201
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Brown JD, Ryan MD. Ribosome “Skipping”: “Stop-Carry On” or “StopGo” Translation. RECODING: EXPANSION OF DECODING RULES ENRICHES GENE EXPRESSION 2010. [DOI: 10.1007/978-0-387-89382-2_5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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202
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Namy O, Rousset JP. Specification of Standard Amino Acids by Stop Codons. RECODING: EXPANSION OF DECODING RULES ENRICHES GENE EXPRESSION 2010. [DOI: 10.1007/978-0-387-89382-2_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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203
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Hetrick B, Lee K, Joseph S. Kinetics of stop codon recognition by release factor 1. Biochemistry 2009; 48:11178-84. [PMID: 19874047 DOI: 10.1021/bi901577d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recognition of stop codons by class I release factors is a fundamental step in the termination phase of protein synthesis. Since premature termination is costly to the cell, release factors have to efficiently discriminate between stop and sense codons. To understand the mechanism of discrimination between stop and sense codons, we developed a new, pre-steady state kinetic assay to monitor the interaction of RF1 with the ribosome. Our results show that RF1 associates with similar association rate constants with ribosomes programmed with stop or sense codons. However, dissociation of RF1 from sense codons is as much as 3 orders of magnitude faster than from stop codons. Interestingly, the affinity of RF1 for ribosomes programmed with different sense codons does not correlate with the defects in peptide release. Thus, discrimination against sense codons is achieved with both an increase in the dissociation rates and a decrease in the rate of peptide release. These results suggest that sense codons inhibit conformational changes necessary for RF1 to stably bind to the ribosome and catalyze peptide release.
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Affiliation(s)
- Byron Hetrick
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0314, USA
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204
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Kimura S, Suzuki T. Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA. Nucleic Acids Res 2009; 38:1341-52. [PMID: 19965768 PMCID: PMC2831307 DOI: 10.1093/nar/gkp1073] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
In bacterial 16S rRNAs, methylated nucleosides are clustered within the decoding center, and these nucleoside modifications are thought to modulate translational fidelity. The N4, 2′-O-dimethylcytidine (m4Cm) at position 1402 of the Escherichia coli 16S rRNA directly interacts with the P-site codon of the mRNA. The biogenesis and function of this modification remain unclear. We have identified two previously uncharacterized genes in E. coli that are required for m4Cm formation. mraW (renamed rsmH) and yraL (renamed rsmI) encode methyltransferases responsible for the N4 and 2′-O-methylations of C1402, respectively. Recombinant RsmH and RsmI proteins employed the 30S subunit (not the 16S rRNA) as a substrate to reconstitute m4Cm1402 in the presence of S-adenosylmethionine (Ado-Met) as the methyl donor, suggesting that m4Cm1402 is formed at a late step during 30S assembly in the cell. A luciferase reporter assay indicated that the lack of N4 methylation of C1402 increased the efficiency of non-AUG initiation and decreased the rate of UGA read-through. These results suggest that m4Cm1402 plays a role in fine-tuning the shape and function of the P-site, thus increasing decoding fidelity.
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Affiliation(s)
- Satoshi Kimura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bldg. 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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205
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Rodnina MV, Wintermeyer W. The ribosome goes Nobel. Trends Biochem Sci 2009; 35:1-5. [PMID: 19962317 DOI: 10.1016/j.tibs.2009.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 11/11/2009] [Indexed: 11/20/2022]
Abstract
The award of this year's Nobel Prize in Chemistry to Ada E. Yonath, Venkatraman Ramakrishnan and Thomas A. Steitz honors their breakthrough achievement in determining the atomic structure of the ribosome.
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Affiliation(s)
- Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany.
