201
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Xiao M, Wang Y. L27-tRNA interaction revealed by mutagenesis and pH titration. Biophys Chem 2012; 167:8-15. [PMID: 22634088 DOI: 10.1016/j.bpc.2012.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 04/23/2012] [Accepted: 04/27/2012] [Indexed: 11/18/2022]
Abstract
The movement of peptidyl tRNA into the P-site after ribosome translocation reduces the ribosome dynamics in the post-translocation complex, which "locks" the ribosome to less conformational fluctuations. Here, we used single molecule FRET method to reveal that ribosomes bearing L27 with N-terminal truncations are less competent to "lock" the tRNA fluctuations after translocation. We found that: (1) truncation of the first three N-terminal residues of L27 increases peptidyl tRNA fluctuation; and (2) increasing the solution pH increases peptidyl tRNA fluctuation in WT and some of the ribosome mutants. We propose that one role of L27 at the catalytic center is to stabilize peptidyl tRNA in the post-translocation complex.
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Affiliation(s)
- Ming Xiao
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Rd, Houston, TX 77214, USA
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202
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Polikanov YS, Blaha GM, Steitz TA. How hibernation factors RMF, HPF, and YfiA turn off protein synthesis. Science 2012; 336:915-8. [PMID: 22605777 DOI: 10.1126/science.1218538] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Eubacteria inactivate their ribosomes as 100S dimers or 70S monomers upon entry into stationary phase. In Escherichia coli, 100S dimer formation is mediated by ribosome modulation factor (RMF) and hibernation promoting factor (HPF), or alternatively, the YfiA protein inactivates ribosomes as 70S monomers. Here, we present high-resolution crystal structures of the Thermus thermophilus 70S ribosome in complex with each of these stationary-phase factors. The binding site of RMF overlaps with that of the messenger RNA (mRNA) Shine-Dalgarno sequence, which prevents the interaction between the mRNA and the 16S ribosomal RNA. The nearly identical binding sites of HPF and YfiA overlap with those of the mRNA, transfer RNA, and initiation factors, which prevents translation initiation. The binding of RMF and HPF, but not YfiA, to the ribosome induces a conformational change of the 30S head domain that promotes 100S dimer formation.
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Affiliation(s)
- Yury S Polikanov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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203
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Wilson DN, Doudna Cate JH. The structure and function of the eukaryotic ribosome. Cold Spring Harb Perspect Biol 2012; 4:4/5/a011536. [PMID: 22550233 DOI: 10.1101/cshperspect.a011536] [Citation(s) in RCA: 215] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Structures of the bacterial ribosome have provided a framework for understanding universal mechanisms of protein synthesis. However, the eukaryotic ribosome is much larger than it is in bacteria, and its activity is fundamentally different in many key ways. Recent cryo-electron microscopy reconstructions and X-ray crystal structures of eukaryotic ribosomes and ribosomal subunits now provide an unprecedented opportunity to explore mechanisms of eukaryotic translation and its regulation in atomic detail. This review describes the X-ray crystal structures of the Tetrahymena thermophila 40S and 60S subunits and the Saccharomyces cerevisiae 80S ribosome, as well as cryo-electron microscopy reconstructions of translating yeast and plant 80S ribosomes. Mechanistic questions about translation in eukaryotes that will require additional structural insights to be resolved are also presented.
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204
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Klinge S, Voigts-Hoffmann F, Leibundgut M, Ban N. Atomic structures of the eukaryotic ribosome. Trends Biochem Sci 2012; 37:189-98. [DOI: 10.1016/j.tibs.2012.02.007] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 02/10/2012] [Accepted: 02/16/2012] [Indexed: 12/20/2022]
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205
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Monajemi H, Omar NYM, Daud MN, Zain SM, Abdullah WATW. The role of initiator tRNAimet in fidelity of initiation of protein synthesis. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2012; 30:726-39. [PMID: 21902474 DOI: 10.1080/15257770.2011.605780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The proper arrangement of amino acids in a protein determines its proper function, which is vital for the cellular metabolism. This indicates that the process of peptide bond formation requires high fidelity. One of the most important processes for this fidelity is kinetic proofreading. As biochemical experiments suggest that kinetic proofreading plays a major role in ensuring the fidelity of protein synthesis, it is not certain whether or not a misacylated tRNA would be corrected by kinetic proofreading during the peptide bond formation. Using 2-layered ONIOM (QM/MM) computational calculations, we studied the behavior of misacylated tRNAs and compared the results with these for cognate aminoacyl-tRNAs during the process of peptide bond formation to investigate the effect of nonnative amino acids on tRNAs. The difference between the behavior of initiator tRNA(i) (met) compared to the one for the elongator tRNAs indicates that only the initiator tRNA(i) (met) specifies the amino acid side chain.
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Affiliation(s)
- Hadieh Monajemi
- Department of Physics, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
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206
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Koc EC, Koc H. Regulation of mammalian mitochondrial translation by post-translational modifications. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:1055-66. [PMID: 22480953 DOI: 10.1016/j.bbagrm.2012.03.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 01/24/2012] [Accepted: 03/16/2012] [Indexed: 11/29/2022]
Abstract
Mitochondria are responsible for the production of over 90% of the energy in eukaryotes through oxidative phosphorylation performed by electron transfer and ATP synthase complexes. Mitochondrial translation machinery is responsible for the synthesis of 13 essential proteins of these complexes encoded by the mitochondrial genome. Emerging data suggest that acetyl-CoA, NAD(+), and ATP are involved in regulation of this machinery through post-translational modifications of its protein components. Recent high-throughput proteomics analyses and mapping studies have provided further evidence for phosphorylation and acetylation of ribosomal proteins and translation factors. Here, we will review our current knowledge related to these modifications and their possible role(s) in the regulation of mitochondrial protein synthesis using the homology between mitochondrial and bacterial translation machineries. However, we have yet to determine the effects of phosphorylation and acetylation of translation components in mammalian mitochondrial biogenesis. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Affiliation(s)
- Emine C Koc
- Department of Biochemistry and Microbiology, Marshall University School of Medicine, Huntington, WV 25755, USA.
