1
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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2
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Byju S, Hassan A, Whitford PC. The energy landscape of the ribosome. Biopolymers 2024; 115:e23570. [PMID: 38051695 DOI: 10.1002/bip.23570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/17/2023] [Accepted: 11/08/2023] [Indexed: 12/07/2023]
Abstract
The ribosome is a prototypical assembly that can be used to establish general principles and techniques for the study of biological molecular machines. Motivated by the fact that the dynamics of every biomolecule is governed by an underlying energy landscape, there has been great interest to understand and quantify ribosome energetics. In the present review, we will focus on theoretical and computational strategies for probing the interactions that shape the energy landscape of the ribosome, with an emphasis on more recent studies of the elongation cycle. These efforts include the application of quantum mechanical methods for describing chemical kinetics, as well as classical descriptions to characterize slower (microsecond to millisecond) large-scale (10-100 Å) rearrangements, where motion is described in terms of diffusion across an energy landscape. Together, these studies provide broad insights into the factors that control a diverse range of dynamical processes in this assembly.
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Affiliation(s)
- Sandra Byju
- Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts, USA
- Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Asem Hassan
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, United States
| | - Paul C Whitford
- Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts, USA
- Department of Physics, Northeastern University, Boston, Massachusetts, USA
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3
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Wang Q, Su H. A Tale of Water Molecules in the Ribosomal Peptidyl Transferase Reaction. Biochemistry 2022; 61:2241-2247. [PMID: 36178262 DOI: 10.1021/acs.biochem.2c00098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The peptidyl transferase center (PTC) in the large subunit of the ribosome plays a critical role in protein synthesis by catalyzing the formation of peptide bonds with an astounding speed of about 15 to 20 peptide bonds per second. The ribosome coordinates the nucleophilic attack and deprotonation in the rate-limiting step at the PTC. However, the details of peptide bond formation within the ribosome, particularly the precise role of the two water molecules in the PTC, remain unclear. Here, we propose a novel stepwise "proton shuttle" mechanism which corroborates all the reported experimental measurements so far. In this mechanism, a water molecule close to A76 of peptidyl-tRNA 2'- and 3'-O stabilizes the transition state. The other one adjacent to the carbonyl oxygen of peptidyl-tRNA actively participates in the proton shuttle, playing the catalytic role of ribosome-catalyzed peptide bond formation.
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Affiliation(s)
- Qiang Wang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China.,HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen 518048, China
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4
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Bose T, Fridkin G, Bashan A, Yonath A. Origin of Life: Chiral Short RNA Chains Capable of Non‐Enzymatic Peptide Bond Formation. Isr J Chem 2022. [DOI: 10.1002/ijch.202100054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tanaya Bose
- Department of Structural Biology Weizmann Institute of Science 76100 Rehovot Israel
| | - Gil Fridkin
- Department of Structural Biology Weizmann Institute of Science 76100 Rehovot Israel
- Department of Organic Chemistry Israel Institute for Biological Research P.O. Box 19 Ness Ziona 7410001 Israel
| | - Anat Bashan
- Department of Structural Biology Weizmann Institute of Science 76100 Rehovot Israel
| | - Ada Yonath
- Department of Structural Biology Weizmann Institute of Science 76100 Rehovot Israel
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5
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Fukushima K, Esaki H. Theoretical Study of the Mechanism of Ribosomal Peptide Bond Formation Using the ONIOM Method. Chem Pharm Bull (Tokyo) 2021; 69:734-740. [PMID: 34334517 DOI: 10.1248/cpb.c21-00148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peptide bond formation in living cells occurs at the peptidyl transferase center (PTC) of the large ribosomal subunit and involves the transfer of the peptidyl group from peptidyl-tRNA to aminoacyl-tRNA. Despite numerous kinetic and theoretical studies, many details of this reaction -such as whether it proceeds via a stepwise or concerted mechanism- remain unclear. In this study, we calculated the geometry and energy of the transition states and intermediates in peptide bond formation in the PTC environment using the ONIOM (our own n-layered integrated molecular orbital and molecular mechanics) method. The calculations indicated that the energy of the transition states of stepwise mechanisms are lower than those of concerted mechanisms and suggested that the reaction involves a neutral tetrahedral intermediate that is stabilized through the hydrogen-bonding network in the PTC environment. The results will lead to a better understanding of the mechanism of peptidyl transfer reaction, and resolve fundamental questions of the steps and molecular intermediates involved in peptide bond formation in the ribosome.
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6
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Metabolic stress promotes stop-codon readthrough and phenotypic heterogeneity. Proc Natl Acad Sci U S A 2020; 117:22167-22172. [PMID: 32839318 DOI: 10.1073/pnas.2013543117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Accurate protein synthesis is a tightly controlled biological process with multiple quality control steps safeguarded by aminoacyl-transfer RNA (tRNA) synthetases and the ribosome. Reduced translational accuracy leads to various physiological changes in both prokaryotes and eukaryotes. Termination of translation is signaled by stop codons and catalyzed by release factors. Occasionally, stop codons can be suppressed by near-cognate aminoacyl-tRNAs, resulting in protein variants with extended C termini. We have recently shown that stop-codon readthrough is heterogeneous among single bacterial cells. However, little is known about how environmental factors affect the level and heterogeneity of stop-codon readthrough. In this study, we have combined dual-fluorescence reporters, mass spectrometry, mathematical modeling, and single-cell approaches to demonstrate that a metabolic stress caused by excess carbon substantially increases both the level and heterogeneity of stop-codon readthrough. Excess carbon leads to accumulation of acid metabolites, which lower the pH and the activity of release factors to promote readthrough. Furthermore, our time-lapse microscopy experiments show that single cells with high readthrough levels are more adapted to severe acid stress conditions and are more sensitive to an aminoglycoside antibiotic. Our work thus reveals a metabolic stress that promotes translational heterogeneity and phenotypic diversity.