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206
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Trobro S, Åqvist J. Mechanism of the Translation Termination Reaction on the Ribosome. Biochemistry 2009; 48:11296-303. [DOI: 10.1021/bi9017297] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefan Trobro
- 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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207
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Seidelt B, Innis CA, Wilson DN, Gartmann M, Armache JP, Villa E, Trabuco LG, Becker T, Mielke T, Schulten K, Steitz TA, Beckmann R. Structural insight into nascent polypeptide chain-mediated translational stalling. Science 2009; 326:1412-5. [PMID: 19933110 DOI: 10.1126/science.1177662] [Citation(s) in RCA: 214] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Expression of the Escherichia coli tryptophanase operon depends on ribosome stalling during translation of the upstream TnaC leader peptide, a process for which interactions between the TnaC nascent chain and the ribosomal exit tunnel are critical. We determined a 5.8 angstrom-resolution cryo-electron microscopy and single-particle reconstruction of a ribosome stalled during translation of the tnaC leader gene. The nascent chain was extended within the exit tunnel, making contacts with ribosomal components at distinct sites. Upon stalling, two conserved residues within the peptidyltransferase center adopted conformations that preclude binding of release factors. We propose a model whereby interactions within the tunnel are relayed to the peptidyltransferase center to inhibit translation. Moreover, we show that nascent chains adopt distinct conformations within the ribosomal exit tunnel.
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Affiliation(s)
- Birgit Seidelt
- Gene Center and Center for Integrated Protein Science Munich (CIPSM), Department for Chemistry and Biochemistry, University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
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208
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Fraser CS. The molecular basis of translational control. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 90:1-51. [PMID: 20374738 DOI: 10.1016/s1877-1173(09)90001-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Our current understanding of eukaryotic protein synthesis has emerged from many years of biochemical, genetic and biophysical approaches. Significant insight into the molecular details of the mechanism has been obtained, although there are clearly many aspects of the process that remain to be resolved. Importantly, our understanding of the mechanism has identified a number of key stages in the pathway that contribute to the regulation of general and gene-specific translation. Not surprisingly, translational control is now widely accepted to play a role in aspects of cell stress, growth, development, synaptic function, aging, and disease. This chapter reviews the mechanism of eukaryotic protein synthesis and its relevance to translational control.
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Affiliation(s)
- Christopher S Fraser
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, California 95616, USA
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209
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What recent ribosome structures have revealed about the mechanism of translation. Nature 2009; 461:1234-42. [DOI: 10.1038/nature08403] [Citation(s) in RCA: 499] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 10/01/2009] [Indexed: 11/08/2022]
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210
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Janssen BD, Hayes CS. Kinetics of paused ribosome recycling in Escherichia coli. J Mol Biol 2009; 394:251-67. [PMID: 19761774 DOI: 10.1016/j.jmb.2009.09.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Revised: 08/09/2009] [Accepted: 09/09/2009] [Indexed: 11/29/2022]
Abstract
The bacterial tmRNA.SmpB system recycles stalled translation complexes in a process termed 'ribosome rescue.' tmRNA.SmpB specifically recognizes ribosomes that are paused at or near the 3' end of truncated mRNA; therefore, nucleolytic mRNA processing is required before paused ribosomes can be rescued from full-length transcripts. Here, we examine the recycling of ribosomes paused on both full-length and truncated mRNAs. Peptidyl-tRNAs corresponding to each paused translation complex were identified, and their turnover kinetics was used to estimate the half-lives of paused ribosomes in vivo. Ribosomes were paused at stop codons on full-length mRNA using a nascent peptide motif that interferes with translation termination and elicits tmRNA.SmpB activity. Peptidyl-tRNA turnover from these termination-paused ribosomes was slightly more rapid in tmRNA(+) cells (T(1/2)=22+/-2.2 s) than in DeltatmRNA cells (T(1/2)=32+/-1.6 s). Overexpression of release factor (RF) 1 greatly accelerated peptidyl-tRNA turnover from termination-paused ribosomes in both tmRNA(+) and DeltatmRNA cells, whereas other termination factors had little or no effect on recycling. In contrast to inefficient translation termination, ribosome recycling from truncated transcripts lacking in-frame stop codons was dramatically accelerated by tmRNA.SmpB. However, peptidyl-tRNA still turned over from nonstop-paused ribosomes at a significant rate (t(1/2)=61+/-7.3 s) in DeltatmRNA cells. Overexpression of RF-1, RF-3, and ribosome recycling factor in DeltatmRNA cells failed to accelerate ribosome recycling from nonstop mRNA. These results indicate that tmRNA.SmpB activity is rate limited by mRNA cleavage, and that RF-3 and ribosome recycling factor do not constitute a tmRNA-independent rescue pathway, as previously suggested. Peptidyl-tRNA turnover from nonstop-paused ribosomes in DeltatmRNA cells suggests the existence of another uncharacterized ribosome rescue pathway.
