity elements that enable the specificity consist of complex sequence and structure motifs, whereas in class II the identity elements are assured by few and simple determinants, which are mostly located in the tRNA acceptor stem. The tRNA(Gly)/glycyl-tRNA-synthetase (GlyRS) system is a special case regarding evolutionary aspects. There exist two different types of GlyRS, namely an archaebacterial/human type and an eubacterial type, reflecting the evolutionary divergence within this system. We previously reported the crystal structures of an Escherichia coli and of a human tRNA(Gly) acceptor stem microhelix. Here we present the crystal structure of a thermophilic tRNA(Gly) aminoacyl stem from Thermus thermophilus at 1.6Å resolution and provide insight into the RNA geometry and hydration.
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Affiliation(s)
- D Oberthür
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, 22603 Hamburg, Germany
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13
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Nozinovic S, Fürtig B, Jonker HRA, Richter C, Schwalbe H. High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA. Nucleic Acids Res 2009; 38:683-94. [PMID: 19906714 PMCID: PMC2811024 DOI: 10.1093/nar/gkp956] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We present a high-resolution nuclear magnetic resonance (NMR) solution structure of a 14-mer RNA hairpin capped by cUUCGg tetraloop. This short and very stable RNA presents an important model system for the study of RNA structure and dynamics using NMR spectroscopy, molecular dynamics (MD) simulations and RNA force-field development. The extraordinary high precision of the structure (root mean square deviation of 0.3 A) could be achieved by measuring and incorporating all currently accessible NMR parameters, including distances derived from nuclear Overhauser effect (NOE) intensities, torsion-angle dependent homonuclear and heteronuclear scalar coupling constants, projection-angle-dependent cross-correlated relaxation rates and residual dipolar couplings. The structure calculations were performed with the program CNS using the ARIA setup and protocols. The structure quality was further improved by a final refinement in explicit water using OPLS force field parameters for non-bonded interactions and charges. In addition, the 2'-hydroxyl groups have been assigned and their conformation has been analyzed based on NOE contacts. The structure currently defines a benchmark for the precision and accuracy amenable to RNA structure determination by NMR spectroscopy. Here, we discuss the impact of various NMR restraints on structure quality and discuss in detail the dynamics of this system as previously determined.
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Affiliation(s)
- Senada Nozinovic
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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14
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Konno M, Sumida T, Uchikawa E, Mori Y, Yanagisawa T, Sekine SI, Yokoyama S, Yokoyama S. Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP). FEBS J 2009; 276:4763-79. [PMID: 19656186 DOI: 10.1111/j.1742-4658.2009.07178.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ATP-pyrophosphate exchange reaction catalyzed by Arg-tRNA, Gln-tRNA and Glu-tRNA synthetases requires the assistance of the cognate tRNA. tRNA also assists Arg-tRNA synthetase in catalyzing the pyrophosphorolysis of synthetic Arg-AMP at low pH. The mechanism by which the 3'-end A76, and in particular its hydroxyl group, of the cognate tRNA is involved with the exchange reaction catalyzed by those enzymes has yet to be established. We determined a crystal structure of a complex of Arg-tRNA synthetase from Pyrococcus horikoshii, tRNA(Arg)(CCU) and an ATP analog with Rfactor = 0.213 (Rfree = 0.253) at 2.0 A resolution. On the basis of newly obtained structural information about the position of ATP bound on the enzyme, we constructed a structural model for a mechanism in which the formation of a hydrogen bond between the 2'-OH group of A76 of tRNA and the carboxyl group of Arg induces both formation of Arg-AMP (Arg + ATP --> Arg-AMP + pyrophosphate) and pyrophosphorolysis of Arg-AMP (Arg-AMP + pyrophosphate --> Arg + ATP) at low pH. Furthermore, we obtained a structural model of the molecular mechanism for the Arg-tRNA synthetase-catalyzed deacylation of Arg-tRNA (Arg-tRNA + AMP --> Arg-AMP + tRNA at high pH), in which the deacylation of aminoacyl-tRNA bound on Arg-tRNA synthetase and Glu-tRNA synthetase is catalyzed by a quite similar mechanism, whereby the proton-donating group (-NH-C+(NH2)2 or -COOH) of Arg and Glu assists the aminoacyl transfer from the 2'-OH group of tRNA to the phosphate group of AMP at high pH.
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Affiliation(s)
- Michiko Konno
- Department of Chemistry and Biochemistry, Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan.
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15
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Eichert A, Schreiber A, Fürste JP, Perbandt M, Betzel C, Erdmann VA, Förster C. Escherichia coli tRNA(Arg) acceptor-stem isoacceptors: comparative crystallization and preliminary X-ray diffraction analysis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:98-101. [PMID: 19193994 DOI: 10.1107/s1744309108042012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Accepted: 12/10/2008] [Indexed: 11/10/2022]
Abstract
The aminoacylation of tRNA is a crucial step in cellular protein biosynthesis. Recognition of the cognate tRNA by the correct aminoacyl-tRNA synthetase is ensured by tRNA identity elements. In tRNA(Arg), the identity elements consist of the anticodon, parts of the D-loop and the discriminator base. The minor groove of the aminoacyl stem interacts with the arginyl-tRNA synthetase. As a consequence of the redundancy of the genetic code, six tRNA(Arg) isoacceptors exist. In the present work, three different Escherichia coli tRNA(Arg) acceptor-stem helices were crystallized. Two of them, the tRNA(Arg) microhelices RR-1660 and RR-1662, were examined by X-ray diffraction analysis and diffracted to 1.7 and 1.8 A resolution, respectively. The tRNA(Arg) RR-1660 helix crystallized in space group P1, with unit-cell parameters a = 26.28, b = 28.92, c = 29.00 A, alpha = 105.74, beta = 99.01, gamma = 97.44 degrees , whereas the tRNA(Arg) RR-1662 helix crystallized in space group C2, with unit-cell parameters a = 33.18, b = 46.16, c = 26.04 A, beta = 101.50 degrees .