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7
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Bowman JC, Petrov AS, Frenkel-Pinter M, Penev PI, Williams LD. Root of the Tree: The Significance, Evolution, and Origins of the Ribosome. Chem Rev 2020; 120:4848-4878. [PMID: 32374986 DOI: 10.1021/acs.chemrev.9b00742] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The ribosome is an ancient molecular fossil that provides a telescope to the origins of life. Made from RNA and protein, the ribosome translates mRNA to coded protein in all living systems. Universality, economy, centrality and antiquity are ingrained in translation. The translation machinery dominates the set of genes that are shared as orthologues across the tree of life. The lineage of the translation system defines the universal tree of life. The function of a ribosome is to build ribosomes; to accomplish this task, ribosomes make ribosomal proteins, polymerases, enzymes, and signaling proteins. Every coded protein ever produced by life on Earth has passed through the exit tunnel, which is the birth canal of biology. During the root phase of the tree of life, before the last common ancestor of life (LUCA), exit tunnel evolution is dominant and unremitting. Protein folding coevolved with evolution of the exit tunnel. The ribosome shows that protein folding initiated with intrinsic disorder, supported through a short, primitive exit tunnel. Folding progressed to thermodynamically stable β-structures and then to kinetically trapped α-structures. The latter were enabled by a long, mature exit tunnel that partially offset the general thermodynamic tendency of all polypeptides to form β-sheets. RNA chaperoned the evolution of protein folding from the very beginning. The universal common core of the ribosome, with a mass of nearly 2 million Daltons, was finalized by LUCA. The ribosome entered stasis after LUCA and remained in that state for billions of years. Bacterial ribosomes never left stasis. Archaeal ribosomes have remained near stasis, except for the superphylum Asgard, which has accreted rRNA post LUCA. Eukaryotic ribosomes in some lineages appear to be logarithmically accreting rRNA over the last billion years. Ribosomal expansion in Asgard and Eukarya has been incremental and iterative, without substantial remodeling of pre-existing basal structures. The ribosome preserves information on its history.
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Affiliation(s)
- Jessica C Bowman
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anton S Petrov
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Moran Frenkel-Pinter
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Petar I Penev
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Loren Dean Williams
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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8
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Le Vay K, Salibi E, Song EY, Mutschler H. Nucleic Acid Catalysis under Potential Prebiotic Conditions. Chem Asian J 2020; 15:214-230. [PMID: 31714665 PMCID: PMC7003795 DOI: 10.1002/asia.201901205] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/05/2019] [Indexed: 01/25/2023]
Abstract
Catalysis by nucleic acids is indispensable for extant cellular life, and it is widely accepted that nucleic acid enzymes were crucial for the emergence of primitive life 3.5-4 billion years ago. However, geochemical conditions on early Earth must have differed greatly from the constant internal milieus of today's cells. In order to explore plausible scenarios for early molecular evolution, it is therefore essential to understand how different physicochemical parameters, such as temperature, pH, and ionic composition, influence nucleic acid catalysis and to explore to what extent nucleic acid enzymes can adapt to non-physiological conditions. In this article, we give an overview of the research on catalysis of nucleic acids, in particular catalytic RNAs (ribozymes) and DNAs (deoxyribozymes), under extreme and/or unusual conditions that may relate to prebiotic environments.
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Affiliation(s)
- Kristian Le Vay
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Elia Salibi
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Emilie Y. Song
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Hannes Mutschler
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
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9
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Kazemi M, Socan J, Himo F, Åqvist J. Mechanistic alternatives for peptide bond formation on the ribosome. Nucleic Acids Res 2019; 46:5345-5354. [PMID: 29746669 PMCID: PMC6009655 DOI: 10.1093/nar/gky367] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 04/26/2018] [Indexed: 02/04/2023] Open
Abstract
The peptidyl transfer reaction on the large ribosomal subunit depends on the protonation state of the amine nucleophile and exhibits a large kinetic solvent isotope effect (KSIE ∼8). In contrast, the related peptidyl-tRNA hydrolysis reaction involved in termination shows a KSIE of ∼4 and a pH-rate profile indicative of base catalysis. It is, however, unclear why these reactions should proceed with different mechanisms, as the experimental data suggests. One explanation is that two competing mechanisms may be operational in the peptidyl transferase center (PTC). Herein, we explored this possibility by re-examining the previously proposed proton shuttle mechanism and testing the feasibility of general base catalysis also for peptide bond formation. We employed a large cluster model of the active site and different reaction mechanisms were evaluated by density functional theory calculations. In these calculations, the proton shuttle and general base mechanisms both yield activation energies comparable to the experimental values. However, only the proton shuttle mechanism is found to be consistent with the experimentally observed pH-rate profile and the KSIE. This suggests that the PTC promotes the proton shuttle mechanism for peptide bond formation, while prohibiting general base catalysis, although the detailed mechanism by which general base catalysis is excluded remains unclear.
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Affiliation(s)
- Masoud Kazemi
- Department of Cell and Molecular Biology, Box 596, Uppsala University, BMC, SE-751 24 Uppsala, Sweden.,Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jaka Socan
- Department of Cell and Molecular Biology, Box 596, Uppsala University, BMC, SE-751 24 Uppsala, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Box 596, Uppsala University, BMC, SE-751 24 Uppsala, Sweden
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10
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Dedkova LM, Hecht SM. Expanding the Scope of Protein Synthesis Using Modified Ribosomes. J Am Chem Soc 2019; 141:6430-6447. [PMID: 30901982 DOI: 10.1021/jacs.9b02109] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The ribosome produces all of the proteins and many of the peptides present in cells. As a macromolecular complex composed of both RNAs and proteins, it employs a constituent RNA to catalyze the formation of peptide bonds rapidly and with high fidelity. Thus, the ribosome can be argued to represent the key link between the RNA World, in which RNAs were the primary catalysts, and present biological systems in which protein catalysts predominate. In spite of the well-known phylogenetic conservation of rRNAs through evolutionary history, rRNAs can be altered readily when placed under suitable pressure, e.g. in the presence of antibiotics which bind to functionally critical regions of rRNAs. While the structures of rRNAs have been altered intentionally for decades to enable the study of their role(s) in the mechanism of peptide bond formation, it is remarkable that the purposeful alteration of rRNA structure to enable the elaboration of proteins and peptides containing noncanonical amino acids has occurred only recently. In this Perspective, we summarize the history of rRNA modifications, and demonstrate how the intentional modification of 23S rRNA in regions critical for peptide bond formation now enables the direct ribosomal incorporation of d-amino acids, β-amino acids, dipeptides and dipeptidomimetic analogues of the normal proteinogenic l-α-amino acids. While proteins containing metabolically important functional groups such as carbohydrates and phosphate groups are normally elaborated by the post-translational modification of nascent polypeptides, the use of modified ribosomes to produce such polymers directly is also discussed. Finally, we describe the elaboration of such modified proteins both in vitro and in bacterial cells, and suggest how such novel biomaterials may be exploited in future studies.