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Affiliation(s)
- Brian D Janssen
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106-9610, USA
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211
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Simonović M, Steitz TA. A structural view on the mechanism of the ribosome-catalyzed peptide bond formation. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1789:612-23. [PMID: 19595805 PMCID: PMC2783306 DOI: 10.1016/j.bbagrm.2009.06.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 06/23/2009] [Accepted: 06/25/2009] [Indexed: 10/20/2022]
Abstract
The ribosome is a large ribonucleoprotein particle that translates genetic information encoded in mRNA into specific proteins. Its highly conserved active site, the peptidyl-transferase center (PTC), is located on the large (50S) ribosomal subunit and is comprised solely of rRNA, which makes the ribosome the only natural ribozyme with polymerase activity. The last decade witnessed a rapid accumulation of atomic-resolution structural data on both ribosomal subunits as well as on the entire ribosome. This has allowed studies on the mechanism of peptide bond formation at a level of detail that surpasses that for the classical protein enzymes. A current understanding of the mechanism of the ribosome-catalyzed peptide bond formation is the focus of this review. Implications on the mechanism of peptide release are discussed as well.
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Affiliation(s)
- Miljan Simonović
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607
| | - Thomas A. Steitz
- Department of Chemistry, Yale University, New Haven, CT 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
- Howard Hughes Medical Institute at Yale University, New Haven, CT 06520
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212
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Abstract
Protein biosynthesis on the ribosome requires repeated cycles of ratcheting, which couples rotation of the two ribosomal subunits with respect to each other, and swiveling of the head domain of the small subunit. However, the molecular basis for how the two ribosomal subunits rearrange contacts with each other during ratcheting while remaining stably associated is not known. Here, we describe x-ray crystal structures of the intact Escherichia coli ribosome, either in the apo-form (3.5 angstrom resolution) or with one (4.0 angstrom resolution) or two (4.0 angstrom resolution) anticodon stem-loop tRNA mimics bound, that reveal intermediate states of intersubunit rotation. In the structures, the interface between the small and large ribosomal subunits rearranges in discrete steps along the ratcheting pathway. Positioning of the head domain of the small subunit is controlled by interactions with the large subunit and with the tRNA bound in the peptidyl-tRNA site. The intermediates observed here provide insight into how tRNAs move into the hybrid state of binding that precedes the final steps of mRNA and tRNA translocation.
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MESH Headings
- Anticodon/chemistry
- Anticodon/metabolism
- Crystallography, X-Ray
- Escherichia coli/chemistry
- Escherichia coli/metabolism
- Escherichia coli/ultrastructure
- Escherichia coli Proteins/biosynthesis
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/metabolism
- Nucleic Acid Conformation
- Protein Biosynthesis
- Protein Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Large, Bacterial/chemistry
- Ribosome Subunits, Large, Bacterial/metabolism
- Ribosome Subunits, Large, Bacterial/ultrastructure
- Ribosome Subunits, Small, Bacterial/chemistry
- Ribosome Subunits, Small, Bacterial/metabolism
- Ribosome Subunits, Small, Bacterial/ultrastructure
- Ribosomes/chemistry
- Ribosomes/metabolism
- Ribosomes/ultrastructure
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Affiliation(s)
- Wen Zhang
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
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213
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Yonath A. Large facilities and the evolving ribosome, the cellular machine for genetic-code translation. J R Soc Interface 2009; 6 Suppl 5:S575-85. [PMID: 19656820 DOI: 10.1098/rsif.2009.0167.focus] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Well-focused X-ray beams, generated by advanced synchrotron radiation facilities, yielded high-resolution diffraction data from crystals of ribosomes, the cellular nano-machines that translate the genetic code into proteins. These structures revealed the decoding mechanism, localized the mRNA path and the positions of the tRNA molecules in the ribosome and illuminated the interactions of the ribosome with initiation, release and recycling factors. They also showed that the ribosome is a ribozyme whose active site is situated within a universal symmetrical region that is embedded in the otherwise asymmetric ribosome structure. As this highly conserved region provides the machinery required for peptide bond formation and for ribosome polymerase activity, it may be the remnant of the proto-ribosome, a dimeric pre-biotic machine that formed peptide bonds and non-coded polypeptide chains. Synchrotron radiation also enabled the determination of structures of complexes of ribosomes with antibiotics targeting them, which revealed the principles allowing for their clinical use, revealed resistance mechanisms and showed the bases for discriminating pathogens from hosts, hence providing valuable structural information for antibiotics improvement.
