151
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Transfer RNA: From pioneering crystallographic studies to contemporary tRNA biology. Arch Biochem Biophys 2016; 602:95-105. [PMID: 26968773 DOI: 10.1016/j.abb.2016.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/29/2016] [Accepted: 03/03/2016] [Indexed: 12/17/2022]
Abstract
Transfer RNAs (tRNAs) play a key role in protein synthesis as adaptor molecules between messenger RNA and protein sequences on the ribosome. Their discovery in the early sixties provoked a worldwide infatuation with the study of their architecture and their function in the decoding of genetic information. tRNAs are also emblematic molecules in crystallography: the determination of the first tRNA crystal structures represented a milestone in structural biology and tRNAs were for a long period the sole source of information on RNA folding, architecture, and post-transcriptional modifications. Crystallographic data on tRNAs in complex with aminoacyl-tRNA synthetases (aaRSs) also provided the first insight into protein:RNA interactions. Beyond the translation process and the history of structural investigations on tRNA, this review also illustrates the renewal of tRNA biology with the discovery of a growing number of tRNA partners in the cell, the involvement of tRNAs in a variety of regulatory and metabolic pathways, and emerging applications in biotechnology and synthetic biology.
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152
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Liu Q, Fredrick K. Intersubunit Bridges of the Bacterial Ribosome. J Mol Biol 2016; 428:2146-64. [PMID: 26880335 DOI: 10.1016/j.jmb.2016.02.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/29/2016] [Accepted: 02/05/2016] [Indexed: 02/02/2023]
Abstract
The ribosome is a large two-subunit ribonucleoprotein machine that translates the genetic code in all cells, synthesizing proteins according to the sequence of the mRNA template. During translation, the primary substrates, transfer RNAs, pass through binding sites formed between the two subunits. Multiple interactions between the ribosomal subunits, termed intersubunit bridges, keep the ribosome intact and at the same time govern dynamics that facilitate the various steps of translation such as transfer RNA-mRNA movement. Here, we review the molecular nature of these intersubunit bridges, how they change conformation during translation, and their functional roles in the process.
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Affiliation(s)
- Qi Liu
- Ohio State Biochemistry Program, Department of Microbiology, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Ohio State Biochemistry Program, Department of Microbiology, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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153
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Rozov A, Demeshkina N, Khusainov I, Westhof E, Yusupov M, Yusupova G. Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code. Nat Commun 2016; 7:10457. [PMID: 26791911 PMCID: PMC4736104 DOI: 10.1038/ncomms10457] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/13/2015] [Indexed: 02/07/2023] Open
Abstract
Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNA(Lys)(UUU) with hypermodified 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm(5)s(2)U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.
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Affiliation(s)
- Alexey Rozov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964; CNRS/University of Strasbourg, UMR7104, 1 rue Laurent Fries, BP 10142, Illkirch 67404, France
| | - Natalia Demeshkina
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964; CNRS/University of Strasbourg, UMR7104, 1 rue Laurent Fries, BP 10142, Illkirch 67404, France
| | - Iskander Khusainov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964; CNRS/University of Strasbourg, UMR7104, 1 rue Laurent Fries, BP 10142, Illkirch 67404, France.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Karl Marx 18, Kazan 420012, Russia
| | - Eric Westhof
- Architecture and Reactivity of RNA, Institute of Molecular and Cellular Biology of the CNRS, University of Strasbourg, UPR9002, 15 rue Rene Descartes, Strasbourg 67084, France
| | - Marat Yusupov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964; CNRS/University of Strasbourg, UMR7104, 1 rue Laurent Fries, BP 10142, Illkirch 67404, France
| | - Gulnara Yusupova
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964; CNRS/University of Strasbourg, UMR7104, 1 rue Laurent Fries, BP 10142, Illkirch 67404, France
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154
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Kondo J. Crystallographic Studies of the Ribosomal A-Site Molecular Switches by Using Model RNA Oligomers. Methods Mol Biol 2016; 1320:315-327. [PMID: 26227052 DOI: 10.1007/978-1-4939-2763-0_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
An RNA molecular switch in the aminoacyl-tRNA decoding site (A site) of the ribosome plays a key role in the decoding process of the protein biosynthesis. The switch discriminates a single cognate-tRNA from near-cognate tRNAs by changing its conformation from "off" to "on" states and recognizing the first two base pairs of codon-anticodon mini-helix to check whether these base pairs are of the canonical Watson-Crick type or not. Aminoglycoside antibiotics specifically target the "on" state of the bacterial A-site molecular switch and disturb the fidelity of the decoding process, resulting to cell death. If it occurs in human who was given aminoglycosides, it can lead to undesirable side effects. In order to understand the molecular bases of the decoding and the antibacterial and toxic side effects of aminoglycosides, it is necessary to determine the three-dimensional structures of the A-site molecular switches both in the presence and absence of aminoglycosides. This chapter focuses on methods in crystallographic studies of the A-site switches by using model RNA oligomers. The methods can be utilized in crystallographic studies of any DNA/RNA oligomers.
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Affiliation(s)
- Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554, Tokyo, Japan,
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155
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Post-Transcriptional Modifications of RNA: Impact on RNA Function and Human Health. MODIFIED NUCLEIC ACIDS IN BIOLOGY AND MEDICINE 2016. [DOI: 10.1007/978-3-319-34175-0_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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156
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Bera S, Mondal D, Palit S, Schweizer F. Structural modifications of the neomycin class of aminoglycosides. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00079g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review encompasses comprehensive literature on synthetic modification and biological activities of clinically used neomycin-class aminoglycoside antibiotics to alleviate dose-related toxicity and pathogenic resistance.
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Affiliation(s)
- Smritilekha Bera
- School of Chemical Sciences
- Central University of Gujarat
- Gandhinagar-382030
- India
| | - Dhananjoy Mondal
- School of Chemical Sciences
- Central University of Gujarat
- Gandhinagar-382030
- India
| | - Subhadeep Palit
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology Campus
- Kolkata-700 032
- India
| | - Frank Schweizer
- Department of Chemistry and Medical Microbiology
- University of Manitoba
- Winnipeg
- Canada
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157
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Abstract
We present a molecular-level model for the origin and evolution of the translation system, using a 3D comparative method. In this model, the ribosome evolved by accretion, recursively adding expansion segments, iteratively growing, subsuming, and freezing the rRNA. Functions of expansion segments in the ancestral ribosome are assigned by correspondence with their functions in the extant ribosome. The model explains the evolution of the large ribosomal subunit, the small ribosomal subunit, tRNA, and mRNA. Prokaryotic ribosomes evolved in six phases, sequentially acquiring capabilities for RNA folding, catalysis, subunit association, correlated evolution, decoding, energy-driven translocation, and surface proteinization. Two additional phases exclusive to eukaryotes led to tentacle-like rRNA expansions. In this model, ribosomal proteinization was a driving force for the broad adoption of proteins in other biological processes. The exit tunnel was clearly a central theme of all phases of ribosomal evolution and was continuously extended and rigidified. In the primitive noncoding ribosome, proto-mRNA and the small ribosomal subunit acted as cofactors, positioning the activated ends of tRNAs within the peptidyl transferase center. This association linked the evolution of the large and small ribosomal subunits, proto-mRNA, and tRNA.
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158
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Aboul-ela F, Huang W, Abd Elrahman M, Boyapati V, Li P. Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design. WILEY INTERDISCIPLINARY REVIEWS. RNA 2015; 6:631-50. [PMID: 26361734 PMCID: PMC5049679 DOI: 10.1002/wrna.1300] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 07/27/2015] [Accepted: 07/28/2015] [Indexed: 11/23/2022]
Abstract
The power of riboswitches in regulation of bacterial metabolism derives from coupling of two characteristics: recognition and folding. Riboswitches contain aptamers, which function as biosensors. Upon detection of the signaling molecule, the riboswitch transduces the signal into a genetic decision. The genetic decision is coupled to refolding of the expression platform, which is distinct from, although overlapping with, the aptamer. Early biophysical studies of riboswitches focused on recognition of the ligand by the aptamer-an important consideration for drug design. A mechanistic understanding of ligand-induced riboswitch RNA folding can further enhance riboswitch ligand design, and inform efforts to tune and engineer riboswitches with novel properties. X-ray structures of aptamer/ligand complexes point to mechanisms through which the ligand brings together distal strand segments to form a P1 helix. Transcriptional riboswitches must detect the ligand and form this P1 helix within the timescale of transcription. Depending on the cell's metabolic state and cellular environmental conditions, the folding and genetic outcome may therefore be affected by kinetics of ligand binding, RNA folding, and transcriptional pausing, among other factors. Although some studies of isolated riboswitch aptamers found homogeneous, prefolded conformations, experimental, and theoretical studies point to functional and structural heterogeneity for nascent transcripts. Recently it has been shown that some riboswitch segments, containing the aptamer and partial expression platforms, can form binding-competent conformers that incorporate an incomplete aptamer secondary structure. Consideration of the free energy landscape for riboswitch RNA folding suggests models for how these conformers may act as transition states-facilitating rapid, ligand-mediated aptamer folding.