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Affiliation(s)
- André Eichert
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
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16
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Binding of DNA-binding alkaloids berberine and palmatine to tRNA and comparison to ethidium: Spectroscopic and molecular modeling studies. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.04.043] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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17
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Korostelev A, Ermolenko DN, Noller HF. Structural dynamics of the ribosome. Curr Opin Chem Biol 2008; 12:674-83. [PMID: 18848900 DOI: 10.1016/j.cbpa.2008.08.037] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 08/23/2008] [Indexed: 01/01/2023]
Abstract
Protein synthesis is inherently a dynamic process, requiring both small-scale and large-scale movements of tRNA and mRNA. It has long been suspected that these movements might be coupled to conformational changes in the ribosome, and in its RNA moieties in particular. Recently, the nature of ribosome structural dynamics has begun to emerge from a combination of approaches, most notably cryo-EM, X-ray crystallography, and FRET. Ribosome movement occurs both on a grand scale, as in the intersubunit rotational movements that are coupled to tRNA-mRNA translocation, and in intricate localized rearrangements such as those that accompany codon-anticodon recognition and peptide bond formation. In spite of much progress, our understanding of the mechanics of translation is now beset with countless new questions, reflecting the vast molecular architecture of the ribosome itself.
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Affiliation(s)
- Andrei Korostelev
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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18
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Radial scan of the molecular electrostatic potential of RNA double helices: an application to the enzyme-tRNA recognition. J Mol Graph Model 2008; 27:255-65. [PMID: 18586541 DOI: 10.1016/j.jmgm.2008.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 04/28/2008] [Accepted: 04/29/2008] [Indexed: 11/24/2022]
Abstract
We introduced a method to characterize quantitatively the molecular electrostatic potential (MEP) of the minor and major grooves of base pairs located at nucleic acid double helices. By means of a radial MEP scan, we obtained a n-tuple of potential values corresponding to each groove, which can be analyzed by plotting the MEP values as a function of the angle in the radial scan. We studied base pairs of two different tRNAs, relevant in the recognition process with their cognate aminoacyl tRNA synthetases (aaRSs), in order to correlate their electrostatic behavior with the corresponding aminoacylation activity. We analyzed the first three base pairs of the Escherichia coli tRNA(Ala) acceptor stem, finding several cases where the MEP profiles obtained from the plots are in agreement with the reported aminoacylation activities. Additionally, a non-hierarchical clustering performed over the MEP n-tuples resulted in meaningful classifications that correlate with the activity and with the predicted stereochemistry of the reaction. We also studied the first two base pairs of the E. coli tRNA(Thr) acceptor stem but constraining the analysis to the angle intervals that seem relevant for the binding sites of the enzyme. These intervals were deduced from the ThrRS-tRNA(Thr) complex crystal structure. In this case, we also found a good agreement between the MEP profiles and the activity, supporting the idea that the tRNA identity elements function is to allow an optimal electrostatic complementarity between the aminoacyl-tRNA synthetase and the tRNA.
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19
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Förster C, Zerressen-Harte A, Fürste JP, Perbandt M, Betzel C, Erdmann VA. Comparative X-ray structure analysis of human and Escherichia coli tRNA(Gly) acceptor stem microhelices. Biochem Biophys Res Commun 2008; 368:1002-6. [PMID: 18275849 DOI: 10.1016/j.bbrc.2008.01.174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Accepted: 01/28/2008] [Indexed: 11/28/2022]
Abstract
tRNA identity elements assure the correct aminoacylation of tRNAs by the aminoacyl-tRNA synthetases with the cognate amino acid. The tRNA(Gly)/glycyl-tRNA sythetase system is member of the so-called 'class II system' in which the tRNA determinants consist of rather simple elements. These are mostly located in the tRNA acceptor stem and in the glycine case additionally the discriminator base at position 73 is required. Within the glycine-tRNA synthetases, the archaebacterial/human and the eubacterial sytems differ with respect to their protein structures and the required tRNA identity elements, suggesting a unique evolutionary divergence. In this study, we present a comparison between the crystal structures of the eubacterial Escherichia coli and the human tRNA(Gly) acceptor stem microhelices and their surrounding hydration patterns.
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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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20
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Förster C, Mankowska M, Fürste J, Perbandt M, Betzel C, Erdmann V. Crystal structure of a human tRNAGly microhelix at 1.2Å resolution. Biochem Biophys Res Commun 2008; 368:996-1001. [DOI: 10.1016/j.bbrc.2008.01.175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Accepted: 01/28/2008] [Indexed: 10/22/2022]
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21
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Papsai P, Snygg ÅS, Aldag J, Elmroth SKC. Platination of full length tRNAAla and truncated versions of the acceptor stem and anticodon loop. Dalton Trans 2008:5225-34. [DOI: 10.1039/b719542g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Förster C, Szkaradkiewicz K, Perbandt M, Brauer ABE, Borowski T, Fürste JP, Betzel C, Erdmann VA. Human tRNA(Gly) acceptor-stem microhelix: crystallization and preliminary X-ray diffraction analysis at 1.2 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:858-61. [PMID: 17909289 PMCID: PMC2339723 DOI: 10.1107/s1744309107041528] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Accepted: 08/23/2007] [Indexed: 11/10/2022]
Abstract
The major dissimilarities between the eukaryotic/archaebacterial-type and eubacterial-type glycyl-tRNA synthetase systems (GlyRS; class II aminoacyl-tRNA synthetases) represent an intriguing example of evolutionarily divergent solutions to similar biological functions. The differences in the identity elements of the respective tRNA(Gly) systems are located within the acceptor stem and include the discriminator base U73. In the present work, the human tRNA(Gly) acceptor-stem microhelix was crystallized in an attempt to analyze the structural features that govern the correct recognition of tRNA(Gly) by the eukaryotic/archaebacterial-type glycyl-tRNA synthetase. The crystals of the human tRNA(Gly) acceptor-stem helix belong to the monoclinic space group C2, with unit-cell parameters a = 37.12, b = 37.49, c = 30.38 A, alpha = gamma = 90, beta = 113.02 degrees, and contain one molecule per asymmetric unit. A high-resolution data set was acquired using synchrotron radiation and the data were processed to 1.2 A resolution.