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Affiliation(s)
- Ada Yonath
- Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel.
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214
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Atkins JF, Gesteland RF. Sequences Promoting Recoding Are Singular Genomic Elements. RECODING: EXPANSION OF DECODING RULES ENRICHES GENE EXPRESSION 2009; 24. [PMCID: PMC7122551 DOI: 10.1007/978-0-387-89382-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The distribution of sequences which induce non-standard decoding, especially of shift-prone sequences, is very unusual. On one hand, since they can disrupt standard genetic readout, they are avoided within the coding regions of most genes. On the other hand, they play important regulatory roles for the expression of those genes where they do occur. As a result, they are preserved among homologs and exhibit deep phylogenetic conservation. The combination of these two constraints results in a characteristic distribution of recoding sequences across genomes: they are highly conserved at specific locations while they are very rare in other locations. We term such sequences singular genomic elements to signify their rare occurrence and biological importance.
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Affiliation(s)
- John F. Atkins
- Molecular Biology Program, University of Utah, N. 2030 E. 15, Salt Late City, 84112-5330 U.S.A
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215
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Davidovich C, Belousoff M, Bashan A, Yonath A. The evolving ribosome: from non-coded peptide bond formation to sophisticated translation machinery. Res Microbiol 2009; 160:487-92. [PMID: 19619641 DOI: 10.1016/j.resmic.2009.07.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 07/02/2009] [Accepted: 07/04/2009] [Indexed: 11/25/2022]
Abstract
Structural analysis supported by biochemical, mutagenesis and computational evidence, revealed that the contemporary ribosome's active site is a universal symmetrical pocket made of ribosomal RNA. This pocket seems to be the remnant of the proto-ribosome, a dimeric RNA assembly evolved by gene duplication, capable of autonomously catalyzing peptide bond formation and non-coded amino acid polymerization.
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Affiliation(s)
- Chen Davidovich
- The Department of Structural Biology, Weizmann Institute, Rehovot, Israel
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216
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Helix 69 in 23S rRNA modulates decoding by wild type and suppressor tRNAs. Mol Genet Genomics 2009; 282:371-80. [PMID: 19603183 DOI: 10.1007/s00438-009-0470-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 06/27/2009] [Indexed: 10/20/2022]
Abstract
Helix 69 of 23S rRNA forms one of the major inter-subunit bridges of the 70S ribosome and interacts with A- and P-site tRNAs and translation factors. Despite the proximity of h69 to the decoding center and tRNAs, the contribution of h69 to the tRNA selection process is unclear: previous genetic analyses have shown that h69 mutations increase frameshifting and readthrough of stop codons. However, a complete deletion of h69 does not affect the selection of cognate tRNAs in vitro. To address these discrepancies, the in vivo effects of a range of single- and multi-base h69 mutations in Escherichia coli 23S rRNA on various translation errors have been determined. While a majority of the h69 mutations examined here affected readthrough of stop codons and frameshifting, the DeltaA1916 single base deletion mutation uniquely influenced missense decoding. Different h69 mutants had either increased or decreased levels of stop codon readthrough. The h69 mutations that decreased UGA readthrough also decreased UGA reading by a mutant, near-cognate tRNA(Trp) carrying a G24A substitution in the D arm, but had far less effect on UGA reading by a suppressor tRNA with a complementary anticodon. These results suggest that h69 interactions with release factors contribute significantly to termination efficiency and that interaction with the D arm of A-site tRNA is important for discrimination between cognate and near-cognate tRNAs.