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Affiliation(s)
- Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
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11
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Routh SB, Sankaranarayanan R. Enzyme action at RNA–protein interface in DTD-like fold. Curr Opin Struct Biol 2018; 53:107-114. [DOI: 10.1016/j.sbi.2018.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 07/24/2018] [Accepted: 07/30/2018] [Indexed: 02/08/2023]
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12
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Wang J, Forster AC. Ribosomal incorporation of unnatural amino acids: lessons and improvements from fast kinetics studies. Curr Opin Chem Biol 2018; 46:180-187. [DOI: 10.1016/j.cbpa.2018.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 05/21/2018] [Accepted: 07/13/2018] [Indexed: 11/30/2022]
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13
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Abstract
This review summarizes our current understanding of translation in prokaryotes, focusing on the mechanistic and structural aspects of each phase of translation: initiation, elongation, termination, and ribosome recycling. The assembly of the initiation complex provides multiple checkpoints for messenger RNA (mRNA) and start-site selection. Correct codon-anticodon interaction during the decoding phase of elongation results in major conformational changes of the small ribosomal subunit and shapes the reaction pathway of guanosine triphosphate (GTP) hydrolysis. The ribosome orchestrates proton transfer during peptide bond formation, but requires the help of elongation factor P (EF-P) when two or more consecutive Pro residues are to be incorporated. Understanding the choreography of transfer RNA (tRNA) and mRNA movements during translocation helps to place the available structures of translocation intermediates onto the time axis of the reaction pathway. The nascent protein begins to fold cotranslationally, in the constrained space of the polypeptide exit tunnel of the ribosome. When a stop codon is reached at the end of the coding sequence, the ribosome, assisted by termination factors, hydrolyzes the ester bond of the peptidyl-tRNA, thereby releasing the nascent protein. Following termination, the ribosome is dissociated into subunits and recycled into another round of initiation. At each step of translation, the ribosome undergoes dynamic fluctuations between different conformation states. The aim of this article is to show the link between ribosome structure, dynamics, and function.
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Affiliation(s)
- Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen 37077, Germany
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14
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Pavlov MY, Liljas A, Ehrenberg M. A recent intermezzo at the Ribosome Club. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0185. [PMID: 28138071 PMCID: PMC5311929 DOI: 10.1098/rstb.2016.0185] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 12/01/2022] Open
Abstract
Two sets of ribosome structures have recently led to two different interpretations of what limits the accuracy of codon translation by transfer RNAs. In this review, inspired by this intermezzo at the Ribosome Club, we briefly discuss accuracy amplification by energy driven proofreading and its implementation in genetic code translation. We further discuss general ways by which the monitoring bases of 16S rRNA may enhance the ultimate accuracy (d-values) and how the codon translation accuracy is reduced by the actions of Mg2+ ions and the presence of error inducing aminoglycoside antibiotics. We demonstrate that complete freezing-in of cognate-like tautomeric states of ribosome-bound nucleotide bases in transfer RNA or messenger RNA is not compatible with recent experiments on initial codon selection by transfer RNA in ternary complex with elongation factor Tu and GTP. From these considerations, we suggest that the sets of 30S subunit structures from the Ramakrishnan group and 70S structures from the Yusupov/Yusupova group may, after all, reflect two sides of the same coin and how the structurally based intermezzo at the Ribosome Club may be resolved simply by taking the dynamic aspects of ribosome function into account. This article is part of the themed issue ‘Perspectives on the ribosome’.
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Affiliation(s)
- Michael Y Pavlov
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala 75124, Sweden
| | - Anders Liljas
- Department of Biochemistry and Structural Biology, Lund University, Box 124, 22100 Lund, Sweden
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala 75124, Sweden
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15
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Mechanistic Insights Into Catalytic RNA-Protein Complexes Involved in Translation of the Genetic Code. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017. [PMID: 28683922 DOI: 10.1016/bs.apcsb.2017.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The contemporary world is an "RNA-protein world" rather than a "protein world" and tracing its evolutionary origins is of great interest and importance. The different RNAs that function in close collaboration with proteins are involved in several key physiological processes, including catalysis. Ribosome-the complex megadalton cellular machinery that translates genetic information encoded in nucleotide sequence to amino acid sequence-epitomizes such an association between RNA and protein. RNAs that can catalyze biochemical reactions are known as ribozymes. They usually employ general acid-base catalytic mechanism, often involving the 2'-OH of RNA that activates and/or stabilizes a nucleophile during the reaction pathway. The protein component of such RNA-protein complexes (RNPCs) mostly serves as a scaffold which provides an environment conducive for the RNA to function, or as a mediator for other interacting partners. In this review, we describe those RNPCs that are involved at different stages of protein biosynthesis and in which RNA performs the catalytic function; the focus of the account is on highlighting mechanistic aspects of these complexes. We also provide a perspective on such associations in the context of proofreading during translation of the genetic code. The latter aspect is not much appreciated and recent works suggest that this is an avenue worth exploring, since an understanding of the subject can provide useful insights into how RNAs collaborate with proteins to ensure fidelity during these essential cellular processes. It may also aid in comprehending evolutionary aspects of such associations.
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16
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Lehmann J. Induced fit of the peptidyl-transferase center of the ribosome and conformational freedom of the esterified amino acids. RNA (NEW YORK, N.Y.) 2017; 23:229-239. [PMID: 27879432 PMCID: PMC5238797 DOI: 10.1261/rna.057273.116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 11/18/2016] [Indexed: 06/06/2023]
Abstract
The catalytic site of most enzymes can efficiently handle only one substrate. In contrast, the ribosome is capable of polymerizing at a similar rate at least 20 different kinds of amino acids from aminoacyl-tRNA carriers while using just one catalytic site, the peptidyl-transferase center (PTC). An induced-fit mechanism has been uncovered in the PTC, but a possible connection between this mechanism and the uniform handling of the substrates has not been investigated. We present an analysis of published ribosome structures supporting the hypothesis that the induced fit eliminates unreactive rotamers predominantly populated for some A-site aminoacyl esters before induction. We show that this hypothesis is fully consistent with the wealth of kinetic data obtained with these substrates. Our analysis reveals that induction constrains the amino acids into a reactive conformation in a side-chain independent manner. It allows us to highlight the rationale of the PTC structural organization, which confers to the ribosome the very unusual ability to handle large as well as small substrates.
