251
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Prestele M, Vogel F, Reichert AS, Herrmann JM, Ott M. Mrpl36 is important for generation of assembly competent proteins during mitochondrial translation. Mol Biol Cell 2009; 20:2615-25. [PMID: 19339279 DOI: 10.1091/mbc.e08-12-1162] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The complexes of the respiratory chain represent mosaics of nuclear and mitochondrially encoded components. The processes by which synthesis and assembly of the various subunits are coordinated remain largely elusive. During evolution, many proteins of the mitochondrial ribosome acquired additional domains pointing at specific properties or functions of the translation machinery in mitochondria. Here, we analyzed the function of Mrpl36, a protein associated with the large subunit of the mitochondrial ribosome. This protein, homologous to the ribosomal protein L31 from bacteria, contains a mitochondria-specific C-terminal domain that is not required for protein synthesis per se; however, its absence decreases stability of Mrpl36. Cells lacking this C-terminal domain can still synthesize proteins, but these translation products fail to be properly assembled into respiratory chain complexes and are rapidly degraded. Surprisingly, overexpression of Mrpl36 seems to even increase the efficiency of mitochondrial translation. Our data suggest that Mrpl36 plays a critical role during translation that determines the rate of respiratory chain assembly. This important function seems to be carried out by a stabilizing activity of Mrpl36 on the interaction between large and small ribosomal subunits, which could influence accuracy of protein synthesis.
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Affiliation(s)
- Martin Prestele
- Zellbiologie, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
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252
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Andér M, Åqvist J. Does Glutamine Methylation Affect the Intrinsic Conformation of the Universally Conserved GGQ Motif in Ribosomal Release Factors? Biochemistry 2009; 48:3483-9. [DOI: 10.1021/bi900117r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martin Andér
- 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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253
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Abstract
The faithful and rapid translation of genetic information into peptide sequences is an indispensable property of the ribosome. The mechanistic understanding of strategies used by the ribosome to achieve both speed and fidelity during translation results from nearly a half century of biochemical and structural studies. Emerging from these studies is the common theme that the ribosome uses local as well as remote conformational switches to govern induced-fit mechanisms that ensure accuracy in codon recognition during both tRNA selection and translation termination.
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254
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Rodnina MV, Wintermeyer W. Recent mechanistic insights into eukaryotic ribosomes. Curr Opin Cell Biol 2009; 21:435-43. [PMID: 19243929 DOI: 10.1016/j.ceb.2009.01.023] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 01/23/2009] [Indexed: 10/21/2022]
Abstract
Ribosomes are supramolecular ribonucleoprotein particles that synthesize proteins in all cells. Protein synthesis proceeds through four major phases: initiation, elongation, termination, and ribosome recycling. In each phase, a number of phase-specific translation factors cooperate with the ribosome. Whereas elongation in prokaryotes and eukaryotes involve similar factors and proceed by similar mechanisms, mechanisms of initiation, termination, and ribosome recycling, as well as the factors involved, appear quite different. Here, we summarize recent progress in deciphering molecular mechanisms of eukaryotic translation. Comparisons with prokaryotic translation are included, emphasizing emerging patterns of common design.
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Affiliation(s)
- Marina V Rodnina
- Max-Planck-Institute for Biophysical Chemistry, Department of Physical Biochemistry, 37077 Göttingen, Germany.
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255
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Abstract
Proofreading mechanisms intrinsic to DNA and RNA polymers that contribute substantially to overall fidelity are lacking in the ribosome. New evidence, however, suggests that quality control in translation can occur after substrate incorporation by an abortive mechanism entailing premature release factor-catalyzed termination. These data shed new light on the importance and ubiquity of retrospective quality control mechanisms in ensuring the overall fidelity of nature's processive enzymes and demonstrate that competitive elongation reactions on the ribosome are kinetically sensitive to compositional features of the translating particle.
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Affiliation(s)
- Scott C. Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, 1300 York Avenue, Whitney 205, New York, New York 10021
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256
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257
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Abstract
Since the mid-1990s, insights obtained from electron microscopy and X-ray crystallography have transformed our understanding of how the most important ribozyme in the cell, the ribosome, catalyzes protein synthesis. This review provides a brief account of how this structural revolution came to pass, and the impact it has had on our understanding of how the ribosome decodes messenger RNAs.
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Affiliation(s)
- Peter B Moore
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.