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Affiliation(s)
- Fareed Aboul-ela
- Center for X-Ray Determination of the Structure of Matter, University of Science and Technology at Zewail City, Giza, Egypt
| | - Wei Huang
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA
| | - Maaly Abd Elrahman
- Center for X-Ray Determination of the Structure of Matter, University of Science and Technology at Zewail City, Giza, Egypt
- Therapeutical Chemistry Department, National Research Center, El Buhouth St., Dokki, Cairo, Egypt
| | - Vamsi Boyapati
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Pan Li
- Department of Biological Sciences, University at Albany-SUNY, Albany, NY, USA
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159
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Abstract
Deciphering AUA codons is a difficult task for organisms, because AUA and AUG specify isoleucine (Ile) and methionine (Met), separately. Each of the other purine-ending sense co-don sets (NNR) specifies a single amino acid in the universal genetic code. In bacteria and archaea, the cytidine derivatives, 2-lysylcytidine (L or lysidine) and 2-agmatinylcytidine (agm(2)C or agmatidine), respectively, are found at the first letter of the anticodon of tRNA(Ile) responsible for AUA codons. These modifications prevent base pairing with G of the third letter of AUG codon, and enable tRNA(Ile) to decipher AUA codon specifically. In addition, these modifications confer a charging ability of tRNA(Ile) with Ile. Despite their similar chemical structures, L and agm(2)C are synthesized by distinctive mechanisms and catalyzed by different classes of enzymes, implying that the analogous decoding systems for AUA codons were established by convergent evolution after the phylogenic split between bacteria and archaea-eukaryotes lineages following divergence from the last universal common ancestor (LUCA).
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Affiliation(s)
- Tsutomu Suzuki
- a Department of Chemistry and Biotechnology; Graduate School of Engineering ; University of Tokyo ; Hongo , Bunkyo-ku , Tokyo , Japan
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160
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Abstract
The bacterial ribosome is a complex macromolecular machine that deciphers the genetic code with remarkable fidelity. During the elongation phase of protein synthesis, the ribosome selects aminoacyl-tRNAs as dictated by the canonical base pairing between the anticodon of the tRNA and the codon of the messenger RNA. The ribosome's participation in tRNA selection is active rather than passive, using conformational changes of conserved bases of 16S rRNA to directly monitor the geometry of codon-anticodon base pairing. The tRNA selection process is divided into an initial selection step and a subsequent proofreading step, with the utilization of two sequential steps increasing the discriminating power of the ribosome far beyond that which could be achieved based on the thermodynamics of codon-anticodon base pairing stability. The accuracy of decoding is impaired by a number of antibiotics and can be either increased or decreased by various mutations in either subunit of the ribosome, in elongation factor Tu, and in tRNA. In this chapter we will review our current understanding of various forces that determine the accuracy of decoding by the bacterial ribosome.
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161
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Shalev M, Rozenberg H, Smolkin B, Nasereddin A, Kopelyanskiy D, Belakhov V, Schrepfer T, Schacht J, Jaffe CL, Adir N, Baasov T. Structural basis for selective targeting of leishmanial ribosomes: aminoglycoside derivatives as promising therapeutics. Nucleic Acids Res 2015; 43:8601-13. [PMID: 26264664 PMCID: PMC4787808 DOI: 10.1093/nar/gkv821] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/01/2015] [Indexed: 11/13/2022] Open
Abstract
Leishmaniasis comprises an array of diseases caused by pathogenic species of Leishmania, resulting in a spectrum of mild to life-threatening pathologies. Currently available therapies for leishmaniasis include a limited selection of drugs. This coupled with the rather fast emergence of parasite resistance, presents a dire public health concern. Paromomycin (PAR), a broad-spectrum aminoglycoside antibiotic, has been shown in recent years to be highly efficient in treating visceral leishmaniasis (VL)—the life-threatening form of the disease. While much focus has been given to exploration of PAR activities in bacteria, its mechanism of action in Leishmania has received relatively little scrutiny and has yet to be fully deciphered. In the present study we present an X-ray structure of PAR bound to rRNA model mimicking its leishmanial binding target, the ribosomal A-site. We also evaluate PAR inhibitory actions on leishmanial growth and ribosome function, as well as effects on auditory sensory cells, by comparing several structurally related natural and synthetic aminoglycoside derivatives. The results provide insights into the structural elements important for aminoglycoside inhibitory activities and selectivity for leishmanial cytosolic ribosomes, highlighting a novel synthetic derivative, compound 3, as a prospective therapeutic candidate for the treatment of VL.
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Affiliation(s)
- Moran Shalev
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Haim Rozenberg
- Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Boris Smolkin
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Abedelmajeed Nasereddin
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Dmitry Kopelyanskiy
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Valery Belakhov
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Thomas Schrepfer
- Kresge Hearing Research Institute, Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jochen Schacht
- Kresge Hearing Research Institute, Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Charles L Jaffe
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Noam Adir
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Timor Baasov
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
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162
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Nord S, Bhatt MJ, Tükenmez H, Farabaugh PJ, Wikström PM. Mutations of ribosomal protein S5 suppress a defect in late-30S ribosomal subunit biogenesis caused by lack of the RbfA biogenesis factor. RNA (NEW YORK, N.Y.) 2015; 21:1454-1468. [PMID: 26089326 PMCID: PMC4509935 DOI: 10.1261/rna.051383.115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/04/2015] [Indexed: 06/04/2023]
Abstract
The in vivo assembly of ribosomal subunits requires assistance by maturation proteins that are not part of mature ribosomes. One such protein, RbfA, associates with the 30S ribosomal subunits. Loss of RbfA causes cold sensitivity and defects of the 30S subunit biogenesis and its overexpression partially suppresses the dominant cold sensitivity caused by a C23U mutation in the central pseudoknot of 16S rRNA, a structure essential for ribosome function. We have isolated suppressor mutations that restore partially the growth of an RbfA-lacking strain. Most of the strongest suppressor mutations alter one out of three distinct positions in the carboxy-terminal domain of ribosomal protein S5 (S5) in direct contact with helix 1 and helix 2 of the central pseudoknot. Their effect is to increase the translational capacity of the RbfA-lacking strain as evidenced by an increase in polysomes in the suppressed strains. Overexpression of RimP, a protein factor that along with RbfA regulates formation of the ribosome's central pseudoknot, was lethal to the RbfA-lacking strain but not to a wild-type strain and this lethality was suppressed by the alterations in S5. The S5 mutants alter translational fidelity but these changes do not explain consistently their effect on the RbfA-lacking strain. Our genetic results support a role for the region of S5 modified in the suppressors in the formation of the central pseudoknot in 16S rRNA.