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Affiliation(s)
- Jean Lehmann
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Campus Paris-Saclay, 91198 Gif-sur-Yvette, France
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17
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Wang J, Kwiatkowski M, Forster AC. Ribosomal Peptide Syntheses from Activated Substrates Reveal Rate Limitation by an Unexpected Step at the Peptidyl Site. J Am Chem Soc 2016; 138:15587-15595. [DOI: 10.1021/jacs.6b06936] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jinfan Wang
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan 3, Box
596, Uppsala 75124, Sweden
| | - Marek Kwiatkowski
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan 3, Box
596, Uppsala 75124, Sweden
| | - Anthony C. Forster
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan 3, Box
596, Uppsala 75124, Sweden
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18
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Kazemi M, Himo F, Åqvist J. Peptide Release on the Ribosome Involves Substrate-Assisted Base Catalysis. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02842] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Masoud Kazemi
- Department
of Cell and Molecular Biology, Uppsala University, Box 596, BMC, SE-751 24 Uppsala, Sweden
| | - Fahmi Himo
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Johan Åqvist
- Department
of Cell and Molecular Biology, Uppsala University, Box 596, BMC, SE-751 24 Uppsala, Sweden
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19
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Gardin J, Yeasmin R, Yurovsky A, Cai Y, Skiena S, Futcher B. Measurement of average decoding rates of the 61 sense codons in vivo. eLife 2014; 3. [PMID: 25347064 PMCID: PMC4371865 DOI: 10.7554/elife.03735] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 10/24/2014] [Indexed: 12/19/2022] Open
Abstract
Most amino acids can be encoded by several synonymous codons, which are used at
unequal frequencies. The significance of unequal codon usage remains unclear. One
hypothesis is that frequent codons are translated relatively rapidly. However, there
is little direct, in vivo, evidence regarding codon-specific translation rates. In
this study, we generate high-coverage data using ribosome profiling in yeast, analyze
using a novel algorithm, and deduce events at the A- and P-sites of the ribosome.
Different codons are decoded at different rates in the A-site. In general, frequent
codons are decoded more quickly than rare codons, and AT-rich codons are decoded more
quickly than GC-rich codons. At the P-site, proline is slow in forming peptide bonds.
We also apply our algorithm to short footprints from a different conformation of the
ribosome and find strong amino acid-specific (not codon-specific) effects that may
reflect interactions with the exit tunnel of the ribosome. DOI:http://dx.doi.org/10.7554/eLife.03735.001 Genes contain the instructions for making proteins from molecules called amino acids.
These instructions are encoded in the order of the four building blocks that make up
DNA, which are symbolized by the letters A, T, C, and G. The DNA of a gene is first
copied to make a molecule of RNA, and then the letters in the RNA are read in groups
of three (called ‘codons’) by a cellular machine called a ribosome.
‘Sense codons’ each specify one amino acid, and the ribosome decodes
hundreds or thousands of these codons into a chain of amino acids to form a protein.
‘Stop codons’ do not encode amino acids but instead instruct the
ribosome to stop building a protein when the chain is completed. Most proteins are built from 20 different kinds of amino acid, but there are 61 sense
codons. As such, up to six codons can code for the same amino acid. The multiple
codons for a single amino acid, however, are not used equally in gene
sequences—some are used much more often than others. Now, Gardin, Yeasmin et al. have instantly halted the on-going processes of decoding
genes and building proteins in yeast cells. Codons being translated into amino acids
are trapped inside the ribosome; and codons that take the longest to decode are
trapped most often. By using a computer algorithm, Gardin, Yeasmin et al. were able
to measure just how often each kind of sense codon was trapped inside the ribosome
and use this as a measure of how quickly each codon is decoded. The more often a
given codon is used in a gene sequence, the less likely it was found to be trapped
inside the ribosome—which suggests that these codons are decoded quicker than
other codons and pass through the ribosome more quickly. Put another way, it appears
that genes tend to use the codons that can be read the fastest. Certain properties of a codon also affected its decoding speed. Codons with more As
and Ts, for example, are decoded faster than codons with more Cs and Gs. Furthermore,
whenever a chemically unusual amino acid called proline has to be added to a new
protein chain, it slowed down the speed at which the protein was built. The method
described by Gardin, Yeasmin et al. for peering into a decoding ribosome may now help
future studies that aim to answer other questions about how proteins are built. DOI:http://dx.doi.org/10.7554/eLife.03735.002
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Affiliation(s)
- Justin Gardin
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, United States
| | - Rukhsana Yeasmin
- Department of Computer Science, Stony Brook University, Stony Brook, United States
| | - Alisa Yurovsky
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, United States
| | - Ying Cai
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, United States
| | - Steve Skiena
- Department of Computer Science, Stony Brook University, Stony Brook, United States
| | - Bruce Futcher
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, United States
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20
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A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome. Nat Struct Mol Biol 2014; 21:787-93. [PMID: 25132179 PMCID: PMC4156881 DOI: 10.1038/nsmb.2871] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 07/14/2014] [Indexed: 11/12/2022]
Abstract
During peptide bond formation on the ribosome the α-amine of an aminoacyl-tRNA attacks the ester carbonyl carbon of a peptidyl-tRNA to yield a peptide lengthened by one amino acid. Although the ribosome's contribution to catalysis is predominantly entropic, the lack of high-resolution structural data for the complete active site in complex with full-length ligands has made it difficult to assess how the ribosome might influence the pathway of the reaction. Here, we present crystal structures of pre-attack and post-catalysis complexes of the Thermus thermophilus 70S ribosome at ∼2.6 Å resolution. These structures reveal a network of hydrogen bonds along which proton transfer could take place to ensure the concerted, rate-limiting formation of a tetrahedral intermediate. Unlike earlier models, we propose that the ribosome and the A-site tRNA facilitate the deprotonation of the nucleophile through the activation of a water molecule.