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Affiliation(s)
- Charlotte Förster
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Karol Szkaradkiewicz
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Markus Perbandt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, c/o DESY, Notkestrasse 85, Building 22a, 22603 Hamburg, Germany
| | - Arnd B. E. Brauer
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Tordis Borowski
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Jens P. Fürste
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg, c/o DESY, Notkestrasse 85, Building 22a, 22603 Hamburg, Germany
| | - Volker A. Erdmann
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
- Correspondence e-mail:
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23
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Korostelev A, Noller HF. The ribosome in focus: new structures bring new insights. Trends Biochem Sci 2007; 32:434-41. [PMID: 17764954 DOI: 10.1016/j.tibs.2007.08.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Revised: 07/02/2007] [Accepted: 08/02/2007] [Indexed: 01/19/2023]
Abstract
Recent all-atom crystal structures of 70S ribosome functional complexes provide a detailed description of how the ribosome interacts with its mRNA and tRNA substrates. The structures support the view that the fundamental steps of translation are based on RNA-RNA interactions, which in some cases underwent further refinement as a result of having recruited proteins. The structural basis of the discrimination of cognate tRNA, the high affinity for tRNA in the peptidyl-tRNA site, the structure of the peptidyl transferase catalytic center, the specificity of the exit site for deacylated tRNA and other functional properties of the ribosome are now explained, confirmed or visualized for the first time in complexes containing full-length tRNAs and defined mRNAs. Clues to the structural dynamics of translation are suggested by conformational changes that occur in both tRNA and the ribosome upon complex formation.
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Affiliation(s)
- Andrei Korostelev
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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24
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Xu D, Landon T, Greenbaum NL, Fenley MO. The electrostatic characteristics of G.U wobble base pairs. Nucleic Acids Res 2007; 35:3836-47. [PMID: 17526525 PMCID: PMC1920249 DOI: 10.1093/nar/gkm274] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
G.U wobble base pairs are the most common and highly conserved non-Watson-Crick base pairs in RNA. Previous surface maps imply uniformly negative electrostatic potential at the major groove of G.U wobble base pairs embedded in RNA helices, suitable for entrapment of cationic ligands. In this work, we have used a Poisson-Boltzmann approach to gain a more detailed and accurate characterization of the electrostatic profile. We found that the major groove edge of an isolated G.U wobble displays distinctly enhanced negativity compared with standard GC or AU base pairs; however, in the context of different helical motifs, the electrostatic pattern varies. G.U wobbles with distinct widening have similar major groove electrostatic potentials to their canonical counterparts, whereas those with minimal widening exhibit significantly enhanced electronegativity, ranging from 0.8 to 2.5 kT/e, depending upon structural features. We propose that the negativity at the major groove of G.U wobble base pairs is determined by the combined effect of the base atoms and the sugar-phosphate backbone, which is impacted by stacking pattern and groove width as a result of base sequence. These findings are significant in that they provide predictive power with respect to which G.U sites in RNA are most likely to bind cationic ligands.
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Affiliation(s)
- Darui Xu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA, Department of Physics, Florida State University, Tallahassee, FL 32306-4390, USA and Institute of Molecular Biophysics Florida State University, Tallahassee, FL 32306-4390, USA
| | - Theresa Landon
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA, Department of Physics, Florida State University, Tallahassee, FL 32306-4390, USA and Institute of Molecular Biophysics Florida State University, Tallahassee, FL 32306-4390, USA
| | - Nancy L. Greenbaum
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA, Department of Physics, Florida State University, Tallahassee, FL 32306-4390, USA and Institute of Molecular Biophysics Florida State University, Tallahassee, FL 32306-4390, USA
- *To whom correspondence should be addressed. Marcia O. Fenley. +1-850-644-7961+1-850-644-7244 Correspondence may also be addressed to Nancy L. Greenbaum. +1-850-644-2005 +1-850-644-8281
| | - Marcia O. Fenley
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA, Department of Physics, Florida State University, Tallahassee, FL 32306-4390, USA and Institute of Molecular Biophysics Florida State University, Tallahassee, FL 32306-4390, USA
- *To whom correspondence should be addressed. Marcia O. Fenley. +1-850-644-7961+1-850-644-7244 Correspondence may also be addressed to Nancy L. Greenbaum. +1-850-644-2005 +1-850-644-8281
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25
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Förster C, Perbandt M, Brauer ABE, Brode S, Fürste JP, Betzel C, Erdmann VA. Crystallization and preliminary X-ray diffraction analysis of an Escherichia coli tRNA(Gly) acceptor-stem microhelix. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 63:46-8. [PMID: 17183173 PMCID: PMC2330105 DOI: 10.1107/s1744309106052870] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Accepted: 12/06/2006] [Indexed: 11/10/2022]
Abstract
The tRNA(Gly) and glycyl-tRNA synthetase (GlyRS) system is an evolutionary special case within the class II aminoacyl-tRNA synthetases because two divergent types of GlyRS exist: an archaebacterial/human type and an eubacterial type. The tRNA identity elements which determine the correct aminoacylation process are located in the aminoacyl domain of tRNA(Gly). To obtain further insight concerning structural investigation of the identity elements, the Escherichia coli seven-base-pair tRNA(Gly) acceptor-stem helix was crystallized. Data were collected to 2.0 A resolution using synchrotron radiation. Crystals belong to space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 35.35, c = 130.82 A, alpha = beta = 90, gamma = 120 degrees and two molecules in the asymmetric unit.
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Affiliation(s)
- Charlotte Förster
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Markus Perbandt
- Institute of Biochemistry and Food Chemistry, University of Hamburg, c/o DESY, Notkestrasse 85, Building 22a, 22603 Hamburg, Germany
| | - Arnd B. E. Brauer
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Svenja Brode
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Jens P. Fürste
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Christian Betzel
- Institute of Biochemistry and Food Chemistry, University of Hamburg, c/o DESY, Notkestrasse 85, Building 22a, 22603 Hamburg, Germany
| | - Volker A. Erdmann
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
- Correspondence e-mail:
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26
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Joli F, Bouchemal N, Laigle A, Hartmann B, Hantz E. Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides. Nucleic Acids Res 2006; 34:5740-51. [PMID: 17041234 PMCID: PMC1694020 DOI: 10.1093/nar/gkl617] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A preferential target of antisense oligonucleotides directed against human PGY/MDR1 mRNA is a hairpin containing a stem with a G*U wobble pair, capped by the purine-rich 5'r(GGGAUG)3' hexaloop. This hairpin is studied by multidimensional NMR and restrained molecular dynamics, with special emphasis on the conformation of south sugars and non-standard phosphate linkages evidenced in both the stem and the loop. The hairpin is found to be highly structured. The G*U wobble pair, a strong counterion binding site, displays structural particularities that are characteristic of this type of mismatch. The upper part of the stem undergoes distortions that optimize its interactions with the beginning of the loop. The loop adopts a new fold in which the single-stranded GGGA purine tract is structured in A-like conformation stacked in continuity of the stem and displays an extensive hydrogen bonding surface for recognition. The remarkable hairpin stability results from classical inter- and intra-strand interactions reinforced by numerous hydrogen bonds involving unusual backbone conformations and ribose 2'-hydroxyl groups. Overall, this work emphasizes numerous features that account for the well-ordered structure of the whole hairpin and highlights the loop properties that facilitate interaction with antisense oligonucleotides.