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Affiliation(s)
- Stefan Nord
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Monika J Bhatt
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21228, USA
| | - Hasan Tükenmez
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Philip J Farabaugh
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21228, USA
| | - P Mikael Wikström
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
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163
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Xie P. Ribosome utilizes the minimum free energy changes to achieve the highest decoding rate and fidelity. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:022716. [PMID: 26382441 DOI: 10.1103/physreve.92.022716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Indexed: 06/05/2023]
Abstract
The performance of ribosome translation can be characterized by two factors, the translation rate and fidelity. Here, we provide analytical studies of the effect of the near-cognate tRNAs on the two factors. It is shown that the increase of the concentration of the near-cognate tRNAs relative to that of the cognate tRNA has negative effects on the ribosome translation by reducing both the translation rate and the translation fidelity. The effect of the near-cognate ternary complexes on the translation rate results mainly from the initial selection phase, whereas the proofreading phase has a minor effect. By contrast, the effect of the near-cognate ternary complexes on the fidelity results almost equally from the two phases. By using two successive phases, the initial selection and the proofreading, the ribosome can achieve higher translation fidelity than the product of the fidelity when only the initial selection is included and when only the proofreading is included, especially at the large ratio of the concentration of the near-cognate tRNAs compared to that of the cognate tRNA. Moreover, we study the changes of the free energy landscape in the tRNA decoding step. It is found that the rate constants of the tRNA decoding step measured experimentally give the minimum energy changes for the ribosomal complex to attain the optimal performance with both the highest decoding rate and fidelity and/or with the maximum value of the decoding fitness function. This suggests that the ribosome has evolved to utilize the minimum free energy changes gained from the conformational changes of the ribosome, EF-Tu, and tRNA to achieve the optimal performance in the tRNA decoding.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
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164
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Caserta E, Liu LC, Grundy FJ, Henkin TM. Codon-Anticodon Recognition in the Bacillus subtilis glyQS T Box Riboswitch: RNA-DEPENDENT CODON SELECTION OUTSIDE THE RIBOSOME. J Biol Chem 2015; 290:23336-47. [PMID: 26229106 DOI: 10.1074/jbc.m115.673236] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Indexed: 12/28/2022] Open
Abstract
Many amino acid-related genes in Gram-positive bacteria are regulated by the T box riboswitch. The leader RNA of genes in the T box family controls the expression of downstream genes by monitoring the aminoacylation status of the cognate tRNA. Previous studies identified a three-nucleotide codon, termed the "Specifier Sequence," in the riboswitch that corresponds to the amino acid identity of the downstream genes. Pairing of the Specifier Sequence with the anticodon of the cognate tRNA is the primary determinant of specific tRNA recognition. This interaction mimics codon-anticodon pairing in translation but occurs in the absence of the ribosome. The goal of the current study was to determine the effect of a full range of mismatches for comparison with codon recognition in translation. Mutations were individually introduced into the Specifier Sequence of the glyQS leader RNA and tRNA(Gly) anticodon to test the effect of all possible pairing combinations on tRNA binding affinity and antitermination efficiency. The functional role of the conserved purine 3' of the Specifier Sequence was also verifiedin this study. We found that substitutions at the Specifier Sequence resulted in reduced binding, the magnitude of which correlates well with the predicted stability of the RNA-RNA pairing. However, the tolerance for specific mismatches in antitermination was generally different from that during decoding, which reveals a unique tRNA recognition pattern in the T box antitermination system.
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Affiliation(s)
- Enrico Caserta
- From the Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
| | - Liang-Chun Liu
- From the Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
| | - Frank J Grundy
- From the Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
| | - Tina M Henkin
- From the Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
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165
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Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions. Nat Commun 2015. [PMID: 26224058 PMCID: PMC4522699 DOI: 10.1038/ncomms8896] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Dynamic remodelling of intersubunit bridge B2, a conserved RNA domain of the bacterial ribosome connecting helices 44 (h44) and 69 (H69) of the small and large subunit, respectively, impacts translation by controlling intersubunit rotation. Here we show that aminoglycosides chemically related to neomycin—paromomycin, ribostamycin and neamine—each bind to sites within h44 and H69 to perturb bridge B2 and affect subunit rotation. Neomycin and paromomycin, which only differ by their ring-I 6′-polar group, drive subunit rotation in opposite directions. This suggests that their distinct actions hinge on the 6′-substituent and the drug's net positive charge. By solving the crystal structure of the paromomycin–ribosome complex, we observe specific contacts between the apical tip of H69 and the 6′-hydroxyl on paromomycin from within the drug's canonical h44-binding site. These results indicate that aminoglycoside actions must be framed in the context of bridge B2 and their regulation of subunit rotation. Ratchet-like rotation of the small ribosomal subunit relative to the large is essential to the translation mechanism. Here, the authors show that chemically related aminoglycoside antibiotics have distinct impacts on the nature and rate of the subunit rotation process within the intact ribosome.
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166
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The importance of codon–anticodon interactions in translation elongation. Biochimie 2015; 114:72-9. [DOI: 10.1016/j.biochi.2015.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 04/16/2015] [Indexed: 11/16/2022]
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167
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Dishler AL, McMichael EL, Serra MJ. Determination of the secondary structure of group II bulge loops using the fluorescent probe 2-aminopurine. RNA (NEW YORK, N.Y.) 2015; 21:975-984. [PMID: 25805856 PMCID: PMC4408803 DOI: 10.1261/rna.048306.114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/17/2015] [Indexed: 06/04/2023]
Abstract
Eleven RNA hairpins containing 2-aminopurine (2-AP) in either base-paired or single nucleotide bulge loop positions were optically melted in 1 M NaCl; and, the thermodynamic parameters ΔH°, ΔS°, ΔG°37, and TM for each hairpin were determined. Substitution of 2-AP for an A (adenosine) at a bulge position (where either the 2-AP or A is the bulge) in the stem of a hairpin, does not affect the stability of the hairpin. For group II bulge loops such as AA/U, where there is ambiguity as to which of the A residues is paired with the U, hairpins with 2-AP substituted for either the 5' or 3' position in the hairpin stem have similar stability. Fluorescent melts were performed to monitor the environment of the 2-AP. When the 2-AP was located distal to the hairpin loop on either the 5' or 3' side of the hairpin stem, the change in fluorescent intensity upon heating was indicative of an unpaired nucleotide. A database of phylogenetically determined RNA secondary structures was examined to explore the presence of naturally occurring bulge loops embedded within a hairpin stem. The distribution of bulge loops is discussed and related to the stability of hairpin structures.
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Affiliation(s)
- Abigael L Dishler
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
| | | | - Martin J Serra
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
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168
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Structural Insights into tRNA Dynamics on the Ribosome. Int J Mol Sci 2015; 16:9866-95. [PMID: 25941930 PMCID: PMC4463622 DOI: 10.3390/ijms16059866] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 11/17/2022] Open
Abstract
High-resolution structures at different stages, as well as biochemical, single molecule and computational approaches have highlighted the elasticity of tRNA molecules when bound to the ribosome. It is well acknowledged that the inherent structural flexibility of the tRNA lies at the heart of the protein synthesis process. Here, we review the recent advances and describe considerations that the conformational changes of the tRNA molecules offer about the mechanisms grounded in translation.
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169
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Saito K, Ito K. Genetic analysis of L123 of the tRNA-mimicking eukaryote release factor eRF1, an amino acid residue critical for discrimination of stop codons. Nucleic Acids Res 2015; 43:4591-601. [PMID: 25897120 PMCID: PMC4482090 DOI: 10.1093/nar/gkv376] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/09/2015] [Indexed: 11/18/2022] Open
Abstract
In eukaryotes, the tRNA-mimicking polypeptide-chain release factor, eRF1, decodes stop codons on the ribosome in a complex with eRF3; this complex exhibits striking structural similarity to the tRNA–eEF1A–GTP complex. Although amino acid residues or motifs of eRF1 that are critical for stop codon discrimination have been identified, the details of the molecular mechanisms involved in the function of the ribosomal decoding site remain obscure. Here, we report analyses of the position-123 amino acid of eRF1 (L123 in Saccharomyces cerevisiae eRF1), a residue that is phylogenetically conserved among species with canonical and variant genetic codes. In vivo readthrough efficiency analysis and genetic growth complementation analysis of the residue-123 systematic mutants suggested that this amino acid functions in stop codon discrimination in a manner coupled with eRF3 binding, and distinctive from previously reported adjacent residues. Furthermore, aminoglycoside antibiotic sensitivity analysis and ribosomal docking modeling of eRF1 in a quasi-A/T state suggested a functional interaction between the side chain of L123 and ribosomal residues critical for codon recognition in the decoding site, as a molecular explanation for coupling with eRF3. Our results provide insights into the molecular mechanisms underlying stop codon discrimination by a tRNA-mimicking protein on the ribosome.
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Affiliation(s)
- Kazuki Saito
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-city, Chiba 277-8562, Japan
| | - Koichi Ito
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-city, Chiba 277-8562, Japan
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170
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Cui Z, Stein V, Tnimov Z, Mureev S, Alexandrov K. Semisynthetic tRNA complement mediates in vitro protein synthesis. J Am Chem Soc 2015; 137:4404-13. [PMID: 25822136 DOI: 10.1021/ja5131963] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Genetic code expansion is a key objective of synthetic biology and protein engineering. Most efforts in this direction are focused on reassigning termination or decoding quadruplet codons. While the redundancy of genetic code provides a large number of potentially reassignable codons, their utility is diminished by the inevitable interaction with cognate aminoacyl-tRNAs. To address this problem, we sought to establish an in vitro protein synthesis system with a simplified synthetic tRNA complement, thereby orthogonalizing some of the sense codons. This quantitative in vitro peptide synthesis assay allowed us to analyze the ability of synthetic tRNAs to decode all of 61 sense codons. We observed that, with the exception of isoacceptors for Asn, Glu, and Ile, the majority of 48 synthetic Escherichia coli tRNAs could support protein translation in the cell-free system. We purified to homogeneity functional Asn, Glu, and Ile tRNAs from the native E. coli tRNA mixture, and by combining them with synthetic tRNAs, we formulated a semisynthetic tRNA complement for all 20 amino acids. We further demonstrated that this tRNA complement could restore the protein translation activity of tRNA-depleted E. coli lysate to a level comparable to that of total native tRNA. To confirm that the developed system could efficiently synthesize long polypeptides, we expressed three different sequences coding for superfolder GFP. This novel semisynthetic translation system is a powerful tool for tRNA engineering and potentially enables the reassignment of at least 9 sense codons coding for Ser, Arg, Leu, Pro, Thr, and Gly.