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217
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Cheng Z, Saito K, Pisarev AV, Wada M, Pisareva VP, Pestova TV, Gajda M, Round A, Kong C, Lim M, Nakamura Y, Svergun DI, Ito K, Song H. Structural insights into eRF3 and stop codon recognition by eRF1. Genes Dev 2009; 23:1106-18. [PMID: 19417105 PMCID: PMC2682955 DOI: 10.1101/gad.1770109] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2008] [Accepted: 03/23/2009] [Indexed: 11/25/2022]
Abstract
Eukaryotic translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act cooperatively to ensure efficient stop codon recognition and fast polypeptide release. The crystal structures of human and Schizosaccharomyces pombe full-length eRF1 in complex with eRF3 lacking the GTPase domain revealed details of the interaction between these two factors and marked conformational changes in eRF1 that occur upon binding to eRF3, leading eRF1 to resemble a tRNA molecule. Small-angle X-ray scattering analysis of the eRF1/eRF3/GTP complex suggested that eRF1's M domain contacts eRF3's GTPase domain. Consistently, mutation of Arg192, which is predicted to come in close contact with the switch regions of eRF3, revealed its important role for eRF1's stimulatory effect on eRF3's GTPase activity. An ATP molecule used as a crystallization additive was bound in eRF1's putative decoding area. Mutational analysis of the ATP-binding site shed light on the mechanism of stop codon recognition by eRF1.
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Affiliation(s)
- Zhihong Cheng
- Cancer and Developmental Cell Biology Division, Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Singapore 138673, Singapore
| | - Kazuki Saito
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Andrey V. Pisarev
- Department of Microbiology and Immunology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Miki Wada
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Vera P. Pisareva
- Department of Microbiology and Immunology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Tatyana V. Pestova
- Department of Microbiology and Immunology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Michal Gajda
- European Molecular Biology Laboratory, Hamburg Outstation, 22603 Hamburg, Germany
| | - Adam Round
- European Molecular Biology Laboratory, Hamburg Outstation, 22603 Hamburg, Germany
| | - Chunguang Kong
- Cancer and Developmental Cell Biology Division, Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Singapore 138673, Singapore
| | - Mengkiat Lim
- Cancer and Developmental Cell Biology Division, Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Singapore 138673, Singapore
| | - Yoshikazu Nakamura
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, 22603 Hamburg, Germany
- Institute of Crystallography, Russian Academy of Sciences, 117333 Moscow, Russia
| | - Koichi Ito
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Haiwei Song
- Cancer and Developmental Cell Biology Division, Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Singapore 138673, Singapore
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218
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Voorhees RM, Weixlbaumer A, Loakes D, Kelley AC, Ramakrishnan V. Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nat Struct Mol Biol 2009; 16:528-33. [PMID: 19363482 PMCID: PMC2679717 DOI: 10.1038/nsmb.1577] [Citation(s) in RCA: 283] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Accepted: 02/19/2009] [Indexed: 11/09/2022]
Abstract
Protein synthesis is catalyzed in the peptidyl transferase center (PTC), located in the large (50S) subunit of the ribosome. No high-resolution structure of the intact ribosome has contained a complete active site including both A- and P-site tRNAs. In addition, although past structures of the 50S subunit have found no ordered proteins at the PTC, biochemical evidence suggests that specific proteins are capable of interacting with the 3' ends of tRNA ligands. Here we present structures, at 3.6-A and 3.5-A resolution respectively, of the 70S ribosome in complex with A- and P-site tRNAs that mimic pre- and post-peptidyl-transfer states. These structures demonstrate that the PTC is very similar between the 50S subunit and the intact ribosome. They also reveal interactions between the ribosomal proteins L16 and L27 and the tRNA substrates, helping to elucidate the role of these proteins in peptidyl transfer.
