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Milón P, Maracci C, Filonava L, Gualerzi CO, Rodnina MV. Real-time assembly landscape of bacterial 30S translation initiation complex. Nat Struct Mol Biol 2012; 19:609-15. [PMID: 22562136 DOI: 10.1038/nsmb.2285] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 05/21/2012] [Indexed: 11/09/2022]
Abstract
Initiation factors guide the ribosome in the selection of mRNA and translational reading frame. We determined the kinetically favored assembly pathway of the 30S preinitiation complex (30S PIC), an early intermediate in 30S initiation complex formation in Escherichia coli. IF3 and IF2 are the first factors to arrive, forming an unstable 30S-IF2-IF3 complex. Subsequently, IF1 joins and locks the factors in a kinetically stable 30S PIC to which fMet-tRNA(fMet) is recruited. Binding of mRNA is independent of initiation factors and can take place at any time during 30S PIC assembly, depending on the cellular concentration of the mRNA and the structural determinants at the ribosome-binding site. The kinetic analysis shows both specific and cumulative effects of initiation factors as well as kinetic checkpoints of mRNA selection at the entry into translation.
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Affiliation(s)
- Pohl Milón
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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52
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Abstract
Translation initiation is a crucial step of protein synthesis which largely defines how the composition of the cellular transcriptome is converted to the proteome and controls the response and adaptation to environmental stimuli. The efficiency of translation of individual mRNAs, and hence the basal shape of the proteome, is defined by the structures of the mRNA translation initiation regions. Initiation efficiency can be regulated by small molecules, proteins, or antisense RNAs, underscoring its importance in translational control. Although initiation has been studied in bacteria for decades, many aspects remain poorly understood. Recent evidence has suggested an unexpected diversity of pathways by which mRNAs can be recruited to the bacterial ribosome, the importance of structural dynamics of initiation intermediates, and the complexity of checkpoints for mRNA selection. In this review, we discuss how the ribosome shapes the landscape of translation initiation by non-linear kinetic processing of the transcriptome information. We summarize the major pathways by which mRNAs enter the ribosome depending on the structure of their 5' untranslated regions, the assembly and the structure of initiation intermediates, the individual and synergistic roles of initiation factors, and the mechanisms of mRNA and initiator tRNA selection.
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Affiliation(s)
- Pohl Milón
- Department of Physical Biochemistry, Max Planck Institute of Biophysical Chemistry, Goettingen, Germany
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53
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Atkinson GC, Kuzmenko A, Kamenski P, Vysokikh MY, Lakunina V, Tankov S, Smirnova E, Soosaar A, Tenson T, Hauryliuk V. Evolutionary and genetic analyses of mitochondrial translation initiation factors identify the missing mitochondrial IF3 in S. cerevisiae. Nucleic Acids Res 2012; 40:6122-34. [PMID: 22457064 PMCID: PMC3401457 DOI: 10.1093/nar/gks272] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Mitochondrial translation is essentially bacteria-like, reflecting the bacterial endosymbiotic ancestry of the eukaryotic organelle. However, unlike the translation system of its bacterial ancestors, mitochondrial translation is limited to just a few mRNAs, mainly coding for components of the respiratory complex. The classical bacterial initiation factors (IFs) IF1, IF2 and IF3 are universal in bacteria, but only IF2 is universal in mitochondria (mIF2). We analyse the distribution of mitochondrial translation initiation factors and their sequence features, given two well-propagated claims: first, a sequence insertion in mitochondrial IF2 (mIF2) compensates for the universal lack of IF1 in mitochondria, and secondly, no homologue of mitochondrial IF3 (mIF3) is identifiable in Saccharomyces cerevisiae. Our comparative sequence analysis shows that, in fact, the mIF2 insertion is highly variable and restricted in length and primary sequence conservation to vertebrates, while phylogenetic and in vivo complementation analyses reveal that an uncharacterized S. cerevisiae mitochondrial protein currently named Aim23p is a bona fide evolutionary and functional orthologue of mIF3. Our results highlight the lineage-specific nature of mitochondrial translation and emphasise that comparative analyses among diverse taxa are essential for understanding whether generalizations from model organisms can be made across eukaryotes.