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258
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Thermus thermophilus as biological model. Extremophiles 2009; 13:213-31. [DOI: 10.1007/s00792-009-0226-6] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 12/31/2008] [Indexed: 10/21/2022]
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259
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Kipper K, Hetényi C, Sild S, Remme J, Liiv A. Ribosomal Intersubunit Bridge B2a Is Involved in Factor-Dependent Translation Initiation and Translational Processivity. J Mol Biol 2009; 385:405-22. [DOI: 10.1016/j.jmb.2008.10.065] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Revised: 10/14/2008] [Accepted: 10/15/2008] [Indexed: 10/21/2022]
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260
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Crystal structure of a translation termination complex formed with release factor RF2. Proc Natl Acad Sci U S A 2008; 105:19684-9. [PMID: 19064930 DOI: 10.1073/pnas.0810953105] [Citation(s) in RCA: 187] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report the crystal structure of a translation termination complex formed by the Thermus thermophilus 70S ribosome bound with release factor RF2, in response to a UAA stop codon, solved at 3 A resolution. The backbone of helix alpha5 and the side chain of serine of the conserved SPF motif of RF2 recognize U1 and A2 of the stop codon, respectively. A3 is unstacked from the first 2 bases, contacting Thr-216 and Val-203 of RF2 and stacking on G530 of 16S rRNA. The structure of the RF2 complex supports our previous proposal that conformational changes in the ribosome in response to recognition of the stop codon stabilize rearrangement of the switch loop of the release factor, resulting in docking of the universally conserved GGQ motif in the PTC of the 50S subunit. As seen for the RF1 complex, the main-chain amide nitrogen of glutamine in the GGQ motif is positioned to contribute directly to catalysis of peptidyl-tRNA hydrolysis, consistent with mutational studies, which show that most side-chain substitutions of the conserved glutamine have little effect. We show that when the H-bonding capability of the main-chain N-H of the conserved glutamine is eliminated by substitution with proline, peptidyl-tRNA esterase activity is abolished, consistent with its proposed role in catalysis.
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261
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Weixlbaumer A, Jin H, Neubauer C, Voorhees RM, Petry S, Kelley AC, Ramakrishnan V. Insights into translational termination from the structure of RF2 bound to the ribosome. Science 2008; 322:953-6. [PMID: 18988853 DOI: 10.1126/science.1164840] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The termination of protein synthesis occurs through the specific recognition of a stop codon in the A site of the ribosome by a release factor (RF), which then catalyzes the hydrolysis of the nascent protein chain from the P-site transfer RNA. Here we present, at a resolution of 3.5 angstroms, the crystal structure of RF2 in complex with its cognate UGA stop codon in the 70S ribosome. The structure provides insight into how RF2 specifically recognizes the stop codon; it also suggests a model for the role of a universally conserved GGQ motif in the catalysis of peptide release.
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Affiliation(s)
- Albert Weixlbaumer
- Medical Research Council (MRC) Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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262
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Liljas A. Biochemistry. Getting close to termination. Science 2008; 322:863-5. [PMID: 18988828 DOI: 10.1126/science.1166913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Anders Liljas
- Department of Molecular Biophysics, Lund University, Sweden.
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263
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Simonović M, Steitz TA. Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA. RNA (NEW YORK, N.Y.) 2008; 14:2372-8. [PMID: 18818369 PMCID: PMC2578858 DOI: 10.1261/rna.1118908] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The last step in ribosome-catalyzed protein synthesis is the hydrolytic release of the newly formed polypeptide from the P-site bound tRNA. Hydrolysis of the ester link of the peptidyl-tRNA is stimulated normally by the binding of release factors (RFs). However, an unacylated tRNA or just CCA binding to the ribosomal A site can also stimulate deacylation under some nonphysiological conditions. Although the sequence of events is well described by biochemical studies, the structural basis of the mechanism underlying this process is not well understood. Two new structures of the large ribosomal subunit of Haloarcula marismortui complexed with a peptidyl-tRNA analog in the P site and two oligonucleotide mimics of unacylated tRNA, CCA and CA, in the A site show that the binding of either CA or CCA induces a very similar conformational change in the peptidyl-transferase center as induced by aminoacyl-CCA. However, only CCA positions a water molecule appropriately to attack the carbonyl carbon of the peptidyl-tRNA and stabilizes the proper orientation of the ester link for hydrolysis. We, thus, conclude that both the ability of the O3'-hydroxyl group of the A-site A76 to position the water and the A-site CCA induced conformational change of the PTC are critical for the catalysis of the deacylation of the peptidyl-tRNA by CCA, and perhaps, an analogous mechanism is used by RFs.