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Affiliation(s)
- Flore Joli
- Laboratoire BioMoCeTi, CNRS UMR 7033UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
- Laboratoire de Biochimie Théorique, CNRS UPR 9080Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
- To whom correspondence should be addressed. Tel: +33 158415167; Fax: +33 158415026;
| | - Nadia Bouchemal
- Laboratoire BioMoCeTi, CNRS UMR 7033UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
| | - Alain Laigle
- Laboratoire BioMoCeTi, CNRS UMR 7033UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
| | - Brigitte Hartmann
- Laboratoire de Biochimie Théorique, CNRS UPR 9080Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
- To whom correspondence should be addressed. Tel: +33 158415167; Fax: +33 158415026;
| | - Edith Hantz
- Laboratoire BioMoCeTi, CNRS UMR 7033UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
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27
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Korostelev A, Trakhanov S, Laurberg M, Noller HF. Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements. Cell 2006; 126:1065-77. [PMID: 16962654 DOI: 10.1016/j.cell.2006.08.032] [Citation(s) in RCA: 382] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 08/10/2006] [Accepted: 08/30/2006] [Indexed: 11/16/2022]
Abstract
Our understanding of the mechanism of protein synthesis has undergone rapid progress in recent years as a result of low-resolution X-ray and cryo-EM structures of ribosome functional complexes and high-resolution structures of ribosomal subunits and vacant ribosomes. Here, we present the crystal structure of the Thermus thermophilus 70S ribosome containing a model mRNA and two tRNAs at 3.7 A resolution. Many structural details of the interactions between the ribosome, tRNA, and mRNA in the P and E sites and the ways in which tRNA structure is distorted by its interactions with the ribosome are seen. Differences between the conformations of vacant and tRNA-bound 70S ribosomes suggest an induced fit of the ribosome structure in response to tRNA binding, including significant changes in the peptidyl-transferase catalytic site.
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Affiliation(s)
- Andrei Korostelev
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
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28
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McClain WH. Surprising contribution to aminoacylation and translation of non-Watson-Crick pairs in tRNA. Proc Natl Acad Sci U S A 2006; 103:4570-5. [PMID: 16537400 PMCID: PMC1450212 DOI: 10.1073/pnas.0600592103] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecules of transfer RNA (tRNA) typically contain four stems composed of Watson-Crick (W-C) base pairs and infrequent mispairs such as G-U and A-C. The latter mispairs are fundamental units of RNA secondary structure found in nearly every class of RNA and are nearly isomorphic to W-C pairs. Therefore, they often substitute for G-C or A-U base pairs. The mispairs also have unique chemical, structural, and dynamic conformational properties, which can only be partially mimicked by W-C base pairs. Here, I characterize the identities and tasks of six mutant G-U and A-C mispairs in Escherichia coli tRNA(Gly) using genetic and bioinformatic tools and show that mispairs are significantly more important for aminoacylation and translation than previously realized. Mispairs boost aminoacylation and translation primarily because they activate tRNA by means of their conformational flexibility. The statistical preservation of the six mutant mispair sites across tRNA(Gly) in many organisms points to a fundamental structure-function signature within tRNA(Gly) with possible analogous missions in other RNAs.
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Affiliation(s)
- William H McClain
- Department of Bacteriology, University of Wisconsin, 420 Henry Mall, Madison, WI 53706-1569, USA.
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29
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Mokdad A, Krasovska MV, Sponer J, Leontis NB. Structural and evolutionary classification of G/U wobble basepairs in the ribosome. Nucleic Acids Res 2006; 34:1326-41. [PMID: 16522645 PMCID: PMC1390688 DOI: 10.1093/nar/gkl025] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We present a comprehensive structural, evolutionary and molecular dynamics (MD) study of the G/U wobble basepairs in the ribosome based on high-resolution crystal structures, including the recent Escherichia coli structure. These basepairs are classified according to their tertiary interactions, and sequence conservation at their positions is determined. G/U basepairs participating in tertiary interactions are more conserved than those lacking any interactions. Specific interactions occurring in the G/U shallow groove pocket--like packing interactions (P-interactions) and some phosphate backbone interactions (phosphate-in-pocket interactions)--lead to higher G/U conservation than others. Two salient cases of unique phylogenetic compensation are discovered. First, a P-interaction is conserved through a series of compensatory mutations involving all four participating nucleotides to preserve or restore the G/U in the optimal orientation. Second, a G/U basepair forming a P-interaction and another one forming a phosphate-in-pocket interaction are replaced by GNRA loops that maintain similar tertiary contacts. MD simulations were carried out on eight P-interactions. The specific GU/CG signature of this interaction observed in structure and sequence analysis was rationalized, and can now be used for improving sequence alignments.
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MESH Headings
- Base Pairing
- Base Sequence
- Conserved Sequence
- Crystallography, X-Ray
- Evolution, Molecular
- Guanine/chemistry
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phosphates/chemistry
- RNA, Archaeal/chemistry
- RNA, Bacterial/chemistry
- RNA, Ribosomal/chemistry
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 5S/chemistry
- Ribosomes/chemistry
- Sequence Analysis, RNA
- Uracil/chemistry
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Affiliation(s)
- Ali Mokdad
- To whom correspondence should be addressed. Tel: +1 419 372 2332; Fax: +1 419 372 2024;
| | - Maryna V. Krasovska
- Institute of Biophysics, Academy of Sciences of the Czech RepublicKralovopolska 135, 612 65, Brno, Czech Republic
| | - Jiri Sponer
- Institute of Biophysics, Academy of Sciences of the Czech RepublicKralovopolska 135, 612 65, Brno, Czech Republic
| | - Neocles B. Leontis
- To whom correspondence should be addressed. Tel: +1 419 372 2332; Fax: +1 419 372 2024;
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30
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Lazar AN, Coleman AW, Terenzi S, Strazewski P. Observation of the formation of supported bilayers by amphiphilic peptidyl-RNA. Chem Commun (Camb) 2006:63-5. [PMID: 16353093 DOI: 10.1039/b509971b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Amphiphilic peptidyl-RNA conjugates, molecules that mimic natural peptidyl-transfer RNA, are capable of self-assembling on glass substrates as vesicles and supported bilayers.