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Affiliation(s)
- Zhenling Cui
- Institute for Molecular Bioscience and the Australian Institute for Bioengeneering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Viktor Stein
- Institute for Molecular Bioscience and the Australian Institute for Bioengeneering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Zakir Tnimov
- Institute for Molecular Bioscience and the Australian Institute for Bioengeneering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Sergey Mureev
- Institute for Molecular Bioscience and the Australian Institute for Bioengeneering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Kirill Alexandrov
- Institute for Molecular Bioscience and the Australian Institute for Bioengeneering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
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171
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Graifer D, Karpova G. Interaction of tRNA with eukaryotic ribosome. Int J Mol Sci 2015; 16:7173-94. [PMID: 25830484 PMCID: PMC4425011 DOI: 10.3390/ijms16047173] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/20/2015] [Accepted: 03/23/2015] [Indexed: 11/16/2022] Open
Abstract
This paper is a review of currently available data concerning interactions of tRNAs with the eukaryotic ribosome at various stages of translation. These data include the results obtained by means of cryo-electron microscopy and X-ray crystallography applied to various model ribosomal complexes, site-directed cross-linking with the use of tRNA derivatives bearing chemically or photochemically reactive groups in the CCA-terminal fragment and chemical probing of 28S rRNA in the region of the peptidyl transferase center. Similarities and differences in the interactions of tRNAs with prokaryotic and eukaryotic ribosomes are discussed with concomitant consideration of the extent of resemblance between molecular mechanisms of translation in eukaryotes and bacteria.
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Affiliation(s)
- Dmitri Graifer
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, pr. Lavrentieva, 8, 630090 Novosibirsk, Russia.
- Department of Natural Sciences, Novosibirsk State University, ul. Pirogova, 2, 630090 Novosibirsk, Russia.
| | - Galina Karpova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, pr. Lavrentieva, 8, 630090 Novosibirsk, Russia.
- Department of Natural Sciences, Novosibirsk State University, ul. Pirogova, 2, 630090 Novosibirsk, Russia.
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172
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Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes. Nature 2015; 519:315-20. [PMID: 25762137 DOI: 10.1038/nature14227] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/09/2015] [Indexed: 11/08/2022]
Abstract
Rare tautomeric and anionic nucleobases are believed to have fundamental biological roles, but their prevalence and functional importance has remained elusive because they exist transiently, in low abundance, and involve subtle movements of protons that are difficult to visualize. Using NMR relaxation dispersion, we show here that wobble dG•dT and rG•rU mispairs in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-populated Watson-Crick-like mispairs that are stabilized by rare enolic or anionic bases. These mispairs can evade Watson-Crick fidelity checkpoints and form with probabilities (10(-3) to 10(-5)) that strongly imply a universal role in replication and translation errors. Our results indicate that rare tautomeric and anionic bases are widespread in nucleic acids, expanding their structural and functional complexity beyond that attainable with canonical bases.
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173
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Carvalho ATP, Szeler K, Vavitsas K, Åqvist J, Kamerlin SCL. Modeling the mechanisms of biological GTP hydrolysis. Arch Biochem Biophys 2015; 582:80-90. [PMID: 25731854 DOI: 10.1016/j.abb.2015.02.027] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/19/2015] [Accepted: 02/21/2015] [Indexed: 01/11/2023]
Abstract
Enzymes that hydrolyze GTP are currently in the spotlight, due to their molecular switch mechanism that controls many cellular processes. One of the best-known classes of these enzymes are small GTPases such as members of the Ras superfamily, which catalyze the hydrolysis of the γ-phosphate bond in GTP. In addition, the availability of an increasing number of crystal structures of translational GTPases such as EF-Tu and EF-G have made it possible to probe the molecular details of GTP hydrolysis on the ribosome. However, despite a wealth of biochemical, structural and computational data, the way in which GTP hydrolysis is activated and regulated is still a controversial topic and well-designed simulations can play an important role in resolving and rationalizing the experimental data. In this review, we discuss the contributions of computational biology to our understanding of GTP hydrolysis on the ribosome and in small GTPases.
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Affiliation(s)
- Alexandra T P Carvalho
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Klaudia Szeler
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Konstantinos Vavitsas
- Copenhagen Plant Science Centre (CPSC), Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Johan Åqvist
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24 Uppsala, Sweden.
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174
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Fan Y, Wu J, Ung MH, De Lay N, Cheng C, Ling J. Protein mistranslation protects bacteria against oxidative stress. Nucleic Acids Res 2015; 43:1740-8. [PMID: 25578967 PMCID: PMC4330365 DOI: 10.1093/nar/gku1404] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Accurate flow of genetic information from DNA to protein requires faithful translation. An increased level of translational errors (mistranslation) has therefore been widely considered harmful to cells. Here we demonstrate that surprisingly, moderate levels of mistranslation indeed increase tolerance to oxidative stress in Escherichia coli. Our RNA sequencing analyses revealed that two antioxidant genes katE and osmC, both controlled by the general stress response activator RpoS, were upregulated by a ribosomal error-prone mutation. Mistranslation-induced tolerance to hydrogen peroxide required rpoS, katE and osmC. We further show that both translational and post-translational regulation of RpoS contribute to peroxide tolerance in the error-prone strain, and a small RNA DsrA, which controls translation of RpoS, is critical for the improved tolerance to oxidative stress through mistranslation. Our work thus challenges the prevailing view that mistranslation is always detrimental, and provides a mechanism by which mistranslation benefits bacteria under stress conditions.
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Affiliation(s)
- Yongqiang Fan
- Department of Microbiology and Molecular Genetics, Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Jiang Wu
- Department of Microbiology and Molecular Genetics, Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Matthew H Ung
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Nicholas De Lay
- Department of Microbiology and Molecular Genetics, Medical School, University of Texas Health Science Center, Houston, TX 77030, USA Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Chao Cheng
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, Medical School, University of Texas Health Science Center, Houston, TX 77030, USA Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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175
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Investigating Bacterial Protein Synthesis Using Systems Biology Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:21-40. [PMID: 26621460 DOI: 10.1007/978-3-319-23603-2_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein synthesis is essential for bacterial growth and survival. Its study in Escherichia coli helped uncover features conserved among bacteria as well as universally. The pattern of discovery and the identification of some of the longest-known components of the protein synthesis machinery, including the ribosome itself, tRNAs, and translation factors proceeded through many stages of successively more refined biochemical purifications, finally culminating in the isolation to homogeneity, identification, and mapping of the smallest unit required for performing the given function. These early studies produced a wealth of information. However, many unknowns remained. Systems biology approaches provide an opportunity to investigate protein synthesis from a global perspective, overcoming the limitations of earlier ad hoc methods to gain unprecedented insights. This chapter reviews innovative systems biology approaches, with an emphasis on those designed specifically for investigating the protein synthesis machinery in E. coli.
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176
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Another look at mutations in ribosomal protein S4 lends strong support to the domain closure model. J Bacteriol 2014; 197:1014-6. [PMID: 25548248 DOI: 10.1128/jb.02579-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Ribosomes employ a "kinetic discrimination" mechanism, in which correct substrates are incorporated more rapidly than incorrect ones. The structural basis of this mechanism may involve 30S domain closure, a global conformational change that coincides with codon recognition. In a direct screen for fidelity-altering mutations, Agarwal and coworkers (D. Agarwal, D. Kamath, S. T. Gregory, and M. O'Connor, J Bacteriol 197:1017-1025, 2015, doi:10.1128/JB.02485-14) isolated mutations that progressively truncate the C terminus of S4. All of these promote miscoding and undoubtedly destabilize the S4-S5 interface, consistent with the domain closure model.