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54
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Quality control of mRNA decoding on the bacterial ribosome. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 86:95-128. [PMID: 22243582 DOI: 10.1016/b978-0-12-386497-0.00003-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The ribosome is a major player in providing accurate gene expression in the cell. The fidelity of substrate selection is tightly controlled throughout the translation process, including the initiation, elongation, and termination phases. Although each phase of translation involves different players, that is, translation factors and tRNAs, the general principles of selection appear surprisingly similar for very different substrates. At essentially every step of translation, differences in complex stabilities as well as induced fit are sources of selectivity. A view starts to emerge of how the ribosome uses local and global conformational switches to govern induced-fit mechanisms that ensure fidelity. This review describes the mechanisms of tRNA and mRNA selection at all phases of protein synthesis in bacteria.
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55
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In vitro and in vivo single-molecule fluorescence imaging of ribosome-catalyzed protein synthesis. Curr Opin Chem Biol 2011; 15:853-63. [PMID: 22104181 DOI: 10.1016/j.cbpa.2011.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 11/01/2011] [Accepted: 11/01/2011] [Indexed: 11/22/2022]
Abstract
Combined with the availability of highly purified, fluorescently labeled in vitro translation systems, the advent of single-molecule fluorescence imaging has ushered in a new era in high-resolution mechanistic studies of ribosome-catalyzed protein synthesis, or translation. Together with ensemble biochemical investigations of translation and structural studies of functional ribosomal complexes, in vitro single-molecule fluorescence imaging of protein synthesis is providing unique mechanistic insight into this fundamental biological process. More recently, rapidly evolving breakthroughs in fluorescence-based molecular imaging in live cells with sub-diffraction-limit spatial resolution and ever-increasing temporal resolution provide great promise for conducting mechanistic studies of translation and its regulation in living cells. Here we review the remarkable recent progress that has been made in these fields, highlight important mechanistic insights that have been gleaned from these studies thus far, and discuss what we envision lies ahead as these approaches continue to evolve and expand to address increasingly complex mechanistic and regulatory aspects of translation.
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56
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Hoskins AA, Gelles J, Moore MJ. New insights into the spliceosome by single molecule fluorescence microscopy. Curr Opin Chem Biol 2011; 15:864-70. [PMID: 22057211 DOI: 10.1016/j.cbpa.2011.10.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 10/10/2011] [Accepted: 10/17/2011] [Indexed: 11/17/2022]
Abstract
Splicing is an essential eukaryotic process in which introns are excised from precursors to messenger RNAs and exons ligated together. This reaction is catalyzed by a multi-MegaDalton machine called the spliceosome, composed of 5 small nuclear RNAs (snRNAs) and a core set of ∼100 proteins minimally required for activity. Because of the spliceosome's size, its low abundance in cellular extracts, and its highly dynamic assembly pathway, analysis of the kinetics of splicing and the conformational rearrangements occurring during spliceosome assembly and disassembly has proven extraordinarily challenging. Here, we review recent progress in combining chemical biology methodologies with single molecule fluorescence techniques to provide a window into splicing in real time. These methods complement ensemble measurements of splicing in vivo and in vitro to facilitate kinetic dissection of pre-mRNA splicing.
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MESH Headings
- Biotin/chemistry
- Biotin/metabolism
- Exons
- Fluorescence Resonance Energy Transfer
- Fluorescent Dyes/analysis
- Fluorescent Dyes/chemistry
- Introns
- Microscopy, Fluorescence/methods
- RNA Precursors/analysis
- RNA Precursors/chemistry
- RNA Precursors/metabolism
- RNA Splicing/genetics
- RNA, Fungal/analysis
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- RNA, Small Nuclear/analysis
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/analysis
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Spliceosomes/chemistry
- Spliceosomes/genetics
- Spliceosomes/metabolism
- Staining and Labeling/methods
- Streptavidin/chemistry
- Streptavidin/metabolism
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Affiliation(s)
- Aaron A Hoskins
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605, USA.