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207
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Acosta-Silva C, Bertran J, Branchadell V, Oliva A. Quantum-Mechanical Study on the Mechanism of Peptide Bond Formation in the Ribosome. J Am Chem Soc 2012; 134:5817-31. [DOI: 10.1021/ja209558d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Carles Acosta-Silva
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Joan Bertran
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Vicenç Branchadell
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Antoni Oliva
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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208
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A new understanding of the decoding principle on the ribosome. Nature 2012; 484:256-9. [PMID: 22437501 DOI: 10.1038/nature10913] [Citation(s) in RCA: 257] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 02/01/2012] [Indexed: 11/09/2022]
Abstract
During protein synthesis, the ribosome accurately selects transfer RNAs (tRNAs) in accordance with the messenger RNA (mRNA) triplet in the decoding centre. tRNA selection is initiated by elongation factor Tu, which delivers tRNA to the aminoacyl tRNA-binding site (A site) and hydrolyses GTP upon establishing codon-anticodon interactions in the decoding centre. At the following proofreading step the ribosome re-examines the tRNA and rejects it if it does not match the A codon. It was suggested that universally conserved G530, A1492 and A1493 of 16S ribosomal RNA, critical for tRNA binding in the A site, actively monitor cognate tRNA, and that recognition of the correct codon-anticodon duplex induces an overall ribosome conformational change (domain closure). Here we propose an integrated mechanism for decoding based on six X-ray structures of the 70S ribosome determined at 3.1-3.4 Å resolution, modelling cognate or near-cognate states of the decoding centre at the proofreading step. We show that the 30S subunit undergoes an identical domain closure upon binding of either cognate or near-cognate tRNA. This conformational change of the 30S subunit forms a decoding centre that constrains the mRNA in such a way that the first two nucleotides of the A codon are limited to form Watson-Crick base pairs. When U·G and G·U mismatches, generally considered to form wobble base pairs, are at the first or second codon-anticodon position, the decoding centre forces this pair to adopt the geometry close to that of a canonical C·G pair. This by itself, or with distortions in the codon-anticodon mini-helix and the anticodon loop, causes the near-cognate tRNA to dissociate from the ribosome.
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209
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Harish A, Caetano-Anollés G. Ribosomal history reveals origins of modern protein synthesis. PLoS One 2012; 7:e32776. [PMID: 22427882 PMCID: PMC3299690 DOI: 10.1371/journal.pone.0032776] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Accepted: 01/30/2012] [Indexed: 02/06/2023] Open
Abstract
The origin and evolution of the ribosome is central to our understanding of the cellular world. Most hypotheses posit that the ribosome originated in the peptidyl transferase center of the large ribosomal subunit. However, these proposals do not link protein synthesis to RNA recognition and do not use a phylogenetic comparative framework to study ribosomal evolution. Here we infer evolution of the structural components of the ribosome. Phylogenetic methods widely used in morphometrics are applied directly to RNA structures of thousands of molecules and to a census of protein structures in hundreds of genomes. We find that components of the small subunit involved in ribosomal processivity evolved earlier than the catalytic peptidyl transferase center responsible for protein synthesis. Remarkably, subunit RNA and proteins coevolved, starting with interactions between the oldest proteins (S12 and S17) and the oldest substructure (the ribosomal ratchet) in the small subunit and ending with the rise of a modern multi-subunit ribosome. Ancestral ribonucleoprotein components show similarities to in vitro evolved RNA replicase ribozymes and protein structures in extant replication machinery. Our study therefore provides important clues about the chicken-or-egg dilemma associated with the central dogma of molecular biology by showing that ribosomal history is driven by the gradual structural accretion of protein and RNA structures. Most importantly, results suggest that functionally important and conserved regions of the ribosome were recruited and could be relics of an ancient ribonucleoprotein world.
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Affiliation(s)
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana-Champaign, Illinois, United States of America
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210
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Agmon IC. A model for the role of isomerization in nascent peptide movement through the ribosomal tunnel. FASEB J 2012; 26:2277-82. [DOI: 10.1096/fj.11-197657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ilana C. Agmon
- Institute for Advanced Studies in Theoretical ChemistrySchulich Faculty of Chemistry, TechnionIsrael Institute of TechnologyHaifaIsrael
- Fritz Haber Research Center for Molecular DynamicsHebrew UniversityJerusalemIsrael
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211
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Pech M, Nierhaus KH. The thorny way to the mechanism of ribosomal peptide-bond formation. Chembiochem 2012; 13:189-92. [PMID: 22213275 DOI: 10.1002/cbic.201100660] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Markus Pech
- Department, AG Ribosomen, Abteilung Vingron, Max-Planck-Insitut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, Germany
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212
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Bulkley D, Johnson F, Steitz TA. The antibiotic thermorubin inhibits protein synthesis by binding to inter-subunit bridge B2a of the ribosome. J Mol Biol 2012; 416:571-8. [PMID: 22240456 DOI: 10.1016/j.jmb.2011.12.055] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 12/13/2011] [Accepted: 12/27/2011] [Indexed: 10/14/2022]
Abstract
Thermorubin is a small-molecule inhibitor of bacterial protein synthesis, but relatively little is known about the molecular mechanism by which it blocks translation. The structure of the complex between thermorubin and the 70S ribosome from Thermus thermophilus reported here shows that thermorubin interacts with the ribosome in a way that is distinct from any other known class of ribosome inhibitor. Though it is structurally similar to tetracycline, it binds to the ribosome at an entirely different location-the interface between the small and large subunits that is formed by inter-subunit bridge B2a. This region of the ribosome is known to play a role in the initiation of translation, and thus, the binding site we observe is consistent with evidence suggesting that thermorubin inhibits the initiation stage of protein synthesis. The binding of thermorubin induces a rearrangement of two bases on helix 69 of the 23S rRNA, and presumably, this rearrangement blocks the binding of an A-site tRNA, thereby inhibiting peptide bond formation. Due in part to its low solubility in aqueous media, thermorubin has not been used clinically, although it is a potent antibacterial agent with low toxicity (Therapeutic Index>200). The interactions between thermorubin and the ribosome, as well as its adjacency to the observed binding sites of three other antibiotic classes, may enable the design of novel derivatives that share thermorubin's mode of action but possess improved pharmacodynamic properties.
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Affiliation(s)
- David Bulkley
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
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213
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Structure and dynamics of the mammalian ribosomal pretranslocation complex. Mol Cell 2011; 44:214-24. [PMID: 22017870 DOI: 10.1016/j.molcel.2011.07.040] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 06/06/2011] [Accepted: 07/24/2011] [Indexed: 11/20/2022]
Abstract
Although the structural core of the ribosome is conserved in all kingdoms of life, eukaryotic ribosomes are significantly larger and more complex than their bacterial counterparts. The extent to which these differences influence the molecular mechanism of translation remains elusive. Multiparticle cryo-electron microscopy and single-molecule FRET investigations of the mammalian pretranslocation complex reveal spontaneous, large-scale conformational changes, including an intersubunit rotation of the ribosomal subunits. Through structurally related processes, tRNA substrates oscillate between classical and at least two distinct hybrid configurations facilitated by localized changes in their L-shaped fold. Hybrid states are favored within the mammalian complex. However, classical tRNA positions can be restored by tRNA binding to the E site or by the eukaryotic-specific antibiotic and translocation inhibitor cycloheximide. These findings reveal critical distinctions in the structural and energetic features of bacterial and mammalian ribosomes, providing a mechanistic basis for divergent translation regulation strategies and species-specific antibiotic action.