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177
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Abstract
Ribosomal proteins S4 and S5 participate in the decoding and assembly processes on the ribosome and the interaction with specific antibiotic inhibitors of translation. Many of the characterized mutations affecting these proteins decrease the accuracy of translation, leading to a ribosomal-ambiguity phenotype. Structural analyses of ribosomal complexes indicate that the tRNA selection pathway involves a transition between the closed and open conformations of the 30S ribosomal subunit and requires disruption of the interface between the S4 and S5 proteins. In agreement with this observation, several of the mutations that promote miscoding alter residues located at the S4-S5 interface. Here, the Escherichia coli rpsD and rpsE genes encoding the S4 and S5 proteins were targeted for mutagenesis and screened for accuracy-altering mutations. While a majority of the 38 mutant proteins recovered decrease the accuracy of translation, error-restrictive mutations were also recovered; only a minority of the mutant proteins affected rRNA processing, ribosome assembly, or interactions with antibiotics. Several of the mutations affect residues at the S4-S5 interface. These include five nonsense mutations that generate C-terminal truncations of S4. These truncations are predicted to destabilize the S4-S5 interface and, consistent with the domain closure model, all have ribosomal-ambiguity phenotypes. A substantial number of the mutations alter distant locations and conceivably affect tRNA selection through indirect effects on the S4-S5 interface or by altering interactions with adjacent ribosomal proteins and 16S rRNA.
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178
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Gumbel M, Fimmel E, Danielli A, Strüngmann L. On models of the genetic code generated by binary dichotomic algorithms. Biosystems 2014; 128:9-18. [PMID: 25530514 DOI: 10.1016/j.biosystems.2014.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/24/2014] [Accepted: 12/16/2014] [Indexed: 11/29/2022]
Abstract
In this paper we introduce the concept of a BDA-generated model of the genetic code which is based on binary dichotomic algorithms (BDAs). A BDA-generated model is based on binary dichotomic algorithms (BDAs). Such a BDA partitions the set of 64 codons into two disjoint classes of size 32 each and provides a generalization of known partitions like the Rumer dichotomy. We investigate what partitions can be generated when a set of different BDAs is applied sequentially to the set of codons. The search revealed that these models are able to generate code tables with very different numbers of classes ranging from 2 to 64. We have analyzed whether there are models that map the codons to their amino acids. A perfect matching is not possible. However, we present models that describe the standard genetic code with only few errors. There are also models that map all 64 codons uniquely to 64 classes showing that BDAs can be used to identify codons precisely. This could serve as a basis for further mathematical analysis using coding theory, for example. The hypothesis that BDAs might reflect a molecular mechanism taking place in the decoding center of the ribosome is discussed. The scan demonstrated that binary dichotomic partitions are able to model different aspects of the genetic code very well. The search was performed with our tool Beady-A. This software is freely available at http://mi.informatik.hs-mannheim.de/beady-a. It requires a JVM version 6 or higher.
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Affiliation(s)
- Markus Gumbel
- Mannheim University of Applied Sciences, Institute for Medical Informatics, Paul-Wittsack-Straße 10, D-68163 Mannheim, Germany.
| | - Elena Fimmel
- Mannheim University of Applied Sciences, Institute for Applied Mathematics, Paul-Wittsack-Straße 10, D-68163 Mannheim, Germany.
| | - Alberto Danielli
- University of Bologna, Department of Pharmacy and Biotechnology, Via Irnerio 42, 40126 Bologna, Italy.
| | - Lutz Strüngmann
- Mannheim University of Applied Sciences, Institute for Applied Mathematics, Paul-Wittsack-Straße 10, D-68163 Mannheim, Germany.
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179
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Fagan CE, Maehigashi T, Dunkle JA, Miles SJ, Dunham CM. Structural insights into translational recoding by frameshift suppressor tRNASufJ. RNA (NEW YORK, N.Y.) 2014; 20:1944-54. [PMID: 25352689 PMCID: PMC4238358 DOI: 10.1261/rna.046953.114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 09/02/2014] [Indexed: 05/25/2023]
Abstract
The three-nucleotide mRNA reading frame is tightly regulated during translation to ensure accurate protein expression. Translation errors that lead to aberrant protein production can result from the uncoupled movement of the tRNA in either the 5' or 3' direction on mRNA. Here, we report the biochemical and structural characterization of +1 frameshift suppressor tRNA(SufJ), a tRNA known to decode four, instead of three, nucleotides. Frameshift suppressor tRNA(SufJ) contains an insertion 5' to its anticodon, expanding the anticodon loop from seven to eight nucleotides. Our results indicate that the expansion of the anticodon loop of either ASL(SufJ) or tRNA(SufJ) does not affect its affinity for the A site of the ribosome. Structural analyses of both ASL(SufJ) and ASL(Thr) bound to the Thermus thermophilus 70S ribosome demonstrate both ASLs decode in the zero frame. Although the anticodon loop residues 34-37 are superimposable with canonical seven-nucleotide ASLs, the single C31.5 insertion between nucleotides 31 and 32 in ASL(SufJ) imposes a conformational change of the anticodon stem, that repositions and tilts the ASL toward the back of the A site. Further modeling analyses reveal that this tilting would cause a distortion in full-length A-site tRNA(SufJ) during tRNA selection and possibly impede gripping of the anticodon stem by 16S rRNA nucleotides in the P site. Together, these data implicate tRNA distortion as a major driver of noncanonical translation events such as frameshifting.
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MESH Headings
- Anticodon/genetics
- Anticodon/ultrastructure
- Crystallography, X-Ray
- Escherichia coli
- Genes, Suppressor
- Nucleic Acid Conformation
- Nucleotides/chemistry
- Nucleotides/genetics
- Protein Biosynthesis/genetics
- RNA, Messenger/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/ultrastructure
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/ultrastructure
- Ribosomes/genetics
- Thermus thermophilus/genetics
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Affiliation(s)
- Crystal E Fagan
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Tatsuya Maehigashi
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Jack A Dunkle
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Stacey J Miles
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Christine M Dunham
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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180
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Simms CL, Hudson BH, Mosior JW, Rangwala AS, Zaher HS. An active role for the ribosome in determining the fate of oxidized mRNA. Cell Rep 2014; 9:1256-64. [PMID: 25456128 DOI: 10.1016/j.celrep.2014.10.042] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/23/2014] [Accepted: 10/15/2014] [Indexed: 11/30/2022] Open
Abstract
Chemical damage to RNA affects its functional properties and thus may pose a significant hurdle to the translational apparatus; however, the effects of damaged mRNA on the speed and accuracy of the decoding process and their interplay with quality-control processes are not known. Here, we systematically explore the effects of oxidative damage on the decoding process using a well-defined bacterial in vitro translation system. We find that the oxidative lesion 8-oxoguanosine (8-oxoG) reduces the rate of peptide-bond formation by more than three orders of magnitude independent of its position within the codon. Interestingly, 8-oxoG had little effect on the fidelity of the selection process, suggesting that the modification stalls the translational machinery. Consistent with these findings, 8-oxoG mRNAs were observed to accumulate and associate with polyribosomes in yeast strains in which no-go decay is compromised. Our data provide compelling evidence that mRNA-surveillance mechanisms have evolved to cope with damaged mRNA.
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Affiliation(s)
- Carrie L Simms
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Benjamin H Hudson
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - John W Mosior
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Ali S Rangwala
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Hani S Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
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181
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Panecka J, Mura C, Trylska J. Interplay of the bacterial ribosomal A-site, S12 protein mutations and paromomycin binding: a molecular dynamics study. PLoS One 2014; 9:e111811. [PMID: 25379961 PMCID: PMC4224418 DOI: 10.1371/journal.pone.0111811] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 10/07/2014] [Indexed: 12/28/2022] Open
Abstract
The conformational properties of the aminoacyl-tRNA binding site (A-site), and its surroundings in the Escherichia coli 30S ribosomal subunit, are of great relevance in designing antibacterial agents. The 30S subunit A-site is near ribosomal protein S12, which neighbors helices h27 and H69; this latter helix, of the 50S subunit, is a functionally important component of an intersubunit bridge. Experimental work has shown that specific point mutations in S12 (K42A, R53A) yield hyper-accurate ribosomes, which in turn confers resistance to the antibiotic 'paromomycin' (even when this aminoglycoside is bound to the A-site). Suspecting that these effects can be elucidated in terms of the local atomic interactions and detailed dynamics of this region of the bacterial ribosome, we have used molecular dynamics simulations to explore the motion of a fragment of the E. coli ribosome, including the A-site. We found that the ribosomal regions surrounding the A-site modify the conformational space of the flexible A-site adenines 1492/93. Specifically, we found that A-site mobility is affected by stacking interactions between adenines A1493 and A1913, and by contacts between A1492 and a flexible side-chain (K43) from the S12 protein. In addition, our simulations reveal possible indirect pathways by which the R53A and K42A mutations in S12 are coupled to the dynamical properties of the A-site. Our work extends what is known about the atomistic dynamics of the A-site, and suggests possible links between the biological effects of hyper-accurate mutations in the S12 protein and conformational properties of the ribosome; the implications for S12 dynamics help elucidate how the miscoding effects of paromomycin may be evaded in antibiotic-resistant mutants of the bacterial ribosome.