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Affiliation(s)
- Rebecca M. Voorhees
- MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom
| | - Albert Weixlbaumer
- MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom
| | - David Loakes
- MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom
| | - Ann C. Kelley
- MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom
| | - V. Ramakrishnan
- MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom
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219
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23S rRNA nucleotides in the peptidyl transferase center are essential for tryptophanase operon induction. J Bacteriol 2009; 191:3445-50. [PMID: 19329641 DOI: 10.1128/jb.00096-09] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Distinct features of the ribosomal peptide exit tunnel are known to be essential for recognition of specific amino acids of a nascent peptidyl-tRNA. Thus, a tryptophan residue at position 12 of the peptidyl-tRNA TnaC-tRNA(Pro) leads to the creation of a free tryptophan binding site within the ribosome at which bound tryptophan inhibits normal ribosome functions. The ribosomal processes that are inhibited are hydrolysis of TnaC-tRNA(Pro) by release factor 2 and peptidyl transfer of TnaC of TnaC-tRNA(Pro) to puromycin. These events are normally performed in the ribosomal peptidyl transferase center. In the present study, changes of 23S rRNA nucleotides in the 2585 region of the peptidyl transferase center, G2583A and U2584C, were observed to reduce maximum induction of tna operon expression by tryptophan in vivo without affecting the concentration of tryptophan necessary to obtain 50% induction. The growth rate of strains with ribosomes with either of these changes was not altered appreciably. In vitro analyses with mutant ribosomes with these changes showed that tryptophan was not as efficient in protecting TnaC-tRNA(Pro) from puromycin action as wild-type ribosomes. However, added tryptophan did prevent sparsomycin action as it normally does with wild-type ribosomes. These findings suggest that these two mutational changes act by reducing the ability of ribosome-bound tryptophan to inhibit peptidyl transferase activity rather than by reducing the ability of the ribosome to bind tryptophan. Thus, the present study identifies specific nucleotides within the ribosomal peptidyl transferase center that appear to be essential for effective tryptophan induction of tna operon expression.
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220
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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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221
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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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222
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Atkins JF, Björk GR. A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment. Microbiol Mol Biol Rev 2009; 73:178-210. [PMID: 19258537 PMCID: PMC2650885 DOI: 10.1128/mmbr.00010-08] [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] [Indexed: 11/20/2022] Open
Abstract
Mutants of translation components which compensate for both -1 and +1 frameshift mutations showed the first evidence for framing malleability. Those compensatory mutants isolated in bacteria and yeast with altered tRNA or protein factors are reviewed here and are considered to primarily cause altered P-site realignment and not altered translocation. Though the first sequenced tRNA mutant which suppressed a +1 frameshift mutation had an extra base in its anticodon loop and led to a textbook "yardstick" model in which the number of anticodon bases determines codon size, this model has long been discounted, although not by all. Accordingly, the reviewed data suggest that reading frame maintenance and translocation are two distinct features of the ribosome. None of the -1 tRNA suppressors have anticodon loops with fewer than the standard seven nucleotides. Many of the tRNA mutants potentially affect tRNA bending and/or stability and can be used for functional assays, and one has the conserved C74 of the 3' CCA substituted. The effect of tRNA modification deficiencies on framing has been particularly informative. The properties of some mutants suggest the use of alternative tRNA anticodon loop stack conformations by individual tRNAs in one translation cycle. The mutant proteins range from defective release factors with delayed decoding of A-site stop codons facilitating P-site frameshifting to altered EF-Tu/EF1alpha to mutant ribosomal large- and small-subunit proteins L9 and S9. Their study is revealing how mRNA slippage is restrained except where it is programmed to occur and be utilized.
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Affiliation(s)
- John F Atkins
- BioSciences Institute, University College, Cork, Ireland.
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223
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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: 5.3] [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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224
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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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225
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Abstract
During protein synthesis, mistakes in adding amino acids to the growing polypeptide chain are usually prevented. If they are not, a quality-control mechanism ensures premature termination of erroneous sequences.
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226
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Ribosome: an Ancient Cellular Nano-Machine for Genetic Code Translation. NATO SCIENCE FOR PEACE AND SECURITY SERIES B: PHYSICS AND BIOPHYSICS 2009. [DOI: 10.1007/978-90-481-2368-1_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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227
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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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