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214
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Wang L, Altman RB, Blanchard SC. Insights into the molecular determinants of EF-G catalyzed translocation. RNA (NEW YORK, N.Y.) 2011; 17:2189-2200. [PMID: 22033333 PMCID: PMC3222131 DOI: 10.1261/rna.029033.111] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 09/16/2011] [Indexed: 05/31/2023]
Abstract
Translocation, the directional movement of transfer RNA (tRNA) and messenger RNA (mRNA) substrates on the ribosome during protein synthesis, is regulated by dynamic processes intrinsic to the translating particle. Using single-molecule fluorescence resonance energy transfer (smFRET) imaging, in combination with site-directed mutagenesis of the ribosome and tRNA substrates, we show that peptidyl-tRNA within the aminoacyl site of the bacterial pretranslocation complex can adopt distinct hybrid tRNA configurations resulting from uncoupled motions of the 3'-CCA terminus and the tRNA body. As expected for an on-path translocation intermediate, the hybrid configuration where both the 3'-CCA end and body of peptidyl-tRNA have moved in the direction of translocation exhibits dramatically enhanced puromycin reactivity, an increase in the rate at which EF-G engages the ribosome, and accelerated rates of translocation. These findings provide compelling evidence that the substrate for EF-G catalyzed translocation is an intermediate wherein the bodies of both tRNA substrates adopt hybrid positions within the translating ribosome.
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Affiliation(s)
- Leyi Wang
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, USA
| | - Roger B. Altman
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, USA
| | - Scott C. Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, USA
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215
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Excited states of ribosome translocation revealed through integrative molecular modeling. Proc Natl Acad Sci U S A 2011; 108:18943-8. [PMID: 22080606 DOI: 10.1073/pnas.1108363108] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The dynamic nature of biomolecules leads to significant challenges when characterizing the structural properties associated with function. While X-ray crystallography and imaging techniques (such as cryo-electron microscopy) can reveal the structural details of stable molecular complexes, strategies must be developed to characterize configurations that exhibit only marginal stability (such as intermediates) or configurations that do not correspond to minima on the energy landscape (such as transition-state ensembles). Here, we present a methodology (MDfit) that utilizes molecular dynamics simulations to generate configurations of excited states that are consistent with available biophysical and biochemical measurements. To demonstrate the approach, we present a sequence of configurations that are suggested to be associated with transfer RNA (tRNA) movement through the ribosome (translocation). The models were constructed by combining information from X-ray crystallography, cryo-electron microscopy, and biochemical data. These models provide a structural framework for translocation that may be further investigated experimentally and theoretically to determine the precise energetic character of each configuration and the transition dynamics between them.
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216
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Abstract
The crystal structures of ribosomes that have been obtained since 2000 have transformed our understanding of protein synthesis. In addition to proving that RNA is responsible for catalyzing peptide bond formation, these structures have provided important insights into the mechanistic details of how the ribosome functions. This review emphasizes what has been learned about the mechanism of peptide bond formation, the antibiotics that inhibit ribosome function, and the fidelity of decoding.
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Affiliation(s)
- Peter B Moore
- Department of Molecular Biophysics, Yale University, New Haven, Connecticut 208114, USA.
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217
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Crystal structure of the hybrid state of ribosome in complex with the guanosine triphosphatase release factor 3. Proc Natl Acad Sci U S A 2011; 108:15798-803. [PMID: 21903932 DOI: 10.1073/pnas.1112185108] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein release factor 3 (RF3), a guanosine triphosphatase, binds to ribosome after release of the nascent peptide and promotes dissociation of the class I release factors during the termination of protein synthesis. Here we present the crystal structure of the 70S ribosome with RF3 in the presence of a nonhydrolyzable GTP analogue, guanosine 5'-β,γ-methylenetriphosphate (GDPCP), refined to 3.8 Å resolution. The structure shows that the subunits of the ribosome are rotated relative to each other compared to the canonical state, resulting in a P/E hybrid state for the transfer RNA. The substantial conformational rearrangements in the complex are described and suggest how RF3, by stabilizing the hybrid state of the ribosome, facilitates the dissociation of class I release factors.
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218
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Korostelev AA. Structural aspects of translation termination on the ribosome. RNA (NEW YORK, N.Y.) 2011; 17:1409-1421. [PMID: 21700725 PMCID: PMC3153966 DOI: 10.1261/rna.2733411] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Translation of genetic information encoded in messenger RNAs into polypeptide sequences is carried out by ribosomes in all organisms. When a full protein is synthesized, a stop codon positioned in the ribosomal A site signals termination of translation and protein release. Translation termination depends on class I release factors. Recently, atomic-resolution crystal structures were determined for bacterial 70S ribosome termination complexes bound with release factors RF1 or RF2. In combination with recent biochemical studies, the structures resolve long-standing questions about translation termination. They bring insights into the mechanisms of recognition of all three stop codons, peptidyl-tRNA hydrolysis, and coordination of stop-codon recognition with peptidyl-tRNA hydrolysis. In this review, the structural aspects of these mechanisms are discussed.
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Affiliation(s)
- Andrei A Korostelev
- RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
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219
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Steger J, Micura R. Functionalized polystyrene supports for solid-phase synthesis of glycyl-, alanyl-, and isoleucyl-RNA conjugates as hydrolysis-resistant mimics of peptidyl-tRNAs. Bioorg Med Chem 2011; 19:5167-74. [PMID: 21807524 PMCID: PMC3162138 DOI: 10.1016/j.bmc.2011.07.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 07/08/2011] [Accepted: 07/10/2011] [Indexed: 12/20/2022]
Abstract
RNA-peptide conjugates that mimic amino acid-charged tRNAs and peptidyl-tRNAs are of high importance for structural and functional investigations of ribosomal complexes. Here, we present the synthesis of glycyl-, alanyl-, and isoleucyladenosine modified solid supports that are eligible for the synthesis of stable 3′-aminoacyl- and 3′-peptidyl-tRNA termini with an amide instead of the natural ester linkage. The present work significantly expands the range of accessible peptidyl-tRNA mimics for ribosomal studies.
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Affiliation(s)
- Jessica Steger
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, University of Innsbruck, Innsbruck, Austria
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220
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The ribosomal tunnel as a functional environment for nascent polypeptide folding and translational stalling. Curr Opin Struct Biol 2011; 21:274-82. [PMID: 21316217 DOI: 10.1016/j.sbi.2011.01.007] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 12/16/2010] [Accepted: 01/19/2011] [Indexed: 12/14/2022]
Abstract
As the nascent polypeptide chain is being synthesized, it passes through a tunnel within the large ribosomal subunit and emerges at the solvent side where protein folding occurs. Despite the universality and conservation of dimensions of the ribosomal tunnel, a functional role for the ribosomal tunnel is only beginning to emerge: Rather than a passive conduit for the nascent chain, accumulating evidence indicates that the tunnel plays a more active role. In this article, we discuss recent structural insights into the role of the tunnel environment, and its implications for protein folding, co-translational targeting and translation regulation.