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Affiliation(s)
- Joanna Panecka
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Warsaw, Poland
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
| | - Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States of America
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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182
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Satpati P, Åqvist J. Why base tautomerization does not cause errors in mRNA decoding on the ribosome. Nucleic Acids Res 2014; 42:12876-84. [PMID: 25352546 PMCID: PMC4227757 DOI: 10.1093/nar/gku1044] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The structure of the genetic code implies strict Watson–Crick base pairing in the first two codon positions, while the third position is known to be degenerate, thus allowing wobble base pairing. Recent crystal structures of near-cognate tRNAs accommodated into the ribosomal A-site, however, show canonical geometry even with first and second position mismatches. This immediately raises the question of whether these structures correspond to tautomerization of the base pairs. Further, if unusual tautomers are indeed trapped why do they not cause errors in decoding? Here, we use molecular dynamics free energy calculations of ribosomal complexes with cognate and near-cognate tRNAs to analyze the structures and energetics of G-U mismatches in the first two codon positions. We find that the enol tautomer of G is almost isoenergetic with the corresponding ketone in the first position, while it is actually more stable in the second position. Tautomerization of U, on the other hand is highly penalized. The presence of the unusual enol form of G thus explains the crystallographic observations. However, the calculations also show that this tautomer does not cause high codon reading error frequencies, as the resulting tRNA binding free energies are significantly higher than for the cognate complex.
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Affiliation(s)
- Priyadarshi Satpati
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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183
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Budkevich TV, Giesebrecht J, Behrmann E, Loerke J, Ramrath DJF, Mielke T, Ismer J, Hildebrand PW, Tung CS, Nierhaus KH, Sanbonmatsu KY, Spahn CMT. Regulation of the mammalian elongation cycle by subunit rolling: a eukaryotic-specific ribosome rearrangement. Cell 2014; 158:121-31. [PMID: 24995983 DOI: 10.1016/j.cell.2014.04.044] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 02/24/2014] [Accepted: 04/18/2014] [Indexed: 11/15/2022]
Abstract
The extent to which bacterial ribosomes and the significantly larger eukaryotic ribosomes share the same mechanisms of ribosomal elongation is unknown. Here, we present subnanometer resolution cryoelectron microscopy maps of the mammalian 80S ribosome in the posttranslocational state and in complex with the eukaryotic eEF1A⋅Val-tRNA⋅GMPPNP ternary complex, revealing significant differences in the elongation mechanism between bacteria and mammals. Surprisingly, and in contrast to bacterial ribosomes, a rotation of the small subunit around its long axis and orthogonal to the well-known intersubunit rotation distinguishes the posttranslocational state from the classical pretranslocational state ribosome. We term this motion "subunit rolling." Correspondingly, a mammalian decoding complex visualized in substates before and after codon recognition reveals structural distinctions from the bacterial system. These findings suggest how codon recognition leads to GTPase activation in the mammalian system and demonstrate that in mammalia subunit rolling occurs during tRNA selection.
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Affiliation(s)
- Tatyana V Budkevich
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Max-Planck Institut für Molekulare Genetik, Abteilung Vingron, AG Ribosomen, 14195 Berlin, Ihnestraße 73, Germany; Institute of Molecular Biology and Genetics, Group of Protein Biosynthesis, 03143 Kiev, Ukraine
| | - Jan Giesebrecht
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Elmar Behrmann
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - David J F Ramrath
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Thorsten Mielke
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Max-Planck Institut für Molekulare Genetik, UltraStrukturNetzwerk, 14195 Berlin, Ihnestraße 73, Germany
| | - Jochen Ismer
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Peter W Hildebrand
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Chang-Shung Tung
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, MK710, Los Alamos, NM 87545, USA
| | - Knud H Nierhaus
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Max-Planck Institut für Molekulare Genetik, Abteilung Vingron, AG Ribosomen, 14195 Berlin, Ihnestraße 73, Germany
| | - Karissa Y Sanbonmatsu
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, MK710, Los Alamos, NM 87545, USA; New Mexico Consortium, 4200 West Jemez Road, Suite 301, Los Alamos, New Mexico 87544, USA
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
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184
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Structural basis for the inhibition of the eukaryotic ribosome. Nature 2014; 513:517-22. [DOI: 10.1038/nature13737] [Citation(s) in RCA: 349] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/06/2014] [Indexed: 11/08/2022]
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185
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Miller MR, Buskirk AR. The SmpB C-terminal tail helps tmRNA to recognize and enter stalled ribosomes. Front Microbiol 2014; 5:462. [PMID: 25228900 PMCID: PMC4151336 DOI: 10.3389/fmicb.2014.00462] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 08/14/2014] [Indexed: 11/13/2022] Open
Abstract
In bacteria, transfer-messenger RNA (tmRNA) and SmpB comprise the most common and effective system for rescuing stalled ribosomes. Ribosomes stall on mRNA transcripts lacking stop codons and are rescued as the defective mRNA is swapped for the tmRNA template in a process known as trans-translation. The tmRNA–SmpB complex is recruited to the ribosome independent of a codon–anticodon interaction. Given that the ribosome uses robust discriminatory mechanisms to select against non-cognate tRNAs during canonical decoding, it has been hard to explain how this can happen. Recent structural and biochemical studies show that SmpB licenses tmRNA entry through its interactions with the decoding center and mRNA channel. In particular, the C-terminal tail of SmpB promotes both EFTu activation and accommodation of tmRNA, the former through interactions with 16S rRNA nucleotide G530 and the latter through interactions with the mRNA channel downstream of the A site. Here we present a detailed model of the earliest steps in trans-translation, and in light of these mechanistic considerations, revisit the question of how tmRNA preferentially reacts with stalled, non-translating ribosomes.
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Affiliation(s)
- Mickey R Miller
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT USA
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD USA
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186
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Sanbonmatsu KY. Flipping through the Genetic Code: New Developments in Discrimination between Cognate and Near-Cognate tRNAs and the Effect of Antibiotics. J Mol Biol 2014; 426:3197-3200. [DOI: 10.1016/j.jmb.2014.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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187
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Phenotypic interactions among mutations in a Thermus thermophilus 16S rRNA gene detected with genetic selections and experimental evolution. J Bacteriol 2014; 196:3776-83. [PMID: 25157075 DOI: 10.1128/jb.02104-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During protein synthesis, the ribosome undergoes conformational transitions between functional states, requiring communication between distant structural elements of the ribosome. Despite advances in ribosome structural biology, identifying the protein and rRNA residues governing these transitions remains a significant challenge. Such residues can potentially be identified genetically, given the predicted deleterious effects of mutations stabilizing the ribosome in discrete conformations and the expected ameliorating effects of second-site compensatory mutations. In this study, we employed genetic selections and experimental evolution to identify interacting mutations in the ribosome of the thermophilic bacterium Thermus thermophilus. By direct genetic selections, we identified mutations in 16S rRNA conferring a streptomycin dependence phenotype and from these derived second-site suppressor mutations relieving dependence. Using experimental evolution of streptomycin-independent pseudorevertants, we identified additional compensating mutations. Similar mutations could be evolved from slow-growing streptomycin-resistant mutants. While some mutations arose close to the site of the original mutation in the three-dimensional structure of the 30S ribosomal subunit and probably act directly by compensating for local structural distortions, the locations of others are consistent with long-range communication between specific structural elements within the ribosome.
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188
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EF-G catalyzes tRNA translocation by disrupting interactions between decoding center and codon-anticodon duplex. Nat Struct Mol Biol 2014; 21:817-24. [PMID: 25108354 DOI: 10.1038/nsmb.2869] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 07/11/2014] [Indexed: 02/01/2023]
Abstract
During translation, elongation factor G (EF-G) catalyzes the translocation of tRNA2-mRNA inside the ribosome. Translocation is coupled to a cycle of conformational rearrangements of the ribosomal machinery, and how EF-G initiates translocation remains unresolved. Here we performed systematic mutagenesis of Escherichia coli EF-G and analyzed inhibitory single-site mutants of EF-G that preserved pretranslocation (Pre)-state ribosomes with tRNAs in A/P and P/E sites (Pre-EF-G). Our results suggest that the interactions between the decoding center and the codon-anticodon duplex constitute the barrier for translocation. Catalysis of translocation by EF-G involves the factor's highly conserved loops I and II at the tip of domain IV, which disrupt the hydrogen bonds between the decoding center and the duplex to release the latter, hence inducing subsequent translocation events, namely 30S head swiveling and tRNA2-mRNA movement on the 30S subunit.