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Affiliation(s)
- Miljan Simonović
- Howard Hughes Medical Institute, New Haven, Connecticut 06520-8114, USA
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264
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Diago-Navarro E, Mora L, Buckingham RH, Díaz-Orejas R, Lemonnier M. Novel Escherichia coli RF1 mutants with decreased translation termination activity and increased sensitivity to the cytotoxic effect of the bacterial toxins Kid and RelE. Mol Microbiol 2008; 71:66-78. [PMID: 19019162 PMCID: PMC2680264 DOI: 10.1111/j.1365-2958.2008.06510.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Novel mutations in prfA, the gene for the polypeptide release factor RF1 of Escherichia coli, were isolated using a positive genetic screen based on the parD (kis, kid) toxin–antitoxin system. This original approach allowed the direct selection of mutants with altered translational termination efficiency at UAG codons. The isolated prfA mutants displayed a ∼10-fold decrease in UAG termination efficiency with no significant changes in RF1 stability in vivo. All three mutations, G121S, G301S and R303H, were situated close to the nonsense codon recognition site in RF1:ribosome complexes. The prfA mutants displayed increased sensitivity to the RelE toxin encoded by the relBE system of E. coli, thus providing in vivo support for the functional interaction between RF1 and RelE. The prfA mutants also showed increased sensitivity to the Kid toxin. Since this toxin can cleave RNA in a ribosome-independent manner, this result was not anticipated and provided first evidence for the involvement of RF1 in the pathway of Kid toxicity. The sensitivity of the prfA mutants to RelE and Kid was restored to normal levels upon overproduction of the wild-type RF1 protein. We discuss these results and their utility for the design of novel antibacterial strategies in the light of the recently reported structure of ribosome-bound RF1.
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Affiliation(s)
- Elizabeth Diago-Navarro
- Department of Molecular Microbiology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
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265
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Korostelev A, Ermolenko DN, Noller HF. Structural dynamics of the ribosome. Curr Opin Chem Biol 2008; 12:674-83. [PMID: 18848900 DOI: 10.1016/j.cbpa.2008.08.037] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 08/23/2008] [Indexed: 01/01/2023]
Abstract
Protein synthesis is inherently a dynamic process, requiring both small-scale and large-scale movements of tRNA and mRNA. It has long been suspected that these movements might be coupled to conformational changes in the ribosome, and in its RNA moieties in particular. Recently, the nature of ribosome structural dynamics has begun to emerge from a combination of approaches, most notably cryo-EM, X-ray crystallography, and FRET. Ribosome movement occurs both on a grand scale, as in the intersubunit rotational movements that are coupled to tRNA-mRNA translocation, and in intricate localized rearrangements such as those that accompany codon-anticodon recognition and peptide bond formation. In spite of much progress, our understanding of the mechanics of translation is now beset with countless new questions, reflecting the vast molecular architecture of the ribosome itself.
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Affiliation(s)
- Andrei Korostelev
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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266
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Egelman EH. Problems in fitting high resolution structures into electron microscopic reconstructions. HFSP JOURNAL 2008; 2:324-31. [PMID: 19436497 DOI: 10.2976/1.2992221] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Indexed: 11/19/2022]
Abstract
Great advances have been made in electron microscopy (EM) over the past decade, with the result that a number of protein complexes have been solved at near-atomic resolution using EM imaging. However, only a limited number of such complexes are expected to have the high degree of internal order needed to achieve this type of resolution. Many other complexes and polymers will be visualized and reconstructed by EM at an intermediate level of resolution, where the polypeptide chain cannot be directly traced. Crystal and nuclear magnetic resonance structures for components or subunits of these higher-order assemblies are frequently available. One of the greatest strengths of EM continues to be the ability to dock high-resolution structures of components into low or intermediate resolution reconstructions of assemblies to build pseudoatomic models for quaternary structure. This review discusses the strengths and limitations of this approach, with particular emphasis on protein polymers. I discuss how limitations in resolution can lead to ambiguities in building models, and these cannot be always be resolved with available data. The use of homology models for quaternary structure are particularly problematic, given accumulating evidence for the divergence of quaternary structures at the same time that tertiary structure can be conserved.
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Affiliation(s)
- Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908-0733
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