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221
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Leung EKY, Suslov N, Tuttle N, Sengupta R, Piccirilli JA. The Mechanism of Peptidyl Transfer Catalysis by the Ribosome. Annu Rev Biochem 2011; 80:527-55. [DOI: 10.1146/annurev-biochem-082108-165150] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Nikolai Suslov
- Department of Biochemistry and Molecular Biology, Chicago, Illinois 60637
| | - Nicole Tuttle
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637;
| | - Raghuvir Sengupta
- Department of Biochemistry, Stanford University, Stanford, California 94305
| | - Joseph Anthony Piccirilli
- Department of Biochemistry and Molecular Biology, Chicago, Illinois 60637
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637;
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222
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Ortiz-Meoz RF, Green R. Helix 69 is key for uniformity during substrate selection on the ribosome. J Biol Chem 2011; 286:25604-10. [PMID: 21622559 DOI: 10.1074/jbc.m111.256255] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Structural studies of ribosome complexes with bound tRNAs and release factors show considerable contacts between these factors and helix 69 (H69) of 23 S rRNA. Although biochemical and genetic studies have provided some general insights into the role of H69 in tRNA and RF selection, a detailed understanding of these contributions remains elusive. Here, we present a pre- steady-state kinetic analysis establishing that two distinct regions of H69 make critical contributions to substrate selection. The loop of H69 (A1913) forms contacts necessary for the efficient accommodation of a subset of natural tRNA species, whereas the base of the stem (G1922) is specifically critical for UGA codon recognition by the class 1 release factor RF2. These data define a broad and critical role for this centrally located intersubunit helix (H69) in accurate and efficient substrate recognition by the ribosome.
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Affiliation(s)
- Rodrigo F Ortiz-Meoz
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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223
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Ohshiro Y, Nakajima E, Goto Y, Fuse S, Takahashi T, Doi T, Suga H. Ribosomal Synthesis of Backbone-Macrocyclic Peptides Containing γ-Amino Acids. Chembiochem 2011; 12:1183-7. [DOI: 10.1002/cbic.201100104] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Indexed: 11/08/2022]
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224
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Scripture JB, Huber PW. Binding site for Xenopus ribosomal protein L5 and accompanying structural changes in 5S rRNA. Biochemistry 2011; 50:3827-39. [PMID: 21446704 DOI: 10.1021/bi200286e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure of the eukaryotic L5-5S rRNA complex was investigated in protection and interference experiments and is compared with the corresponding structure (L18-5S rRNA) in the Haloarcula marismortui 50S subunit. In close correspondence with the archaeal structure, the contact sites for the eukaryotic ribosomal protein are located primarily in helix III and loop C and secondarily in loop A and helix V. While the former is unique to L5, the latter is also a critical contact site for transcription factor IIIA (TFIIIA), accounting for the mutually exclusive binding of these two proteins to 5S RNA. The binding of L5 causes structural changes in loops B and C that expose nucleotides that contact the Xenopus L11 ortholog in H. marismortui. This induced change in the structure of the RNA reveals the origins of the cooperative binding to 5S rRNA that has been observed for the bacterial counterparts of these proteins. The native structure of helix IV and loop D antagonizes binding of L5, indicating that this region of the RNA is dynamic and also influenced by the protein. Examination of the crystal structures of Thermus thermophilus ribosomes in the pre- and post-translocation states identified changes in loop D and in the surrounding region of 23S rRNA that support the proposal that 5S rRNA acts to transmit information between different functional domains of the large subunit.
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Affiliation(s)
- J Benjamin Scripture
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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225
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Abstract
Metal ions are the salt in the soup of essentially every biological system. Also in the ribosome, the largest natural ribozyme that produces all proteins in every living cell, metal ions have been found contributing significantly to the highly dynamic and accurate process of translation. The ribosome is considered a molecular fossil of the 'RNA world' and it could be shown that the evolutionarily oldest parts of the particle, which build the catalytic center and surrounding domains, are densely packed with divalent metal ions. Nevertheless, metal ions do not seem to directly participate in ribosomal catalysis, their important roles in the ribosome, however, cannot be denied. It is probable that mono- and divalent metal ions primarily promote the functionally competent architecture of the ribosomal RNAs, but more direct roles in mRNA decoding and reading frame maintenance are likely. Decades of biochemical studies and the recent high resolution crystallographic structures of the ribosome strongly indicate that metal ions are involved in essentially every phase of the ribosomal elongation cycle, thus contributing significantly to the precise translation of the genetic code.
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Affiliation(s)
- Krista Trappl
- Innsbruck Biocenter, Division of Genomics and RNomics, Medical University Innsbruck, Fritz-Pregl-Strasse 3, 6020 Innsbruck, Austria.
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226
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Ramu H, Vázquez-Laslop N, Klepacki D, Dai Q, Piccirilli J, Micura R, Mankin AS. Nascent peptide in the ribosome exit tunnel affects functional properties of the A-site of the peptidyl transferase center. Mol Cell 2011; 41:321-30. [PMID: 21292164 DOI: 10.1016/j.molcel.2010.12.031] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 10/30/2010] [Accepted: 11/11/2010] [Indexed: 11/28/2022]
Abstract
The ability to monitor the nascent peptide structure and to respond functionally to specific nascent peptide sequences is a fundamental property of the ribosome. An extreme manifestation of such response is nascent peptide-dependent ribosome stalling, involved in the regulation of gene expression. The molecular mechanisms of programmed translation arrest are unclear. By analyzing ribosome stalling at the regulatory cistron of the antibiotic resistance gene ermA, we uncovered a carefully orchestrated cooperation between the ribosomal exit tunnel and the A-site of the peptidyl transferase center (PTC) in halting translation. The presence of an inducing antibiotic and a specific nascent peptide in the exit tunnel abrogate the ability of the PTC to catalyze peptide bond formation with a particular subset of amino acids. The extent of the conferred A-site selectivity is modulated by the C-terminal segment of the nascent peptide, where the third-from-last residue plays a critical role.
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Affiliation(s)
- Haripriya Ramu
- Center for Pharmaceutical Biotechnology, University of Illinois, Chicago, IL 60607, USA
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227
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Huang Y, Sprinzl M. Peptide Bond Formation on the Ribosome: The Role of the 2′-OH Group on the Terminal Adenosine of Peptidyl-tRNA and of the Length of Nascent Peptide Chain. Angew Chem Int Ed Engl 2011; 50:7287-9. [DOI: 10.1002/anie.201005245] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2010] [Revised: 09/27/2010] [Indexed: 11/09/2022]
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228
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Huang Y, Sprinzl M. Bildung der Peptidbindung im Ribosom: die Rolle der 2′-OH-Gruppe des terminalen Adenosins der Peptidyl-tRNA und der Länge der entstehenden Peptidkette. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201005245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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229
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Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation. Proc Natl Acad Sci U S A 2011; 108:4817-21. [PMID: 21383139 DOI: 10.1073/pnas.1101503108] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
mRNA-tRNA translocation is a central and highly regulated process during translational elongation. Along with the mRNA, tRNA moves through the ribosome in a stepwise fashion. Using cryoelectron microscopy on ribosomes with a P-loop mutation, we have identified novel structural intermediates likely to exist transiently during translocation. Our observations suggest a mechanism by which the rate of translocation can be regulated.