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189
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Satpati P, Bauer P, Åqvist J. Energetic Tuning by tRNA Modifications Ensures Correct Decoding of Isoleucine and Methionine on the Ribosome. Chemistry 2014; 20:10271-5. [DOI: 10.1002/chem.201404016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Indexed: 11/11/2022]
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190
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Flipping of the ribosomal A-site adenines provides a basis for tRNA selection. J Mol Biol 2014; 426:3201-3213. [PMID: 24813122 DOI: 10.1016/j.jmb.2014.04.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/13/2014] [Accepted: 04/14/2014] [Indexed: 11/22/2022]
Abstract
Ribosomes control the missense error rate of ~10(-4) during translation though quantitative contributions of individual mechanistic steps of the conformational changes yet to be fully determined. Biochemical and biophysical studies led to a qualitative tRNA selection model in which ribosomal A-site residues A1492 and A1493 (A1492/3) flip out in response to cognate tRNA binding, promoting the subsequent reactions, but not in the case of near-cognate or non-cognate tRNA. However, this model was recently questioned by X-ray structures revealing conformations of extrahelical A1492/3 and domain closure of the decoding center in both cognate and near-cognate tRNA bound ribosome complexes, suggesting that the non-specific flipping of A1492/3 has no active role in tRNA selection. We explore this question by carrying out molecular dynamics simulations, aided with fluorescence and NMR experiments, to probe the free energy cost of extrahelical flipping of 1492/3 and the strain energy associated with domain conformational change. Our rigorous calculations demonstrate that the A1492/3 flipping is indeed a specific response to the binding of cognate tRNA, contributing 3kcal/mol to the specificity of tRNA selection. Furthermore, the different A-minor interactions in cognate and near-cognate complexes propagate into the conformational strain and contribute another 4kcal/mol in domain closure. The recent structure of ribosome with features of extrahelical A1492/3 and closed domain in near-cognate complex is reconciled by possible tautomerization of the wobble base pair in mRNA-tRNA. These results quantitatively rationalize other independent experimental observations and explain the ribosomal discrimination mechanism of selecting cognate versus near-cognate tRNA.
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191
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Wald N, Margalit H. Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics. Nucleic Acids Res 2014; 42:6552-66. [PMID: 24782525 PMCID: PMC4041420 DOI: 10.1093/nar/gku245] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Decoding of all codons can be achieved by a subset of tRNAs. In bacteria, certain tRNA species are mandatory, while others are auxiliary and are variably used. It is currently unknown how this variability has evolved and whether it provides an adaptive advantage. Here we shed light on the subset of auxiliary tRNAs, using genomic data from 319 bacteria. By reconstructing the evolution of tRNAs we show that the auxiliary tRNAs are highly dynamic, being frequently gained and lost along the phylogenetic tree, with a clear dominance of loss events for most auxiliary tRNA species. We reveal distinct co-gain and co-loss patterns for subsets of the auxiliary tRNAs, suggesting that they are subjected to the same selection forces. Controlling for phylogenetic dependencies, we find that the usage of these tRNA species is positively correlated with GC content and may derive directly from nucleotide bias or from preference of Watson-Crick codon-anticodon interactions. Our results highlight the highly dynamic nature of these tRNAs and their complicated balance with codon usage.
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Affiliation(s)
- Naama Wald
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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192
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Shimizu Y. Biochemical aspects of bacterial strategies for handling the incomplete translation processes. Front Microbiol 2014; 5:170. [PMID: 24782856 PMCID: PMC3989591 DOI: 10.3389/fmicb.2014.00170] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/28/2014] [Indexed: 11/13/2022] Open
Abstract
During protein synthesis in cells, translating ribosomes may encounter abnormal situations that lead to retention of immature peptidyl-tRNA on the ribosome due to failure of suitable termination processes. Bacterial cells handle such situations by employing three systems that rescue the stalled translation machinery. The transfer messenger RNA/small protein B (tmRNA/SmpB) system, also called the trans-translation system, rescues stalled ribosomes by initiating template switching from the incomplete mRNA to the short open reading frame of tmRNA, leading to the production of a protein containing a C-terminal tag that renders it susceptible to proteolysis. The ArfA/RF2 and ArfB systems rescue stalled ribosomes directly by hydrolyzing the immature peptidyl-tRNA remaining on the ribosome. Here, the biochemical aspects of these systems, as clarified by recent studies, are reviewed.
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Affiliation(s)
- Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, Quantitative Biology Center - RIKEN Kobe, Hyogo, Japan
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193
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McClory SP, Devaraj A, Fredrick K. Distinct functional classes of ram mutations in 16S rRNA. RNA (NEW YORK, N.Y.) 2014; 20:496-504. [PMID: 24572811 PMCID: PMC3964911 DOI: 10.1261/rna.043331.113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 01/20/2014] [Indexed: 06/03/2023]
Abstract
During decoding, the ribosome selects the correct (cognate) aminoacyl-tRNA (aa-tRNA) from a large pool of incorrect aa-tRNAs through a two-stage mechanism. In the initial selection stage, aa-tRNA is delivered to the ribosome as part of a ternary complex with elongation factor EF-Tu and GTP. Interactions between codon and anticodon lead to activation of the GTPase domain of EF-Tu and GTP hydrolysis. Then, in the proofreading stage, aa-tRNA is released from EF-Tu and either moves fully into the A/A site (a step termed "accommodation") or dissociates from the ribosome. Cognate codon-anticodon pairing not only stabilizes aa-tRNA at both stages of decoding but also stimulates GTP hydrolysis and accommodation, allowing the process to be both accurate and fast. In previous work, we isolated a number of ribosomal ambiguity (ram) mutations in 16S rRNA, implicating particular regions of the ribosome in the mechanism of decoding. Here, we analyze a representative subset of these mutations with respect to initial selection, proofreading, RF2-dependent termination, and overall miscoding in various contexts. We find that mutations that disrupt inter-subunit bridge B8 increase miscoding in a general way, causing defects in both initial selection and proofreading. Mutations in or near the A site behave differently, increasing miscoding in a codon-anticodon-dependent manner. These latter mutations may create spurious favorable interactions in the A site for certain near-cognate aa-tRNAs, providing an explanation for their context-dependent phenotypes in the cell.
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MESH Headings
- Anticodon/genetics
- Codon/genetics
- Guanosine Triphosphate/metabolism
- Kinetics
- Models, Molecular
- Mutation/genetics
- Nucleic Acid Conformation
- Peptide Termination Factors/chemistry
- Peptide Termination Factors/genetics
- Peptide Termination Factors/metabolism
- Protein Biosynthesis
- RNA, Messenger/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
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Affiliation(s)
- Sean P. McClory
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Aishwarya Devaraj
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Kurt Fredrick
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
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194
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Giudice E, Macé K, Gillet R. Trans-translation exposed: understanding the structures and functions of tmRNA-SmpB. Front Microbiol 2014; 5:113. [PMID: 24711807 PMCID: PMC3968760 DOI: 10.3389/fmicb.2014.00113] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 03/05/2014] [Indexed: 11/13/2022] Open
Abstract
Ribosome stalling is a serious issue for cell survival. In bacteria, the primary rescue system is trans-translation, performed by tmRNA and its protein partner small protein B (SmpB). Since its discovery almost 20 years ago, biochemical, genetic, and structural studies have paved the way to a better understanding of how this sophisticated process takes place at the cellular and molecular levels. Here we describe the molecular details of trans-translation, with special mention of recent cryo-electron microscopy and crystal structures that have helped explain how the huge tmRNA-SmpB complex targets and delivers stalled ribosomes without interfering with canonical translation.