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Affiliation(s)
- Adina N Lazar
- Assemblages Moléculaires d'Intérêt Biologique (UMR CNRS 5086), Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, F-69367 Lyon, France
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31
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Łobocka MB, Rose DJ, Plunkett G, Rusin M, Samojedny A, Lehnherr H, Yarmolinsky MB, Blattner FR. Genome of bacteriophage P1. J Bacteriol 2004; 186:7032-68. [PMID: 15489417 PMCID: PMC523184 DOI: 10.1128/jb.186.21.7032-7068.2004] [Citation(s) in RCA: 200] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2004] [Accepted: 07/09/2004] [Indexed: 11/20/2022] Open
Abstract
P1 is a bacteriophage of Escherichia coli and other enteric bacteria. It lysogenizes its hosts as a circular, low-copy-number plasmid. We have determined the complete nucleotide sequences of two strains of a P1 thermoinducible mutant, P1 c1-100. The P1 genome (93,601 bp) contains at least 117 genes, of which almost two-thirds had not been sequenced previously and 49 have no homologs in other organisms. Protein-coding genes occupy 92% of the genome and are organized in 45 operons, of which four are decisive for the choice between lysis and lysogeny. Four others ensure plasmid maintenance. The majority of the remaining 37 operons are involved in lytic development. Seventeen operons are transcribed from sigma(70) promoters directly controlled by the master phage repressor C1. Late operons are transcribed from promoters recognized by the E. coli RNA polymerase holoenzyme in the presence of the Lpa protein, the product of a C1-controlled P1 gene. Three species of P1-encoded tRNAs provide differential controls of translation, and a P1-encoded DNA methyltransferase with putative bifunctionality influences transcription, replication, and DNA packaging. The genome is particularly rich in Chi recombinogenic sites. The base content and distribution in P1 DNA indicate that replication of P1 from its plasmid origin had more impact on the base compositional asymmetries of the P1 genome than replication from the lytic origin of replication.
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Affiliation(s)
- Małgorzata B Łobocka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Ul. Pawinskiego 5A, 02-106 Warsaw, Poland.
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32
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Chandrasekhar K, Malathhi R. Non-Watson Crick base pairs might stabilize RNA structural motifs in ribozymes -- a comparative study of group-I intron structures. J Biosci 2004; 28:547-55. [PMID: 14517358 DOI: 10.1007/bf02703330] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In recent decades studies on RNA structure and function have gained significance due to discoveries on diversified functions of RNA. A common element for RNA secondary structure formed by series of non- Watson/Watson Crick base pairs, internal loops and pseudoknots have been the highlighting feature of recent structural determination of RNAs. The recent crystal structure of group-I introns has demonstrated that these might constitute RNA structural motifs in ribozymes, playing a crucial role in their enzymatic activity. To understand the functional significance of these non-canonical base pairs in catalytic RNA, we analysed the sequences of group-I introns from nuclear genes. The results suggest that they might form the building blocks of folded RNA motifs which are crucial to the catalytic activity of the ribozyme. The conservation of these, as observed from divergent organisms, argues for the presence of non-canonical base pairs as an important requisite for the structure and enzymatic property of ribozymes by enabling them to carry out functions such as replication, polymerase activity etc. in primordial conditions in the absence of proteins.
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Affiliation(s)
- K Chandrasekhar
- Department of Genetics, Dr ALM PG Institute of Basic Medical Sciences, University of Madras,Taramani Campus, Chennai 600 113, India
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33
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Ramos A, Lane AN, Hollingworth D, Fan TWM. Secondary structure and stability of the selenocysteine insertion sequences (SECIS) for human thioredoxin reductase and glutathione peroxidase. Nucleic Acids Res 2004; 32:1746-55. [PMID: 15026534 PMCID: PMC390329 DOI: 10.1093/nar/gkh331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have used high resolution NMR and thermodynamics to characterize the secondary structure and stability of the selenocysteine insertion sequences (SECIS) of human glutathione peroxidase (58 nt) and thioredoxin reductase (51 nt). These sequences are members of the two classes of SECIS recently identified with two distinct structures capable of directing selenocysteine incorporation into proteins in eukaryotes. UV melting experiments showed a single cooperative and reversible transition for each RNA, which indicates the presence of stable secondary structures. Despite their large size, the RNAs gave well resolved NMR spectra for the exchangeable protons. Using NOESY, the imino protons as well as the cytosine amino protons of all of the Watson-Crick base pairs were assigned. In addition, a number of non-canonical base pairs including the wobble G.U pairs were identified. The interbase-pair NOEs allowed definition of the hydrogen-bonded structure of the oligonucleotides, providing an experimental model of the secondary structure of these elements. The derived secondary structures are consistent with several features of the predicted models, but with some important differences, especially regarding the conserved sequence motifs.
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Affiliation(s)
- Andres Ramos
- Division of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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34
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Wodrich H, Guan T, Cingolani G, Von Seggern D, Nemerow G, Gerace L. Switch from capsid protein import to adenovirus assembly by cleavage of nuclear transport signals. EMBO J 2004; 22:6245-55. [PMID: 14633984 PMCID: PMC291855 DOI: 10.1093/emboj/cdg614] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Replication and assembly of adenovirus occurs in the nucleus of infected cells, requiring the nuclear import of all viral structural proteins. In this report we show that nuclear import of the major capsid protein, hexon, is mediated by protein VI, a structural protein located underneath the 12 vertices of the adenoviral capsid. Our data indicate that protein VI shuttles between the nucleus and the cytoplasm and that it links hexon to the nuclear import machinery via an importin alpha/beta-dependent mechanism. Key nuclear import and export signals of protein VI are located in a short C-terminal segment, which is proteolytically removed during virus maturation. The removal of these C-terminal transport signals appears to trigger a functional transition in protein VI, from a role in supporting hexon nuclear import to a structural role in virus assembly.