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230
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Krishnakumar KS, Goudedranche S, Bouchu D, Strazewski P. The Shortest Synthetic Route to Puromycin Analogues Using a Modified Robins Approach. J Org Chem 2011; 76:2253-6. [DOI: 10.1021/jo102178h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kollappillil S. Krishnakumar
- Laboratoire de Synthèse de Biomolécules (UMR 5246, ICBMS), Université Claude Bernard Lyon 1, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Sébastien Goudedranche
- Laboratoire de Synthèse de Biomolécules (UMR 5246, ICBMS), Université Claude Bernard Lyon 1, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Denis Bouchu
- Laboratoire de Synthèse de Biomolécules (UMR 5246, ICBMS), Université Claude Bernard Lyon 1, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Peter Strazewski
- Laboratoire de Synthèse de Biomolécules (UMR 5246, ICBMS), Université Claude Bernard Lyon 1, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France
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231
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Altuntop ME, Ly CT, Wang Y. Single-molecule study of ribosome hierarchic dynamics at the peptidyl transferase center. Biophys J 2011; 99:3002-9. [PMID: 21044598 DOI: 10.1016/j.bpj.2010.08.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 08/11/2010] [Accepted: 08/13/2010] [Indexed: 12/01/2022] Open
Abstract
During protein biosynthesis the ribosome moves along mRNA in steps of precisely three nucleotides. The mechanism for this ribosome motion remains elusive. Using a classification algorithm to sort single-molecule fluorescence resonance energy transfer data into subpopulations, we found that the ribosome dynamics detected at the peptidyl transferase center are highly inhomogeneous. The pretranslocation complex has at least four subpopulations that sample two hybrid states, whereas the posttranslocation complex is mainly static. We observed transitions among the ribosome subpopulations under various conditions, including 1), in the presence of EF-G; 2), spontaneously; 3), in different buffers, and 4), bound to antibiotics. Therefore, these subpopulations represent biologically active ribosomes. One key observation indicates that the Hy2 hybrid state only exists in a fluctuating ribosome subpopulation, which prompts us to propose that ribosome dynamics are hierarchically arranged. This proposal may have important implications for the regulation of cellular translation rates.
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Affiliation(s)
- Mediha Esra Altuntop
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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232
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O'Brien EP, Christodoulou J, Vendruscolo M, Dobson CM. New scenarios of protein folding can occur on the ribosome. J Am Chem Soc 2011; 133:513-26. [PMID: 21204555 DOI: 10.1021/ja107863z] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Identifying and understanding the differences between protein folding in bulk solution and in the cell is a crucial challenge facing biology. Using Langevin dynamics, we have simulated intact ribosomes containing five different nascent chains arrested at different stages of their synthesis such that each nascent chain can fold and unfold at or near the exit tunnel vestibule. We find that the native state is destabilized close to the ribosome surface due to an increase in unfolded state entropy and a decrease in native state entropy; the former arises because the unfolded ensemble tends to behave as an expanded random coil near the ribosome and a semicompact globule in bulk solution. In addition, the unfolded ensemble of the nascent chain adopts a highly anisotropic shape near the ribosome surface and the cooperativity of the folding-unfolding transition is decreased due to the appearance of partially folded structures that are not populated in bulk solution. The results show, in light of these effects, that with increasing nascent chain length folding rates increase in a linear manner and unfolding rates decrease, with larger and topologically more complex folds being the most highly perturbed by the ribosome. Analysis of folding trajectories, initiated by temperature quench, reveals the transition state ensemble is driven toward compaction and greater native-like structure by interactions with the ribosome surface and exit vestibule. Furthermore, the diversity of folding pathways decreases and the probability increases of initiating folding via the N-terminus on the ribosome. We show that all of these findings are equally applicable to the situation in which protein folding occurs during continuous (non-arrested) translation provided that the time scales of folding and unfolding are much faster than the time scale of monomer addition to the growing nascent chain, which results in a quasi-equilibrium process. These substantial ribosome-induced perturbations to almost all aspects of protein folding indicate that folding scenarios that are distinct from those of bulk solution can occur on the ribosome.
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Affiliation(s)
- Edward P O'Brien
- Department of Chemistry, Lensfield Road, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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233
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Activation of initiation factor 2 by ligands and mutations for rapid docking of ribosomal subunits. EMBO J 2010; 30:289-301. [PMID: 21151095 DOI: 10.1038/emboj.2010.328] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 11/17/2010] [Indexed: 11/08/2022] Open
Abstract
We previously identified mutations in the GTPase initiation factor 2 (IF2), located outside its tRNA-binding domain, compensating strongly (A-type) or weakly (B-type) for initiator tRNA formylation deficiency. We show here that rapid docking of 30S with 50S subunits in initiation of translation depends on switching 30S subunit-bound IF2 from its inactive to active form. Activation of wild-type IF2 requires GTP and formylated initiator tRNA (fMet-tRNA(i)). In contrast, extensive activation of A-type IF2 occurs with only GTP or with GDP and fMet-tRNA(i), implying a passive role for initiator tRNA as activator of IF2 in subunit docking. The theory of conditional switching of GTPases quantitatively accounts for all our experimental data. We find that GTP, GDP, fMet-tRNA(i) and A-type mutations multiplicatively increase the equilibrium ratio, K, between active and inactive forms of IF2 from a value of 4 × 10(-4) for wild-type apo-IF2 by factors of 300, 8, 80 and 20, respectively. Functional characterization of the A-type mutations provides keys to structural interpretation of conditional switching of IF2 and other multidomain GTPases.
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234
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Mikulík K, Bobek J, Ziková A, Smětáková M, Bezoušková S. Phosphorylation of ribosomal proteins influences subunit association and translation of poly (U) in Streptomyces coelicolor. MOLECULAR BIOSYSTEMS 2010; 7:817-23. [PMID: 21152561 DOI: 10.1039/c0mb00174k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The occurrence of phosphorylated proteins in ribosomes of Streptomyces coelicolor was investigated. Little is known about which biological functions these posttranslational modifications might fulfil. A protein kinase associated with ribosomes phosphorylated six ribosomal proteins of the small subunit (S3, S4, S12, S13, S14 and S18) and seven ribosomal proteins of the large subunit (L2, L3, L7/L12, L16, L17, L23 and L27). The ribosomal proteins were phosphorylated mainly on the Ser/Thr residues. Phosphorylation of the ribosomal proteins influences ribosomal subunits association. Ribosomes with phosphorylated proteins were used to examine poly (U) translation activity. Phosphorylation induced about 50% decrease in polyphenylalanine synthesis. After preincubation of ribosomes with alkaline phosphatase the activity of ribosomes was greatly restored. Small differences were observed between phosphorylated and unphosphorylated ribosomes in the kinetic parameters of the binding of Phe-tRNA to the A-site of poly (U) programmed ribosomes, suggesting that the initial binding of Phe-tRNA is not significantly affected by phosphorylation. On contrary, the rate of peptidyl transferase was about two-fold lower than that in unphosphorylated ribosomes. The data presented demonstrate that phosphorylation of ribosomal proteins affects critical steps of protein synthesis.