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21
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Wang J, Kwiatkowski M, Pavlov MY, Ehrenberg M, Forster AC. Peptide formation by N-methyl amino acids in translation is hastened by higher pH and tRNA(Pro). ACS Chem Biol 2014; 9:1303-11. [PMID: 24673854 DOI: 10.1021/cb500036a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Applications of N-methyl amino acids (NMAAs) in drug discovery are limited by their low efficiencies of ribosomal incorporation, and little is known mechanistically about the steps leading to incorporation. Here, we demonstrate that a synthetic tRNA body based on a natural N-alkyl amino acid carrier, tRNA(Pro), increases translation incorporation rates of all three studied NMAAs compared with tRNA(Phe)- and tRNA(Ala)-based bodies. We also investigate the pH dependence of the incorporation rates and find that the rates increase dramatically in the range of pH 7 to 8.5 with the titration of a single proton. Results support a rate-limiting peptidyl transfer step dependent on deprotonation of the N-nucleophile of the NMAA. Competition experiments demonstrate that several futile cycles of delivery and rejection of A-site NMAA-tRNA are required per peptide bond formed and that increasing magnesium ion concentration increases incorporation yield. Data clarify the mechanism of ribosomal NMAA incorporation and provide three generalizable ways to improve incorporation of NMAAs in translation.
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Affiliation(s)
- Jinfan Wang
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan 3, Box
596, Uppsala 75124, Sweden
| | - Marek Kwiatkowski
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan 3, Box
596, Uppsala 75124, Sweden
| | - Michael Y. Pavlov
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan 3, Box
596, Uppsala 75124, Sweden
| | - Måns Ehrenberg
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan 3, Box
596, Uppsala 75124, Sweden
| | - Anthony C. Forster
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan 3, Box
596, Uppsala 75124, Sweden
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22
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Ieong KW, Pavlov MY, Kwiatkowski M, Ehrenberg M, Forster AC. A tRNA body with high affinity for EF-Tu hastens ribosomal incorporation of unnatural amino acids. RNA (NEW YORK, N.Y.) 2014; 20:632-43. [PMID: 24671767 PMCID: PMC3988565 DOI: 10.1261/rna.042234.113] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 01/27/2014] [Indexed: 05/25/2023]
Abstract
There is evidence that tRNA bodies have evolved to reduce differences between aminoacyl-tRNAs in their affinity to EF-Tu. Here, we study the kinetics of incorporation of L-amino acids (AAs) Phe, Ala allyl-glycine (aG), methyl-serine (mS), and biotinyl-lysine (bK) using a tRNA(Ala)-based body (tRNA(AlaB)) with a high affinity for EF-Tu. Results are compared with previous data on the kinetics of incorporation of the same AAs using a tRNA(PheB) body with a comparatively low affinity for EF-Tu. All incorporations exhibited fast and slow phases, reflecting the equilibrium fraction of AA-tRNA in active ternary complex with EF-Tu:GTP before the incorporation reaction. Increasing the concentration of EF-Tu increased the amplitude of the fast phase and left its rate unaltered. This allowed estimation of the affinity of each AA-tRNA to EF-Tu:GTP during translation, showing about a 10-fold higher EF-Tu affinity for AA-tRNAs formed from the tRNA(AlaB) body than from the tRNA(PheB) body. At ∼1 µM EF-Tu, tRNA(AlaB) conferred considerably faster incorporation kinetics than tRNA(PheB), especially in the case of the bulky bK. In contrast, the swap to the tRNA(AlaB) body did not increase the fast phase fraction of N-methyl-Phe incorporation, suggesting that the slow incorporation of N-methyl-Phe had a different cause than low EF-Tu:GTP affinity. The total time for AA-tRNA release from EF-Tu:GDP, accommodation, and peptidyl transfer on the ribosome was similar for the tRNA(AlaB) and tRNA(PheB) bodies. We conclude that a tRNA body with high EF-Tu affinity can greatly improve incorporation of unnatural AAs in a potentially generalizable manner.
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23
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Affiliation(s)
| | - V. Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; ,
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24
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Rodnina MV. The ribosome as a versatile catalyst: reactions at the peptidyl transferase center. Curr Opin Struct Biol 2013; 23:595-602. [PMID: 23711800 DOI: 10.1016/j.sbi.2013.04.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 04/10/2013] [Indexed: 11/29/2022]
Abstract
In all contemporary organisms, the active site of the ribosome--the peptidyl transferase center--catalyzes two distinct reactions, peptide bond formation between peptidyl-tRNA and aminoacyl-tRNA as well as the hydrolysis of peptidyl-tRNA with the help of a release factor. However, when provided with appropriate substrates, ribosomes can also catalyze a broad range of other chemical reaction, which provides the basis for orthogonal translation and synthesis of alloproteins from unnatural building blocks. Advances in understanding the mechanisms of the two ubiquitous reactions, the peptide bond formation and peptide release, provide insights into the versatility of the active site of the ribosome. Release factors 1 and 2 and elongation factor P are auxiliary factors that augment the intrinsic catalytic activity of the ribosome in special cases.
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Affiliation(s)
- Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany.
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25
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A Vestige of an RNA Apparatus With Ribozyme Capabilities Embedded and Functions Within the Modern Ribosome. SOCIAL AND ECOLOGICAL INTERACTIONS IN THE GALAPAGOS ISLANDS 2013. [DOI: 10.1007/978-1-4614-6732-8_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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26
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Shaw JJ, Trobro S, He SL, Åqvist J, Green R. A Role for the 2' OH of peptidyl-tRNA substrate in peptide release on the ribosome revealed through RF-mediated rescue. ACTA ACUST UNITED AC 2012; 19:983-93. [PMID: 22921065 DOI: 10.1016/j.chembiol.2012.06.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 05/12/2012] [Accepted: 06/01/2012] [Indexed: 11/25/2022]
Abstract
The 2' OH of the peptidyl-tRNA substrate is thought to be important for catalysis of both peptide bond formation and peptide release in the ribosomal active site. The release reaction also specifically depends on a release factor protein (RF) to hydrolyze the ester linkage of the peptidyl-tRNA upon recognition of stop codons in the A site. Here, we demonstrate that certain amino acid substitutions (in particular those containing hydroxyl or thiol groups) in the conserved GGQ glutamine of release factor RF1 can rescue defects in the release reaction associated with peptidyl-tRNA substrates lacking a 2' OH. We explored this rescue effect through biochemical and computational approaches that support a model where the 2' OH of the P-site substrate is critical for orienting the nucleophile in a hydrogen-bonding network productive for catalysis.