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Affiliation(s)
- Harald Wodrich
- Department of Cell Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
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35
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Seetharaman M, Williams C, Cramer CJ, Musier-Forsyth K. Effect of G-1 on histidine tRNA microhelix conformation. Nucleic Acids Res 2004; 31:7311-21. [PMID: 14654706 PMCID: PMC291870 DOI: 10.1093/nar/gkg930] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Histidine tRNAs (tRNA(His)) are unique in that they possess an extra 5'-base (G-1) not found in other tRNAs. Deletion of G-1 results in at least a 250-fold reduction in the rate of histidine charging in vitro. To better understand the role of the G-1 nucleotide in defining the structure of tRNA(His), and to correlate structure with cognate amino acid charging, NMR and molecular dynamics (MD) studies were performed on the wild-type and a DeltaG-1 mutant Escherichia coli histidine tRNA acceptor stem microhelix. Using NMR-derived distance restraints, global structural characteristics are described and interpreted to rationalize experimental observations with respect to aminoacylation activity. The quality of the NMR-derived solution conformations of the wild-type and DeltaG-1 histidine microhelices (micro helix(His)) is assessed using a variety of MD-based computational protocols. Most of the duplex regions of the acceptor stem and the UUCG tetraloop are well defined and effectively superimposable for the wild-type and DeltaG-1 mutant microhelix(His). Differences, however, are observed at the end of the helix and in the single-stranded CCCA-3' tail. The wild-type microhelix(His) structure is more well defined than the mutant and folds into a 'stacked fold-back' conformation. In contrast, we observe fraying of the first two base pairs and looping back of the single-stranded region in the DeltaG-1 mutant resulting in a much less well defined conformation. Thus the role of the extra G-1 base of the unique G-1:C73 base pair in tRNA(His) may be to prevent end-fraying and stabilize the stacked fold-back conformation of the CCCA-3' region.
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36
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Choi H, Otten S, Schneider J, McClain WH. Genetic perturbations of RNA reveal structure-based recognition in protein-RNA interaction. J Mol Biol 2002; 324:573-6. [PMID: 12460561 DOI: 10.1016/s0022-2836(02)01098-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Protein-RNA recognition is an essential foundation of cellular processes, yet much remains unknown about these important interactions. The recognition between aminoacyl-tRNA synthetases and their cognate tRNA substrates is highly specific and essential for cell viability, due to the necessity for accurate translation of the genetic code into protein sequences. We selected an active tRNA that is highly mutated in the recognition nucleotides of the acceptor stem region in the alanine system. The functional properties of this mutant and its secondary derivatives demonstrate that recognition cannot be reduced to isolated structural elements, but rather the amino acid acceptor stem is being recognized as a unit.
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MESH Headings
- Amino Acyl-tRNA Synthetases/chemistry
- Amino Acyl-tRNA Synthetases/genetics
- Amino Acyl-tRNA Synthetases/metabolism
- Bacterial Proteins/chemistry
- Bacterial Proteins/metabolism
- Escherichia coli/genetics
- Mutagenesis, Site-Directed
- Protein Binding
- Protein Conformation
- Protein Structure, Secondary
- RNA/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Structure-Activity Relationship
- Substrate Specificity
- Transformation, Bacterial
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Affiliation(s)
- Hyunsic Choi
- Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, E.B. Fred Hall, Madison, WI 53706-1567, USA
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37
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Kallick DA, Nagan MC, Beuning PJ, Kerimo S, Tessmer MR, Cramer CJ, Musier-Forsyth K. Discrimination of C1:G72 MicrohelixAla by AlaRS Is Based on Specific Atomic Groups Rather Than Conformational Effects: An NMR and MD Analysis. J Phys Chem B 2002. [DOI: 10.1021/jp020956r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Deborah A. Kallick
- Department of Medicinal Chemistry and Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455
| | - Maria C. Nagan
- Department of Medicinal Chemistry and Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455
| | - Penny J. Beuning
- Department of Medicinal Chemistry and Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455
| | - Stephanie Kerimo
- Department of Medicinal Chemistry and Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455
| | - Michael R. Tessmer
- Department of Medicinal Chemistry and Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455
| | - Christopher J. Cramer
- Department of Medicinal Chemistry and Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455
| | - Karin Musier-Forsyth
- Department of Medicinal Chemistry and Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455
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38
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Choi H, Otten S, McClain WH. Isolation of novel tRNA(Ala) mutants by library selection in a tRNA(Ala) knockout strain. Biochimie 2002; 84:705-11. [PMID: 12457558 DOI: 10.1016/s0300-9084(02)01407-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The relationship between tRNA structure and function has been widely investigated by site-directed mutagenesis. This method has been a very useful tool to reveal the critical bases in tRNAs that are important for recognition and aminoacylation, but has been limited by the large number of possible base combinations in tRNA molecules. We have devised a new method that uses tRNA knockout cells for selection of functional tRNAs from a mutant tRNA gene library to overcome this limitation. To explore the mechanism of tRNA(Ala) recognition, the bases of the acceptor-stem region were randomized and active mutants were selected in a tRNA(Ala) knockout strain. Mutants of tRNA(Ala) having diverse sequence combinations in the acceptor-stem region and a broad range of functional activity to support knockout cell growth were isolated. The mutant tRNAs selected by the method included molecules containing novel base substitutions as well as extensively altered base combinations that would not be readily generated by rationally designed site-directed mutagenesis. Our results emphasize the importance of the acceptor stem as a structural unit in which some nucleotides may carry more weight than others, but in summation every nucleotide contributes to the interaction with the enzyme.
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Affiliation(s)
- H Choi
- Department of Bacteriology, University of Wisconsin, WI Madison 53706-1567, USA
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39
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Beuning PJ, Nagan MC, Cramer CJ, Musier-Forsyth K, Gelpí JL, Bashford D. Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair. RNA (NEW YORK, N.Y.) 2002; 8:659-670. [PMID: 12022232 PMCID: PMC1370286 DOI: 10.1017/s1355838202020277] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Specific aminoacylation by aminoacyl-tRNA synthetases requires accurate recognition of cognate tRNA substrates. In the case of alanyl-tRNA synthetase (AlaRS), RNA duplexes that mimic the acceptor stem of the tRNA are efficient substrates for aminoacylation in vitro. It was previously shown that recognition by AlaRS is severely affected by a simple base pair transversion of the G2:C71 pair at the second position in the RNA helix. In this study, we determined the aminoacylation efficiencies of 50 variants of the tRNA(Ala) acceptor stem containing substitutions at the 2:71 position. We find that there is not a single functional group of the wild-type G2:C71 base pair that is critical for positive recognition. Rather, we observed that base-pair orientation plays an important role in recognition. In particular, pyrimidine2:purine71 combinations generally resulted in decreased aminoacylation efficiency compared to the corresponding purine:pyrimidine pair. Moreover, the activity of a pyrimidine:purine variant could be partially restored by the presence of a major groove amino group at position 71. In an attempt to understand this result further, dielectric continuum electrostatic calculations were carried out, in some cases with additional inclusion of van der Waals interaction energies, to determine interaction potentials of the wild-type duplexAla and seven 2:71 variants. This analysis revealed a positive correlation between major groove negative electrostatic potential in the vicinity of the 3:70 base pair and measured aminoacylation efficiency.