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Affiliation(s)
- Karel Mikulík
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 4, Videnská 1083, Czech Republic.
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235
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Márquez V, Fröhlich T, Armache JP, Sohmen D, Dönhöfer A, Mikolajka A, Berninghausen O, Thomm M, Beckmann R, Arnold GJ, Wilson DN. Proteomic characterization of archaeal ribosomes reveals the presence of novel archaeal-specific ribosomal proteins. J Mol Biol 2010; 405:1215-32. [PMID: 21134383 DOI: 10.1016/j.jmb.2010.11.055] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 11/19/2010] [Accepted: 11/27/2010] [Indexed: 10/18/2022]
Abstract
Protein synthesis occurs in macromolecular particles called ribosomes. All ribosomes are composed of RNA and proteins. While the protein composition of bacterial and eukaryotic ribosomes has been well-characterized, a systematic analysis of archaeal ribosomes has been lacking. Here we report the first comprehensive two-dimensional PAGE and mass spectrometry analysis of archaeal ribosomes isolated from the thermophilic Pyrobaculum aerophilum and the thermoacidophilic Sulfolobus acidocaldarius Crenarchaeota. Our analysis identified all 66 ribosomal proteins (r-proteins) of the P. aerophilum small and large subunits, as well as all but two (62 of 64; 97%) r-proteins of the S. acidocaldarius small and large subunits that are predicted genomically. Some r-proteins were identified with one or two lysine methylations and N-terminal acetylations. In addition, we identify three hypothetical proteins that appear to be bona fide r-proteins of the S. acidocaldarius large subunit. Dissociation of r-proteins from the S. acidocaldarius large subunit indicates that the novel r-proteins establish tighter interactions with the large subunit than some integral r-proteins. Furthermore, cryo electron microscopy reconstructions of the S. acidocaldarius and P. aerophilum 50S subunits allow for a tentative localization of the binding site of the novel r-proteins. This study illustrates not only the potential diversity of the archaeal ribosomes but also the necessity to experimentally analyze the archaeal ribosomes to ascertain their protein composition. The discovery of novel archaeal r-proteins and factors may be the first step to understanding how archaeal ribosomes cope with extreme environmental conditions.
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Affiliation(s)
- Viter Márquez
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Feodor Lynen Str. 25, 81377 Munich, Germany
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236
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Proteome evolution and the metabolic origins of translation and cellular life. J Mol Evol 2010; 72:14-33. [PMID: 21082171 DOI: 10.1007/s00239-010-9400-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 10/25/2010] [Indexed: 12/27/2022]
Abstract
The origin of life has puzzled molecular scientists for over half a century. Yet fundamental questions remain unanswered, including which came first, the metabolic machinery or the encoding nucleic acids. In this study we take a protein-centric view and explore the ancestral origins of proteins. Protein domain structures in proteomes are highly conserved and embody molecular functions and interactions that are needed for cellular and organismal processes. Here we use domain structure to study the evolution of molecular function in the protein world. Timelines describing the age and function of protein domains at fold, fold superfamily, and fold family levels of structural complexity were derived from a structural phylogenomic census in hundreds of fully sequenced genomes. These timelines unfold congruent hourglass patterns in rates of appearance of domain structures and functions, functional diversity, and hierarchical complexity, and revealed a gradual build up of protein repertoires associated with metabolism, translation and DNA, in that order. The most ancient domain architectures were hydrolase enzymes and the first translation domains had catalytic functions for the aminoacylation and the molecular switch-driven transport of RNA. Remarkably, the most ancient domains had metabolic roles, did not interact with RNA, and preceded the gradual build-up of translation. In fact, the first translation domains had also a metabolic origin and were only later followed by specialized translation machinery. Our results explain how the generation of structure in the protein world and the concurrent crystallization of translation and diversified cellular life created further opportunities for proteomic diversification.
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237
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Armache JP, Jarasch A, Anger AM, Villa E, Becker T, Bhushan S, Jossinet F, Habeck M, Dindar G, Franckenberg S, Marquez V, Mielke T, Thomm M, Berninghausen O, Beatrix B, Söding J, Westhof E, Wilson DN, Beckmann R. Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome. Proc Natl Acad Sci U S A 2010; 107:19754-9. [PMID: 20974910 PMCID: PMC2993421 DOI: 10.1073/pnas.1010005107] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Protein synthesis in all living organisms occurs on ribonucleoprotein particles, called ribosomes. Despite the universality of this process, eukaryotic ribosomes are significantly larger in size than their bacterial counterparts due in part to the presence of 80 r proteins rather than 54 in bacteria. Using cryoelectron microscopy reconstructions of a translating plant (Triticum aestivum) 80S ribosome at 5.5-Å resolution, together with a 6.1-Å map of a translating Saccharomyces cerevisiae 80S ribosome, we have localized and modeled 74/80 (92.5%) of the ribosomal proteins, encompassing 12 archaeal/eukaryote-specific small subunit proteins as well as the complete complement of the ribosomal proteins of the eukaryotic large subunit. Near-complete atomic models of the 80S ribosome provide insights into the structure, function, and evolution of the eukaryotic translational apparatus.
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Affiliation(s)
- Jean-Paul Armache
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Alexander Jarasch
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Andreas M. Anger
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Elizabeth Villa
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Thomas Becker
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Shashi Bhushan
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Fabrice Jossinet
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Michael Habeck
- Department of Empirical Inference, Max Planck Institute for Biological Cybernetics, Spemannstrasse 38, 72076 Tübingen, Germany
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Gülcin Dindar
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Sibylle Franckenberg
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Viter Marquez
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Thorsten Mielke
- UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
- Institut für Medizinische Physik und Biophysik, Charité, Ziegelstrasse 5-8, 10117 Berlin, Germany; and
| | - Michael Thomm
- Universität Regensburg, Lehrstuhl für Mikrobiologie, Universitätstrasse 31, 93053 Regensburg, Germany
| | - Otto Berninghausen
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Birgitta Beatrix
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Johannes Söding
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Eric Westhof
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Daniel N. Wilson
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Roland Beckmann
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
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238
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O'Brien EP, Hsu STD, Christodoulou J, Vendruscolo M, Dobson CM. Transient tertiary structure formation within the ribosome exit port. J Am Chem Soc 2010; 132:16928-37. [PMID: 21062068 DOI: 10.1021/ja106530y] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The exit tunnel of the ribosome is commonly considered to be sufficiently narrow that co-translational folding can begin only when specific segments of nascent chains are fully extruded from the tunnel. Here we show, on the basis of molecular simulations and comparison with experiment, that the long-range contacts essential for initiating protein folding can form within a nascent chain when it reaches the last 20 Å of the exit tunnel. We further show that, in this "exit port", a significant proportion of native and non-native tertiary structure can form without steric overlap with the ribosome itself, and provide a library of structural elements that our simulations predict can form in the exit tunnel and is amenable to experimental testing. Our results show that these elements of folded tertiary structure form only transiently and are at their midpoints of stability at the boundary region between the inside and the outside of the tunnel. These findings provide a framework for interpreting a range of recent experimental studies of ribosome nascent chain complexes and for understanding key aspects of the nature of co-translational folding.