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Affiliation(s)
- Jeffrey J Shaw
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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27
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Ieong KW, Pavlov MY, Kwiatkowski M, Forster AC, Ehrenberg M. Inefficient Delivery but Fast Peptide Bond Formation of Unnatural l-Aminoacyl-tRNAs in Translation. J Am Chem Soc 2012; 134:17955-62. [DOI: 10.1021/ja3063524] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ka-Weng Ieong
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan
3, Box 596, Uppsala
75124, Sweden
| | - Michael Y. Pavlov
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan
3, Box 596, Uppsala
75124, Sweden
| | - Marek Kwiatkowski
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan
3, Box 596, Uppsala
75124, Sweden
| | - Anthony C. Forster
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan
3, Box 596, Uppsala
75124, Sweden
| | - Måns Ehrenberg
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan
3, Box 596, Uppsala
75124, Sweden
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28
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Xu J, Zhang JZH, Xiang Y. Ab Initio QM/MM Free Energy Simulations of Peptide Bond Formation in the Ribosome Support an Eight-Membered Ring Reaction Mechanism. J Am Chem Soc 2012; 134:16424-9. [DOI: 10.1021/ja3076605] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jun Xu
- State Key Laboratory of Precision
Spectroscopy, Institute of Theoretical and Computational Science,
Department of Physics, East China Normal University, Shanghai 200062, China
| | - John Z. H. Zhang
- State Key Laboratory of Precision
Spectroscopy, Institute of Theoretical and Computational Science,
Department of Physics, East China Normal University, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10003, United
States
| | - Yun Xiang
- State Key Laboratory of Precision
Spectroscopy, Institute of Theoretical and Computational Science,
Department of Physics, East China Normal University, Shanghai 200062, China
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29
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Aqvist J, Lind C, Sund J, Wallin G. Bridging the gap between ribosome structure and biochemistry by mechanistic computations. Curr Opin Struct Biol 2012; 22:815-23. [PMID: 22884263 DOI: 10.1016/j.sbi.2012.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 06/14/2012] [Accepted: 07/09/2012] [Indexed: 11/18/2022]
Abstract
The wealth of structural and biochemical data now available for protein synthesis on the ribosome presents major new challenges for computational biochemistry. Apart from technical difficulties in modeling ribosome systems, the complexity of the overall translation cycle with a multitude of different kinetic steps presents a formidable problem for computational efforts where we have only seen the beginning. However, a range of methodologies including molecular dynamics simulations, free energy calculations, molecular docking and quantum chemical approaches have already been put to work with promising results. In particular, the combined efforts of structural biology, biochemistry, kinetics and computational modeling can lead towards a quantitative structure-based description of translation.
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Affiliation(s)
- Johan Aqvist
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden.
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30
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Forster AC. Synthetic biology challenges long-held hypotheses in translation, codon bias and transcription. Biotechnol J 2012; 7:835-45. [DOI: 10.1002/biot.201200002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 04/28/2012] [Accepted: 05/08/2012] [Indexed: 11/09/2022]
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31
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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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32
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Abstract
Proteins, the main players in current biological systems, are produced on ribosomes by sequential amide bond (peptide bond) formations between amino-acid-bearing tRNAs. The ribosome is an exquisite super-complex of RNA-proteins, containing more than 50 proteins and at least 3 kinds of RNAs. The combination of a variety of side chains of amino acids (typically 20 kinds with some exceptions) confers proteins with extraordinary structure and functions. The origin of peptide bond formation and the ribosome is crucial to the understanding of life itself. In this article, a possible evolutionary pathway to peptide bond formation machinery (proto-ribosome) will be discussed, with a special focus on the RNA minihelix (primordial form of modern tRNA) as a starting molecule. Combining the present data with recent experimental data, we can infer that the peptidyl transferase center (PTC) evolved from a primitive system in the RNA world comprising tRNA-like molecules formed by duplication of minihelix-like small RNA.
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Affiliation(s)
- Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510 Japan.
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33
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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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34
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Watts RE, Forster AC. Update on pure translation display with unnatural amino acid incorporation. Methods Mol Biol 2012; 805:349-365. [PMID: 22094816 DOI: 10.1007/978-1-61779-379-0_20] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The identification of peptide and protein ligands by directed evolution in vitro has been of enormous utility in molecular biology and biotechnology. However, the translation step in almost all polypeptide selection methods is performed in vivo or in crude extracts, restricting applications. These restrictions include a limited library size due to transformation efficiency, unwanted competing reactions in translation, and an inability to incorporate multiple unnatural amino acids (AAs) with high fidelity and efficiency. These restrictions can be addressed by "pure translation display" where the translation step is performed in a purified system. To date, all pure translation display selections have coupled genotype to phenotype in a ribosome display format, though other formats also should be practical. Here, we detail the original, proof-of-principle, pure-translation-display method because this version should be the most suitable for encoding multiple unnatural AAs per peptide product toward the goal of "peptidomimetic evolution." Challenges and progress toward this ultimate goal are discussed and are mainly associated with improving the efficiency of ribosomal polymerization of multiple unnatural AAs.
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Affiliation(s)
- R Edward Watts
- Department of Pharmacology, Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, TN, USA
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35
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Monajemi H, Zain SM, Wan Abdullah WAT. Computational outlook on the ribosome as an entropy trap. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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36
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Firdaus-Raih M, Harrison AM, Willett P, Artymiuk PJ. Novel base triples in RNA structures revealed by graph theoretical searching methods. BMC Bioinformatics 2011; 12 Suppl 13:S2. [PMID: 22373013 PMCID: PMC3278836 DOI: 10.1186/1471-2105-12-s13-s2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Highly hydrogen bonded base interactions play a major part in stabilizing the tertiary structures of complex RNA molecules, such as transfer-RNAs, ribozymes and ribosomal RNAs. Results We describe the graph theoretical identification and searching of highly hydrogen bonded base triples, where each base is involved in at least two hydrogen bonds with the other bases. Our approach correlates theoretically predicted base triples with literature-based compilations and other actual occurrences in crystal structures. The use of ‘fuzzy’ search tolerances has enabled us to discover a number of triple interaction types that have not been previously recorded nor predicted theoretically. Conclusions Comparative analyses of different ribosomal RNA structures reveal several conserved base triple motifs in 50S rRNA structures, indicating an important role in structural stabilization and ultimately RNA function.