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MESH Headings
- Acylation
- Alanine-tRNA Ligase/metabolism
- Base Pairing
- Base Sequence
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Hydrogen Bonding
- Mutagenesis, Site-Directed
- Nucleic Acid Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer, Ala/chemistry
- RNA, Transfer, Ala/genetics
- RNA, Transfer, Ala/metabolism
- Static Electricity
- Thermodynamics
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Affiliation(s)
- Penny J Beuning
- Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis 55455-0431, USA
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40
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Sherer EC, Cramer CJ. Internal Loop−Helix Coupling in the Dynamics of the RNA Duplex (GC*C*AGUUCGCUGGC)2. J Phys Chem B 2002. [DOI: 10.1021/jp014494d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Edward C. Sherer
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431
| | - Christopher J. Cramer
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431
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41
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Gerdeman MS, Henkin TM, Hines JV. In vitro structure-function studies of the Bacillus subtilis tyrS mRNA antiterminator: evidence for factor-independent tRNA acceptor stem binding specificity. Nucleic Acids Res 2002; 30:1065-72. [PMID: 11842119 PMCID: PMC100339 DOI: 10.1093/nar/30.4.1065] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2001] [Revised: 12/04/2001] [Accepted: 12/04/2001] [Indexed: 11/14/2022] Open
Abstract
Expression of many aminoacyl-tRNA synthetase, amino acid biosynthesis and transport genes in Bacillus subtilis is controlled at the level of transcription termination using the T box system and requires the formation of specific secondary structures in the mRNA leader region. One structure functions as a transcriptional terminator, while an alternate form, the antiterminator, is necessary for transcription of the downstream coding regions. We have investigated the interaction of antiterminator model RNAs, based on the B.subtilis tyrS antiterminator with tRNA(Tyr) and tRNA acceptor stem models, using a gel shift assay. Binding of the antiterminator RNA to tRNA(Tyr) was dependent on complimentarity with the acceptor end of the tRNA or microhelix; affinity for the microhelix RNA was reduced relative to the tRNA. Alteration of a conserved position in the non-base pairing region of the bulge greatly reduced tRNA binding, consistent with in vivo studies. Therefore, it appears that some of the antiterminator-tRNA binding specificity is dependent on the structure of the antiterminator bulge alone and the complex it forms with tRNA in the absence of additional trans-acting factors. During the course of these studies we also discovered that the antiterminator can form a 'kissing' bulge complex, a unique RNA motif. The ease of formation of this RNA homodimer illustrates the propensity for the bulge of the antiterminator to bind RNA.
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MESH Headings
- 5' Untranslated Regions
- Bacillus subtilis/genetics
- Base Pairing
- Base Sequence
- Binding Sites
- Dimerization
- Electrophoretic Mobility Shift Assay
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Bacterial/physiology
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- RNA, Messenger/physiology
- RNA, Transfer, Tyr/chemistry
- RNA, Transfer, Tyr/metabolism
- Structure-Activity Relationship
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Affiliation(s)
- Melinda S Gerdeman
- Division of Medicinal Chemistry, College of Pharmacy and Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
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42
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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: 2.0] [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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43
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Schlosser A, Nawrot B, Grillenbeck N, Sprinzl M. Fluorescence-monitored conformational change on the 3'-end of tRNA upon aminoacylation. J Biomol Struct Dyn 2001; 19:285-91. [PMID: 11697733 DOI: 10.1080/07391102.2001.10506739] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Fluorescent tRNAs species with formycine in the 3'-terminal position (tRNA-CCF) were derived from Escherichia coli tRNA(Val). Thermus thermophilus tRNA(Aap) and Thermus thermophilus tRNA(Phe). The fluorescence of formycine was used to monitor the conformational changes at the 3'-terminus of tRNA caused by aminoacylation and hydrolysis of aminoacyl residue from aminoacyl-tRNAs. An increase of about 15% in the fluorescence intensity was observed after aminoacylation of the three tRNA-CCF. This change in fluorescence amplitude that is reversed by hydrolysis of the aminoacyl residue, does not depend on the structure of the amino acid or tRNA sequence. A local conformational change at the 3'-terminal formycine probably involving a partial destacking of the base moiety in the ACCF end takes place as a consequence of aminoacylation. A structural change at the 3'-terminus of tRNA induced by attachment and detachment of the acyl residue may be important in controlling the substrate/product relationship in reactions in which tRNA participates during protein biosynthesis.
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Affiliation(s)
- A Schlosser
- Laboratorium für Biochemie Universität Bayreuth, Germany
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44
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Lovato MA, Chihade JW, Schimmel P. Translocation within the acceptor helix of a major tRNA identity determinant. EMBO J 2001; 20:4846-53. [PMID: 11532948 PMCID: PMC125604 DOI: 10.1093/emboj/20.17.4846] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The genetic code is defined by the specific aminoacylations of tRNAs by aminoacyl-tRNA synthetases. Although the synthetases are widely conserved through evolution, aminoacylation of a given tRNA is often system specific-a synthetase from one source will not acylate its cognate tRNA from another. This system specificity is due commonly to variations in the sequence of a critical tRNA identity element. In bacteria and the cytoplasm of eukaryotes, an acceptor stem G3:U70 base pair marks a tRNA for aminoacylation with alanine. In contrast, Drosophila melanogaster (Dm) mitochondrial (mt) tRNA(Ala) has a G2:U71 but not a G3:U70 pair. Here we show that this translocated G:U and the adjacent G3:C70 are major determinants for recognition by Dm mt alanyl-tRNA synthetase (AlaRS). Additionally, G:U at the 3:70 position serves as an anti-determinant for Dm mt AlaRS. Consequently, the mitochondrial enzyme cannot charge cytoplasmic tRNA(Ala). All insect mitochondrial AlaRSs appear to have split apart recognition of mitochondrial from cytoplasmic tRNA(Ala) by translocation of G:U. This split may be essential for preventing introduction of ambiguous states into the genetic code.