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Affiliation(s)
- Edward P O'Brien
- Department of Chemistry, Lensfield Road, University of Cambridge, UK
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239
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Blanchard SC, Cooperman BS, Wilson DN. Probing translation with small-molecule inhibitors. ACTA ACUST UNITED AC 2010; 17:633-45. [PMID: 20609413 DOI: 10.1016/j.chembiol.2010.06.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 05/14/2010] [Accepted: 06/07/2010] [Indexed: 10/19/2022]
Abstract
The translational apparatus of the bacterial cell remains one of the principal targets of antibiotics for the clinical treatment of infection worldwide. Since the introduction of specific translation inhibitors into clinical practice in the late 1940s, intense efforts have been made to understand their precise mechanisms of action. Such research has often revealed significant and sometimes unexpected insights into many fundamental aspects of the translation mechanism. Central to progress in this area, high-resolution crystal structures of the bacterial ribosome identifying the sites of antibiotic binding are now available, which, together with recent developments in single-molecule and fast-kinetic approaches, provide an integrated view of the dynamic translation process. Assays employing these approaches and focusing on specific steps of the overall translation process are amenable for drug screening. Such assays, coupled with structural studies, have the potential not only to accelerate the discovery of novel and effective antimicrobial agents, but also to refine our understanding of the mechanisms of translation. Antibiotics often stabilize specific functional states of the ribosome and therefore allow distinct translation steps to be dissected in molecular detail.
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Affiliation(s)
- Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA
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240
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Ng CL, Lang K, Meenan NAG, Sharma A, Kelley AC, Kleanthous C, Ramakrishnan V. Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3. Nat Struct Mol Biol 2010; 17:1241-1246. [PMID: 20852642 PMCID: PMC3755339 DOI: 10.1038/nsmb.1896] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 07/26/2010] [Indexed: 11/08/2022]
Abstract
The toxin colicin E3 targets the 30S subunit of bacterial ribosomes and cleaves a phosphodiester bond in the decoding center. We present the crystal structure of the 70S ribosome in complex with the cytotoxic domain of colicin E3 (E3-rRNase). The structure reveals how the rRNase domain of colicin binds to the A site of the decoding center in the 70S ribosome and cleaves the 16S ribosomal RNA (rRNA) between A1493 and G1494. The cleavage mechanism involves the concerted action of conserved residues Glu62 and His58 of the cytotoxic domain of colicin E3. These residues activate the 16S rRNA for 2' OH-induced hydrolysis. Conformational changes observed for E3-rRNase, 16S rRNA and helix 69 of 23S rRNA suggest that a dynamic binding platform is required for colicin E3 binding and function.
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MESH Headings
- Amino Acid Sequence
- Catalysis
- Colicins/chemistry
- Colicins/metabolism
- Conserved Sequence
- Crystallography, X-Ray
- Escherichia coli/metabolism
- Macromolecular Substances
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Conformation
- Protein Structure, Tertiary
- RNA, Messenger/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/metabolism
- RNA, Transfer, Met/metabolism
- Ribosomes/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Structure-Activity Relationship
- Thermus thermophilus/metabolism
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Affiliation(s)
- C Leong Ng
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Kathrin Lang
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | | | - Amit Sharma
- Department of Biology (Area 10), University of York, York, UK
| | - Ann C Kelley
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | | | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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241
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Revisiting the structures of several antibiotics bound to the bacterial ribosome. Proc Natl Acad Sci U S A 2010; 107:17158-63. [PMID: 20876130 DOI: 10.1073/pnas.1008685107] [Citation(s) in RCA: 207] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The increasing prevalence of antibiotic-resistant pathogens reinforces the need for structures of antibiotic-ribosome complexes that are accurate enough to enable the rational design of novel ribosome-targeting therapeutics. Structures of many antibiotics in complex with both archaeal and eubacterial ribosomes have been determined, yet discrepancies between several of these models have raised the question of whether these differences arise from species-specific variations or from experimental problems. Our structure of chloramphenicol in complex with the 70S ribosome from Thermus thermophilus suggests a model for chloramphenicol bound to the large subunit of the bacterial ribosome that is radically different from the prevailing model. Further, our structures of the macrolide antibiotics erythromycin and azithromycin in complex with a bacterial ribosome are indistinguishable from those determined of complexes with the 50S subunit of Haloarcula marismortui, but differ significantly from the models that have been published for 50S subunit complexes of the eubacterium Deinococcus radiodurans. Our structure of the antibiotic telithromycin bound to the T. thermophilus ribosome reveals a lactone ring with a conformation similar to that observed in the H. marismortui and D. radiodurans complexes. However, the alkyl-aryl moiety is oriented differently in all three organisms, and the contacts observed with the T. thermophilus ribosome are consistent with biochemical studies performed on the Escherichia coli ribosome. Thus, our results support a mode of macrolide binding that is largely conserved across species, suggesting that the quality and interpretation of electron density, rather than species specificity, may be responsible for many of the discrepancies between the models.
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242
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Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action. Proc Natl Acad Sci U S A 2010; 107:17152-7. [PMID: 20876128 DOI: 10.1073/pnas.1007988107] [Citation(s) in RCA: 330] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Differences between the structures of bacterial, archaeal, and eukaryotic ribosomes account for the selective action of antibiotics. Even minor variations in the structure of ribosomes of different bacterial species may lead to idiosyncratic, species-specific interactions of the drugs with their targets. Although crystallographic structures of antibiotics bound to the peptidyl transferase center or the exit tunnel of archaeal (Haloarcula marismortui) and bacterial (Deinococcus radiodurans) large ribosomal subunits have been reported, it remains unclear whether the interactions of antibiotics with these ribosomes accurately reflect those with the ribosomes of pathogenic bacteria. Here we report X-ray crystal structures of the Escherichia coli ribosome in complexes with clinically important antibiotics of four major classes, including the macrolide erythromycin, the ketolide telithromycin, the lincosamide clindamycin, and a phenicol, chloramphenicol, at resolutions of ∼3.3 Å-3.4 Å. Binding modes of three of these antibiotics show important variations compared to the previously determined structures. Biochemical and structural evidence also indicates that interactions of telithromycin with the E. coli ribosome more closely resembles drug binding to ribosomes of bacterial pathogens. The present data further argue that the identity of nucleotides 752, 2609, and 2055 of 23S ribosomal RNA explain in part the spectrum and selectivity of antibiotic action.