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Affiliation(s)
- Mohd Firdaus-Raih
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
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37
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Kuhlenkoetter S, Wintermeyer W, Rodnina MV. Different substrate-dependent transition states in the active site of the ribosome. Nature 2011; 476:351-4. [PMID: 21804565 DOI: 10.1038/nature10247] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 06/03/2011] [Indexed: 11/09/2022]
Abstract
The active site of the ribosome, the peptidyl transferase centre, catalyses two reactions, namely, peptide bond formation between peptidyl-tRNA and aminoacyl-tRNA as well as the release-factor-dependent hydrolysis of peptidyl-tRNA. Unlike peptide bond formation, peptide release is strongly impaired by mutations of nucleotides within the active site, in particular by base exchanges at position A2602 (refs 1, 2). The 2'-OH group of A76 of the peptidyl-tRNA substrate seems to have a key role in peptide release. According to computational analysis, the 2'-OH may take part in a concerted 'proton shuttle' by which the leaving group is protonated, in analogy to similar current models of peptide bond formation. Here we report kinetic solvent isotope effects and proton inventories (reaction rates measured in buffers with increasing content of deuterated water, D(2)O) of the two reactions catalysed by the active site of the Escherichia coli ribosome. The transition state of the release factor 2 (RF2)-dependent hydrolysis reaction is characterized by the rate-limiting formation of a single strong hydrogen bond. This finding argues against a concerted proton shuttle in the transition state of the hydrolysis reaction. In comparison, the proton inventory for peptide bond formation indicates the rate-limiting formation of three hydrogen bonds with about equal contributions, consistent with a concerted eight-membered proton shuttle in the transition state. Thus, the ribosome supports different rate-limiting transition states for the two reactions that take place in the peptidyl transferase centre.
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Affiliation(s)
- Stephan Kuhlenkoetter
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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38
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A two-step chemical mechanism for ribosome-catalysed peptide bond formation. Nature 2011; 476:236-9. [PMID: 21765427 PMCID: PMC3154986 DOI: 10.1038/nature10248] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 06/03/2011] [Indexed: 01/18/2023]
Abstract
The chemical step of natural protein synthesis, peptide bond formation, is catalysed by the large subunit of the ribosome. Crystal structures have shown that the active site for peptide bond formation is composed entirely of RNA. Recent work has focused on how an RNA active site is able to catalyse this fundamental biological reaction at a suitable rate for protein synthesis. On the basis of the absence of important ribosomal functional groups, lack of a dependence on pH, and the dominant contribution of entropy to catalysis, it has been suggested that the role of the ribosome is limited to bringing the substrates into close proximity. Alternatively, the importance of the 2'-hydroxyl of the peptidyl-transfer RNA and a Brønsted coefficient near zero have been taken as evidence that the ribosome coordinates a proton-transfer network. Here we report the transition state of peptide bond formation, based on analysis of the kinetic isotope effect at five positions within the reaction centre of a peptidyl-transfer RNA mimic. Our results indicate that in contrast to the uncatalysed reaction, formation of the tetrahedral intermediate and proton transfer from the nucleophilic nitrogen both occur in the rate-limiting step. Unlike in previous proposals, the reaction is not fully concerted; instead, breakdown of the tetrahedral intermediate occurs in a separate fast step. This suggests that in addition to substrate positioning, the ribosome is contributing to chemical catalysis by changing the rate-limiting transition state.
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39
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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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40
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Kaur J, Raj M, Cooperman BS. Fluorescent labeling of tRNA dihydrouridine residues: Mechanism and distribution. RNA (NEW YORK, N.Y.) 2011; 17:1393-1400. [PMID: 21628433 PMCID: PMC3138574 DOI: 10.1261/rna.2670811] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 04/27/2011] [Indexed: 05/26/2023]
Abstract
Dihydrouridine (DHU) positions within tRNAs have long been used as sites to covalently attach fluorophores, by virtue of their unique chemical reactivity toward reduction by NaBH(4), their abundance within prokaryotic and eukaryotic tRNAs, and the biochemical functionality of the labeled tRNAs so produced. Interpretation of experiments employing labeled tRNAs can depend on knowing the distribution of dye among the DHU positions present in a labeled tRNA. Here we combine matrix-assisted laser desorption/ionization mass spectroscopy (MALDI-MS) analysis of oligonucleotide fragments and thin layer chromatography to resolve and quantify sites of DHU labeling by the fluorophores Cy3, Cy5, and proflavin in Escherichia coli tRNA(Phe) and E. coli tRNA(Arg). The MALDI-MS results led us to re-examine the precise chemistry of the reactions that result in fluorophore introduction into tRNA. We demonstrate that, in contrast to an earlier suggestion that has long been unchallenged in the literature, such introduction proceeds via a substitution reaction on tetrahydrouridine, the product of NaBH(4) reduction of DHU, resulting in formation of substituted tetrahydrocytidines within tRNA.
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Affiliation(s)
- Jaskiran Kaur
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
- Anima Cell Metrology, Inc., Bernardsville, New Jersey 07924-2270, USA
| | - Monika Raj
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
| | - Barry S. Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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41
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Zaher HS, Shaw JJ, Strobel SA, Green R. The 2'-OH group of the peptidyl-tRNA stabilizes an active conformation of the ribosomal PTC. EMBO J 2011; 30:2445-53. [PMID: 21552203 DOI: 10.1038/emboj.2011.142] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 04/06/2011] [Indexed: 11/09/2022] Open
Abstract
The ribosome accelerates the rate of peptidyl transfer by >10(6)-fold relative to the background rate. A widely accepted model for this rate enhancement invokes entropic effects whereby the ribosome and the 2'-OH of the peptidyl-tRNA substrate precisely position the reactive moieties through an extensive network of hydrogen bonds that allows proton movement through them. Some studies, however, have called this model into question because they find the 2'-OH of the peptidyl-tRNA to be dispensable for catalysis. Here, we use an in vitro reconstituted translation system to resolve these discrepancies. We find that catalysis is at least 100-fold slower with the dA76-substituted peptidyl-tRNA substrate and that the peptidyl transferase centre undergoes a slow inactivation when the peptidyl-tRNA lacks the 2'-OH group. Additionally, the 2'-OH group was found to be critical for EFTu binding and peptide release. These findings reconcile the conflict in the literature, and support a model where interactions between active site residues and the 2'-OH of A76 of the peptidyl-tRNA are pivotal in orienting substrates in this active site for optimal catalysis.