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Affiliation(s)
| | - Joseph W. Chihade
- Departments of Molecular Biology and Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
Present address: Department of Chemistry, Williams College, Williamstown, MA 01267, USA Corresponding author e-mail:
| | - Paul Schimmel
- Departments of Molecular Biology and Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
Present address: Department of Chemistry, Williams College, Williamstown, MA 01267, USA Corresponding author e-mail:
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45
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Zuleeg T, Hartmann RK, Kreutzer R, Limmer S. NMR spectroscopic evidence for Mn(2+)(Mg(2+)) binding to a precursor-tRNA microhelix near the potential RNase P cleavage site. J Mol Biol 2001; 305:181-9. [PMID: 11124898 DOI: 10.1006/jmbi.2000.4299] [Citation(s) in RCA: 19] [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
The binding of Mg(2+)/Mn(2+) to acceptor stem microhelices as minimal models for precursor-tRNA(Gly) is demonstrated by NMR spectroscopy. From the evaluation of COSY and NOESY spectra, binding sites for Mg(2+)/Mn(2+) can be inferred. In particular, one binding site exists near the ribose moiety of nucleotide -1 at the position of cleavage by RNase P. From comparison with a variant possessing a deoxynucleotide at this position, it is concluded that the 2'-OH group of this nucleotide is indispensable for coordinating the divalent metal ion. Hence, this catalytically important metal ion is "pre-bound" to the precursor-tRNA before complexation with RNase P.
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Affiliation(s)
- T Zuleeg
- Laboratorium für Biochemie, der Universität Bayreuth, Universitätsstr 30, Bayreuth, D-95440, Germany
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46
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Varani G, McClain WH. The G x U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems. EMBO Rep 2000; 1:18-23. [PMID: 11256617 PMCID: PMC1083677 DOI: 10.1093/embo-reports/kvd001] [Citation(s) in RCA: 328] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The G x U wobble base pair is a fundamental unit of RNA secondary structure that is present in nearly every class of RNA from organisms of all three phylogenetic domains. It has comparable thermodynamic stability to Watson-Crick base pairs and is nearly isomorphic to them. Therefore, it often substitutes for G x C or A x U base pairs. The G x U wobble base pair also has unique chemical, structural, dynamic and ligand-binding properties, which can only be partially mimicked by Watson-Crick base pairs or other mispairs. These features mark sites containing G x U pairs for recognition by proteins and other RNAs and allow the wobble pair to play essential functional roles in a remarkably wide range of biological processes.
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Affiliation(s)
- G Varani
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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47
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Nagan MC, Beuning P, Musier-Forsyth K, Cramer CJ. Importance of discriminator base stacking interactions: molecular dynamics analysis of A73 microhelix(Ala) variants. Nucleic Acids Res 2000; 28:2527-34. [PMID: 10871402 PMCID: PMC102696 DOI: 10.1093/nar/28.13.2527] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transfer of alanine from Escherichia coli alanyl-tRNA synthetase (AlaRS) to RNA minihelices that mimic the amino acid acceptor stem of tRNA(Ala) has been shown, by analysis of variant minihelix aminoacylation activities, to involve a transition state sensitive to changes in the 'discriminator' base at position 73. Solution NMR has indicated that this single-stranded nucleotide is predominantly stacked onto G1 of the first base pair of the alanine acceptor stem helix. We report the activity of a new variant with the adenine at position 73 substituted by its non-polar isostere 4-methylindole (M). Despite lacking N7, this analog is well tolerated by AlaRS. Molecular dynamics (MD) simulations show that the M substitution improves position 73 base stacking over G1, as measured by a stacking lifetime analysis. Additional MD simulations of wild-type microhelix(Ala) and six variants reveal a positive correlation between N73 base stacking propensity over G1 and aminoacylation activity. For the two DeltaN7 variants simulated we found that the propensity to stack over G1 was similar to the analogous variants that contain N7 and we conclude that the decrease in aminoacylation efficiency observed upon deletion of N7 is likely due to loss of a direct stabilizing interaction with the synthetase.
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Affiliation(s)
- M C Nagan
- Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis 55455-0431, USA
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48
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Abstract
Computer simulation methods are increasingly being used to study possible conformations and dynamics of structural motifs in RNA. Recent results of molecular dynamics simulations and continum solvent studies of RNA structures and RNA-ligand complexes show promising agreement with experimental data. Combined with the ongoing progress in the experimental characterization of RNA structure and thermodynamics, these computational approaches can help to better understand the mechanism of RNA structure formation and the binding of ligands.
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Affiliation(s)
- M Zacharias
- AG Theoretische Biophysik, Institut für Molekulare Biotechnologie, Jena, D-07745, Germany.
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49
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Abstract
The aminoacyl-tRNA synthetases are an ancient group of enzymes that catalyze the covalent attachment of an amino acid to its cognate transfer RNA. The question of specificity, that is, how each synthetase selects the correct individual or isoacceptor set of tRNAs for each amino acid, has been referred to as the second genetic code. A wealth of structural, biochemical, and genetic data on this subject has accumulated over the past 40 years. Although there are now crystal structures of sixteen of the twenty synthetases from various species, there are only a few high resolution structures of synthetases complexed with cognate tRNAs. Here we review briefly the structural information available for synthetases, and focus on the structural features of tRNA that may be used for recognition. Finally, we explore in detail the insights into specific recognition gained from classical and atomic group mutagenesis experiments performed with tRNAs, tRNA fragments, and small RNAs mimicking portions of tRNAs.
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Affiliation(s)
- P J Beuning
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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50
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Zuleeg T, Vogtherr M, Schübel H, Limmer S. The C-A mismatch base pair and the single-strand terminus in the E. coli initiator tRNA(fMet) acceptor stem adopt unusual conformations. FEBS Lett 2000; 472:247-53. [PMID: 10788620 DOI: 10.1016/s0014-5793(00)01459-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Acceptor stem variants of tRNA(fMet) (Escherichia coli) have been characterized by nuclear magnetic resonance. The wild type contains a C1-A72 mismatch pair which is crucial for its biological function. For comparison, the mismatch was replaced by regular pairs U1-A72 and C1-G72. Further variants contain an altered discriminator base, G73, or a G1-C72/U73 combination. The stems of variants U1-A72/A73 and C1-G72/A73 have A-RNA geometry, which extends essentially to the single-strand terminus. C1-A72/G73 variant and wild type are structurally almost identical. C1 and A72 adopt peculiar conformations with C1 being largely destacked with respect to G2, while A73 stacks upon C1. The unique arrangement of the mismatch causes a distinctly different orientation of the single-strand terminus compared to variants with regular 1-72 base pairs, and to formyltransferase-complexed tRNA(fMet).
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Affiliation(s)
- T Zuleeg
- Laboratorium für Biochemie, Universität Bayreuth, Universitätsstrasse 30, D-95440, Bayreuth, Germany
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