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243
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Ramakrishnan V. Unraveling the structure of the ribosome (Nobel Lecture). Angew Chem Int Ed Engl 2010; 49:4355-80. [PMID: 20535836 DOI: 10.1002/anie.201001436] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- V Ramakrishnan
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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244
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Agirrezabala X, Frank J. From DNA to proteins via the ribosome: structural insights into the workings of the translation machinery. Hum Genomics 2010; 4:226-37. [PMID: 20511136 PMCID: PMC2976604 DOI: 10.1186/1479-7364-4-4-226] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Understanding protein synthesis in bacteria and humans is important for understanding the origin of many human diseases and devising treatments for them. Over the past decade, the field of structural biology has made significant advances in the visualisation of the molecular machinery involved in protein synthesis. It is now possible to discern, at least in outline, the way that interlocking ribosomal components and factors adapt their conformations throughout this process. The determination of structures in various functional contexts, along with the application of kinetic and fluorescent resonance energy transfer approaches to the problem, has given researchers the frame of reference for what remains as the greatest challenge: the complete dynamic portrait of protein synthesis in the cell.
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245
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Steger J, Graber D, Moroder H, Geiermann AS, Aigner M, Micura R. Efficient Access to Nonhydrolyzable Initiator tRNA Based on the Synthesis of 3′-Azido-3′-Deoxyadenosine RNA. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201003424] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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246
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Steger J, Graber D, Moroder H, Geiermann AS, Aigner M, Micura R. Efficient Access to Nonhydrolyzable Initiator tRNA Based on the Synthesis of 3′-Azido-3′-Deoxyadenosine RNA. Angew Chem Int Ed Engl 2010; 49:7470-2. [DOI: 10.1002/anie.201003424] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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247
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Kurland CG. The RNA dreamtime: modern cells feature proteins that might have supported a prebiotic polypeptide world but nothing indicates that RNA world ever was. Bioessays 2010; 32:866-71. [PMID: 20806270 DOI: 10.1002/bies.201000058] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Modern cells present no signs of a putative prebiotic RNA world. However, RNA coding is not a sine qua non for the accumulation of catalytic polypeptides. Thus, cellular proteins spontaneously fold into active structures that are resistant to proteolysis. The law of mass action suggests that binding domains are stabilized by specific interactions with their substrates. Random polypeptide synthesis in a prebiotic world has the potential to initially produce only a very small fraction of polypeptides that can fold spontaneously into catalytic domains. However, that fraction can be enriched by proteolytic activities that destroy the unfolded polypeptides and regenerate amino acids that can be recycled into polypeptides. In this open system scenario the stable domains that accumulate and the chemical environment in which they are accumulated are linked through self coding of polypeptide structure. Such open polypeptide systems may have been the precursors to the cellular ribonucleoprotein (RNP) world that evolved subsequently.
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Affiliation(s)
- Charles G Kurland
- Department of Microbial Ecology, University of Lund, Sölvegatan, Lund, Sweden.
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248
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Jenner L, Demeshkina N, Yusupova G, Yusupov M. Structural rearrangements of the ribosome at the tRNA proofreading step. Nat Struct Mol Biol 2010; 17:1072-8. [PMID: 20694005 DOI: 10.1038/nsmb.1880] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Accepted: 06/25/2010] [Indexed: 01/01/2023]
Abstract
Discrimination of tRNA on the ribosome occurs in two consecutive steps: initial selection and proofreading. Here we propose a proofreading mechanism based on comparison of crystal structures of the 70S ribosome with an empty A site or with the A site occupied by uncharged cognate or near-cognate tRNA. We observe that ribosomal proteins S13, S19, L16, L25, L27 and L31 are actively involved in the proofreading of tRNA. We suggest that proofreading begins with the monitoring of the entire anticodon loop of tRNA by nucleotides from 16S rRNA (helices 18 and 44) of the small subunit and 23S rRNA (helix 69) of the large subunit with involvement of magnesium ions. Subsequently, the elbow region is scanned by rRNA (helices 38 and 89) and proteins from the large subunit determining whether to accommodate the acceptor end of tRNA in the peptidyl transferase center or not.
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Affiliation(s)
- Lasse Jenner
- Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
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249
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Vázquez-Laslop N, Ramu H, Klepacki D, Kannan K, Mankin AS. The key function of a conserved and modified rRNA residue in the ribosomal response to the nascent peptide. EMBO J 2010; 29:3108-17. [PMID: 20676057 DOI: 10.1038/emboj.2010.180] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2010] [Accepted: 07/06/2010] [Indexed: 11/09/2022] Open
Abstract
The ribosome is able to monitor the structure of the nascent peptide and can stall in response to specific peptide sequences. Such programmed stalling is used for the regulation of gene expression. The molecular mechanisms of the nascent-peptide recognition and ribosome stalling are unknown. We identified the conserved and posttranscriptionally modified 23S rRNA nucleotide m(2)A2503 located at the entrance of the ribosome exit tunnel as a key component of the ribosomal response mechanism. A2503 mutations abolish nascent-peptide-dependent stalling at the leader cistrons of several inducible antibiotic resistance genes and at the secM regulatory gene. Remarkably, lack of the C2 methylation of A2503 significantly function induction of expression of the ermC gene, indicating that the functional role of posttranscriptional modification is to fine-tune ribosome-nascent peptide interactions. Structural and biochemical evidence suggest that m(2)A2503 may act in concert with the previously identified nascent-peptide sensor, A2062, in the ribosome exit tunnel to relay the stalling signal to the peptidyl transferase centre.
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Affiliation(s)
- Nora Vázquez-Laslop
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL, USA.
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250
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Hardin JW, Hu YX, McKay DB. Structure of the RNA binding domain of a DEAD-box helicase bound to its ribosomal RNA target reveals a novel mode of recognition by an RNA recognition motif. J Mol Biol 2010; 402:412-27. [PMID: 20673833 DOI: 10.1016/j.jmb.2010.07.040] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Revised: 07/02/2010] [Accepted: 07/20/2010] [Indexed: 01/30/2023]
Abstract
DEAD-box RNA helicases of the bacterial DbpA subfamily are localized to their biological substrate when a carboxy-terminal RNA recognition motif domain binds tightly and specifically to a segment of 23S ribosomal RNA (rRNA) that includes hairpin 92 of the peptidyl transferase center. A complex between a fragment of 23S rRNA and the RNA binding domain (RBD) of the Bacillus subtilis DbpA protein YxiN was crystallized and its structure was determined to 2.9 A resolution, revealing an RNA recognition mode that differs from those observed with other RNA recognition motifs. The RBD is bound between two RNA strands at a three-way junction. Multiple phosphates of the RNA backbone interact with an electropositive band generated by lysines of the RBD. Nucleotides of the single-stranded loop of hairpin 92 interact with the RBD, including the guanosine base of G2553, which forms three hydrogen bonds with the peptide backbone. A G2553U mutation reduces the RNA binding affinity by 2 orders of magnitude, confirming that G2553 is a sequence specificity determinant in RNA binding. Binding of the RBD to 23S rRNA in the late stages of ribosome subunit maturation would position the ATP-binding duplex destabilization fragment of the protein for interaction with rRNA in the peptidyl transferase cleft of the subunit, allowing it to "melt out" unstable secondary structures and allow proper folding.
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Affiliation(s)
- John W Hardin
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80301, USA
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