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Affiliation(s)
- Hani S Zaher
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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42
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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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43
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pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA. Proc Natl Acad Sci U S A 2010; 108:79-84. [PMID: 21169502 DOI: 10.1073/pnas.1012612107] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We studied the pH-dependence of ribosome catalyzed peptidyl transfer from fMet-tRNA(fMet) to the aa-tRNAs Phe-tRNA(Phe), Ala-tRNA(Ala), Gly-tRNA(Gly), Pro-tRNA(Pro), Asn-tRNA(Asn), and Ile-tRNA(Ile), selected to cover a large range of intrinsic pK(a)-values for the α-amino group of their amino acids. The peptidyl transfer rates were different at pH 7.5 and displayed different pH-dependence, quantified as the pH-value, pK(a)(obs), at which the rate was half maximal. The pK(a)(obs)-values were downshifted relative to the intrinsic pK(a)-value of aa-tRNAs in bulk solution. Gly-tRNA(Gly) had the smallest downshift, while Ile-tRNA(Ile) and Ala-tRNA(Ala) had the largest downshifts. These downshifts correlate strongly with molecular dynamics (MD) estimates of the downshifts in pK(a)-values of these aa-tRNAs upon A-site binding. Our data show the chemistry of peptide bond formation to be rate limiting for peptidyl transfer at pH 7.5 in the Gly and Pro cases and indicate rate limiting chemistry for all six aa-tRNAs.
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44
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Validating a new proton shuttle reaction pathway for formation of the peptide bond in ribosomes: A theoretical investigation. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.10.048] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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45
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Optimization of speed and accuracy of decoding in translation. EMBO J 2010; 29:3701-9. [PMID: 20842102 DOI: 10.1038/emboj.2010.229] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 08/24/2010] [Indexed: 11/08/2022] Open
Abstract
The speed and accuracy of protein synthesis are fundamental parameters for understanding the fitness of living cells, the quality control of translation, and the evolution of ribosomes. In this study, we analyse the speed and accuracy of the decoding step under conditions reproducing the high speed of translation in vivo. We show that error frequency is close to 10⁻³, consistent with the values measured in vivo. Selectivity is predominantly due to the differences in k(cat) values for cognate and near-cognate reactions, whereas the intrinsic affinity differences are not used for tRNA discrimination. Thus, the ribosome seems to be optimized towards high speed of translation at the cost of fidelity. Competition with near- and non-cognate ternary complexes reduces the rate of GTP hydrolysis in the cognate ternary complex, but does not appreciably affect the rate-limiting tRNA accommodation step. The GTP hydrolysis step is crucial for the optimization of both the speed and accuracy, which explains the necessity for the trade-off between the two fundamental parameters of translation.
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Burakovsky DE, Sergiev PV, Steblyanko MA, Kubarenko AV, Konevega AL, Bogdanov AA, Rodnina MV, Dontsova OA. Mutations at the accommodation gate of the ribosome impair RF2-dependent translation termination. RNA (NEW YORK, N.Y.) 2010; 16:1848-1853. [PMID: 20668033 PMCID: PMC2924543 DOI: 10.1261/rna.2185710] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 06/16/2010] [Indexed: 05/29/2023]
Abstract
During protein synthesis, aminoacyl-tRNA (aa-tRNA) and release factors 1 and 2 (RF1 and RF2) have to bind at the catalytic center of the ribosome on the 50S subunit where they take part in peptide bond formation or peptidyl-tRNA hydrolysis, respectively. Computer simulations of aa-tRNA movement into the catalytic site (accommodation) suggested that three nucleotides of 23S rRNA, U2492, C2556, and C2573, form a "gate" at which aa-tRNA movement into the A site is retarded. Here we examined the role of nucleotides C2573 of 23S rRNA, a part of the putative accommodation gate, and of the neighboring A2572 for aa-tRNA binding followed by peptide bond formation and for the RF2-dependent peptide release. Mutations at the two positions did not affect aa-tRNA accommodation, peptide bond formation, or the fidelity of aa-tRNA selection, but impaired RF2-catalyzed peptide release. The data suggest that the ribosome is a robust machine that allows rapid aa-tRNA accommodation despite the defects at the accommodation gate. In comparison, peptide release by RF2 appears more sensitive to these mutations, due to slower accommodation of the factor or effects on RF2 positioning in the A site.
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Meskauskas A, Dinman JD. A molecular clamp ensures allosteric coordination of peptidyltransfer and ligand binding to the ribosomal A-site. Nucleic Acids Res 2010; 38:7800-13. [PMID: 20660012 PMCID: PMC2995063 DOI: 10.1093/nar/gkq641] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Although the ribosome is mainly comprised of rRNA and many of its critical functions occur through RNA–RNA interactions, distinct domains of ribosomal proteins also participate in switching the ribosome between different conformational/functional states. Prior studies demonstrated that two extended domains of ribosomal protein L3 form an allosteric switch between the pre- and post-translocational states. Missing was an explanation for how the movements of these domains are communicated among the ribosome's functional centers. Here, a third domain of L3 called the basic thumb, that protrudes roughly perpendicular from the W-finger and is nestled in the center of a cagelike structure formed by elements from three separate domains of the large subunit rRNA is investigated. Mutagenesis of basically charged amino acids of the basic thumb to alanines followed by detailed analyses suggests that it acts as a molecular clamp, playing a role in allosterically communicating the ribosome's tRNA occupancy status to the elongation factor binding region and the peptidyltransferase center, facilitating coordination of their functions through the elongation cycle. The observation that these mutations affected translational fidelity, virus propagation and cell growth demonstrates how small structural changes at the atomic scale can propagate outward to broadly impact the biology of cell.
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Affiliation(s)
- Arturas Meskauskas
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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48
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Yonath A. Winterschlafende Bären, Antibiotika und die Evolution des Ribosoms (Nobel-Aufsatz). Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001297] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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49
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Yonath A. Hibernating Bears, Antibiotics, and the Evolving Ribosome (Nobel Lecture). Angew Chem Int Ed Engl 2010; 49:4341-54. [DOI: 10.1002/anie.201001297] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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50
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