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Affiliation(s)
- Emmanuel Giudice
- Translation and Folding Team, Université de Rennes 1, CNRS UMR 6290 IGDR Rennes, France
| | - Kevin Macé
- Translation and Folding Team, Université de Rennes 1, CNRS UMR 6290 IGDR Rennes, France
| | - Reynald Gillet
- Translation and Folding Team, Université de Rennes 1, CNRS UMR 6290 IGDR Rennes, France ; Institut Universitaire de France France
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195
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Satpati P, Sund J, Aqvist J. Structure-based energetics of mRNA decoding on the ribosome. Biochemistry 2014; 53:1714-22. [PMID: 24564511 DOI: 10.1021/bi5000355] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The origin of high fidelity in bacterial protein synthesis on the ribosome remains a fundamental unsolved problem despite available three-dimensional structures of different stages of the translation process. However, these structures open up the possibility of directly computing the energetics of tRNA selection that is required for an authentic understanding of fidelity in decoding. Here, we report extensive computer simulations that allow us to quantitatively calculate tRNA discrimination and uncover the energetics underlying accuracy in code translation. We show that the tRNA-mRNA interaction energetics varies drastically along the path from initial selection to peptide bond formation. While the selection process is obviously controlled by kinetics, the underlying thermodynamics explains the origin of the high degree of accuracy. The existence of both low- and high-selectivity states provides an efficient mechanism for initial selection and proofreading that does not require codon-dependent long-range structural signaling within the ribosome. It is instead the distinctly unequal population of the high-selectivity states for cognate and noncognate substrates that is the key discriminatory factor. The simulations reveal the essential roles played both by the 30S subunit conformational switch and by the common tRNA modification at position 37 in amplifying the accuracy.
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Affiliation(s)
- Priyadarshi Satpati
- Department of Cell and Molecular Biology, Uppsala University , Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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196
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Abstract
RNA dynamics play a fundamental role in many cellular functions. However, there is no general framework to describe these complex processes, which typically consist of many structural maneuvers that occur over timescales ranging from picoseconds to seconds. Here, we classify RNA dynamics into distinct modes representing transitions between basins on a hierarchical free-energy landscape. These transitions include large-scale secondary-structural transitions at >0.1-s timescales, base-pair/tertiary dynamics at microsecond-to-millisecond timescales, stacking dynamics at timescales ranging from nanoseconds to microseconds, and other "jittering" motions at timescales ranging from picoseconds to nanoseconds. We review various modes within these three different tiers, the different mechanisms by which they are used to regulate function, and how they can be coupled together to achieve greater functional complexity.
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197
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Calidas D, Lyon H, Culver GM. The N-terminal extension of S12 influences small ribosomal subunit assembly in Escherichia coli. RNA (NEW YORK, N.Y.) 2014; 20:321-30. [PMID: 24442609 PMCID: PMC3923127 DOI: 10.1261/rna.042432.113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The small subunit (SSU) of the ribosome of E. coli consists of a core of ribosomal RNA (rRNA) surrounded peripherally by ribosomal proteins (r-proteins). Ten of the 15 universally conserved SSU r-proteins possess nonglobular regions called extensions. The N-terminal noncanonically structured extension of S12 traverses from the solvent to intersubunit surface of the SSU and is followed by a more C-terminal globular region that is adjacent to the decoding center of the SSU. The role of the globular region in maintaining translational fidelity is well characterized, but a role for the S12 extension in SSU structure and function is unknown. We examined the effect of stepwise truncation of the extension of S12 in SSU assembly and function in vitro and in vivo. Examination of in vitro assembly in the presence of sequential N-terminal truncated variants of S12 reveals that N-terminal deletions of greater than nine amino acids exhibit decreased tRNA-binding activity and altered 16S rRNA architecture particularly in the platform of the SSU. While wild-type S12 expressed from a plasmid can rescue a genomic deletion of the essential gene for S12, rpsl; N-terminal deletions of S12 exhibit deleterious phenotypic consequences. Partial N-terminal deletions of S12 are slow growing and cold sensitive. Strains bearing these truncations as the sole copy of S12 have increased levels of free SSUs and immature 16S rRNA as compared with the wild-type S12. These differences are hallmarks of SSU biogenesis defects, indicating that the extension of S12 plays an important role in SSU assembly.
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Affiliation(s)
- Deepika Calidas
- Department of Biology, Center for RNA Biology: From Genome to Therapeutics, University of Rochester Medical Center, Rochester, New York 14627, USA
| | - Hiram Lyon
- Department of Biology, Center for RNA Biology: From Genome to Therapeutics, University of Rochester Medical Center, Rochester, New York 14627, USA
| | - Gloria M. Culver
- Department of Biology, Center for RNA Biology: From Genome to Therapeutics, University of Rochester Medical Center, Rochester, New York 14627, USA
- Corresponding authorE-mail
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198
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Miller MR, Buskirk AR. An unusual mechanism for EF-Tu activation during tmRNA-mediated ribosome rescue. RNA (NEW YORK, N.Y.) 2014; 20:228-235. [PMID: 24345396 PMCID: PMC3895274 DOI: 10.1261/rna.042226.113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 11/07/2013] [Indexed: 06/03/2023]
Abstract
In bacteria, ribosomes stalled on truncated mRNAs are rescued by transfer-messenger RNA (tmRNA) and its protein partner SmpB. Acting like tRNA, the aminoacyl-tmRNA/SmpB complex is delivered to the ribosomal A site by EF-Tu and accepts the transfer of the nascent polypeptide. Although SmpB binding within the decoding center is clearly critical for licensing tmRNA entry into the ribosome, it is not known how activation of EF-Tu occurs in the absence of a codon-anticodon interaction. A recent crystal structure revealed that SmpB residue His136 stacks on 16S rRNA nucleotide G530, a critical player in the canonical decoding mechanism. Here we use pre-steady-state kinetic methods to probe the role of this interaction in ribosome rescue. We find that although mutation of His136 does not reduce SmpB's affinity for the ribosomal A-site, it dramatically reduces the rate of GTP hydrolysis by EF-Tu. Surprisingly, the same mutation has little effect on the apparent rate of peptide-bond formation, suggesting that release of EF-Tu from the tmRNA/SmpB complex on the ribosome may occur prior to GTP hydrolysis. Consistent with this idea, we find that peptidyl transfer to tmRNA is relatively insensitive to the antibiotic kirromycin. Taken together, our studies provide a model for the initial stages of ribosomal rescue by tmRNA.
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199
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Synthesis of triazole-functionalized 2-DOS analogues and their evaluation as A-site binders. Bioorg Med Chem Lett 2014; 24:1122-6. [DOI: 10.1016/j.bmcl.2013.12.125] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 12/30/2013] [Accepted: 12/31/2013] [Indexed: 11/19/2022]
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200
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Bulkley D, Brandi L, Polikanov YS, Fabbretti A, O'Connor M, Gualerzi CO, Steitz TA. The antibiotics dityromycin and GE82832 bind protein S12 and block EF-G-catalyzed translocation. Cell Rep 2014; 6:357-65. [PMID: 24412368 PMCID: PMC5331365 DOI: 10.1016/j.celrep.2013.12.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 11/23/2013] [Accepted: 12/13/2013] [Indexed: 01/23/2023] Open
Abstract
The translocation of mRNA and tRNA through the ribosome is catalyzed by elongation factor G (EF-G), a universally conserved guanosine triphosphate hydrolase (GTPase). The mechanism by which the closely related decapeptide antibiotics dityromycin and GE82832 inhibit EF-G-catalyzed translocation is elucidated in this study. Using crystallographic and biochemical experiments, we demonstrate that these antibiotics bind to ribosomal protein S12 in solution alone as well as within the small ribosomal subunit, inducing long-range effects on the ribosomal head. The crystal structure of the antibiotic in complex with the 70S ribosome reveals that the binding involves conserved amino acid residues of S12 whose mutations result in in vitro and in vivo antibiotic resistance and loss of antibiotic binding. The data also suggest that GE82832/dityromycin inhibits EF-G-catalyzed translocation by disrupting a critical contact between EF-G and S12 that is required to stabilize the posttranslocational conformation of EF-G, thereby preventing the ribosome-EF-G complex from entering a conformation productive for translocation.
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Affiliation(s)
- David Bulkley
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Letizia Brandi
- Laboratory of Genetics, Department of Biosciences and Biotechnology, University of Camerino, 62032 Camerino, Italy
| | - Yury S Polikanov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, New Haven, CT 06511, USA
| | - Attilio Fabbretti
- Laboratory of Genetics, Department of Biosciences and Biotechnology, University of Camerino, 62032 Camerino, Italy
| | - Michael O'Connor
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Claudio O Gualerzi
- Laboratory of Genetics, Department of Biosciences and Biotechnology, University of Camerino, 62032 Camerino, Italy.
| | - Thomas A Steitz
- Department of Chemistry, Yale University, New Haven, CT 06511, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, New Haven, CT 06511, USA.
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