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57
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Vohlander Rasmussen LC, Oliveira CLP, Pedersen JS, Sperling-Petersen HU, Mortensen KK. Structural transitions of translation initiation factor IF2 upon GDPNP and GDP binding in solution. Biochemistry 2011; 50:9779-87. [PMID: 21988058 DOI: 10.1021/bi200938q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three protein factors ensure rapid and accurate initiation of translation in bacteria. Translation initiation factor IF2 is a ribosome-dependent GTPase, which is important for correct positioning of initiator tRNA on the 30S subunit as well as ribosomal subunit joining. The solution structure of the free C-terminal part of IF2 (IF2C, comprising domains IV to VI-2) was previously determined by small-angle X-ray scattering (SAXS) [Rasmussen, L. C., et al. (2008) Biochemistry 47, 5590-5598]. In this study, adding GDP or nonhydrolyzable GTP analogue GDPNP to the protein in solution caused structural changes in the protein, in agreement with recent data determined via isothermal titration calorimetry [Hauryliuk, V., et al. (2009) J. Mol. Biol. 394, 621-626]. The p(r) function indicated an elongated conformation supported by radii of gyration of 40.1 and 44.9 Å and maximum dimensions of ~125 and ~150 Å for IF2C with GDPNP and GDP, respectively. The SAXS data were used to model the structure of IF2C bound to either GDPNP or GDP. The structural transitions of IF2C upon GDPNP binding and following nucleotide hydrolysis support the concept of cofactor-dependent conformational switching rather than the classical model for GTPase activity.
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58
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Julián P, Milon P, Agirrezabala X, Lasso G, Gil D, Rodnina MV, Valle M. The Cryo-EM structure of a complete 30S translation initiation complex from Escherichia coli. PLoS Biol 2011; 9:e1001095. [PMID: 21750663 PMCID: PMC3130014 DOI: 10.1371/journal.pbio.1001095] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 05/24/2011] [Indexed: 12/04/2022] Open
Abstract
Formation of the 30S initiation complex (30S IC) is an important checkpoint in regulation of gene expression. The selection of mRNA, correct start codon, and the initiator fMet-tRNAfMet requires the presence of three initiation factors (IF1, IF2, IF3) of which IF3 and IF1 control the fidelity of the process, while IF2 recruits fMet-tRNAfMet. Here we present a cryo-EM reconstruction of the complete 30S IC, containing mRNA, fMet-tRNAfMet, IF1, IF2, and IF3. In the 30S IC, IF2 contacts IF1, the 30S subunit shoulder, and the CCA end of fMet-tRNAfMet, which occupies a novel P/I position (P/I1). The N-terminal domain of IF3 contacts the tRNA, whereas the C-terminal domain is bound to the platform of the 30S subunit. Binding of initiation factors and fMet-tRNAfMet induces a rotation of the head relative to the body of the 30S subunit, which is likely to prevail through 50S subunit joining until GTP hydrolysis and dissociation of IF2 take place. The structure provides insights into the mechanism of mRNA selection during translation initiation. Translation is the process by which a ribosome converts the sequence of a messenger RNA (mRNA)—produced from a gene—into the sequence of amino acids that comprise a protein. Bacterial ribosomes each have one large and one small subunit: the 50S and 30S subunits. Initiation of translation entails selection of an mRNA, identification of the correct starting point from which to read its code, and engagement of the initial amino acid carrier (tRNA). These events take place in the 30S subunit and require the presence of three initiation factors (IF1, IF2, IF3). Formation of this 30S initiation complex precedes joining with the 50S subunit to assemble the functional ribosome. By using a cryo-electron microscopy approach to visualize the structures without fixation or staining, we have determined the structure of a complete 30S initiation complex and identified the positions and orientations of the tRNA and all three initiation factors. We found that the presence of the initiation factors and tRNA induces rotation of the head relative to the body of the 30S subunit, which may be essential for rapid binding to the 50S subunit and for regulating selection of the mRNA. IF3 had not been seen previously in the context of the 30S structure and its visualization gives insight into a potential role in preventing association of the two ribosomal subunits. These findings are important for understanding how the interplay of elements during the early stages of translation selects the mRNA and regulates formation of functional ribosomes.
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Affiliation(s)
- Patricia Julián
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Parque Tecnológico de Bizkaia, Derio, Spain
| | - Pohl Milon
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Xabier Agirrezabala
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Parque Tecnológico de Bizkaia, Derio, Spain
| | - Gorka Lasso
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Parque Tecnológico de Bizkaia, Derio, Spain
| | - David Gil
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Parque Tecnológico de Bizkaia, Derio, Spain
| | - Marina V. Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Mikel Valle
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Parque Tecnológico de Bizkaia, Derio, Spain
- Department of Biochemistry and Molecular Biology. Faculty of Science and Technology, University of the Basque Country, Bilbao, Spain
- * E-mail:
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59
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Abstract
The last 15 years have witnessed the development of tools that allow the observation and manipulation of single molecules. The rapidly expanding application of these technologies for investigating biological systems of ever-increasing complexity is revolutionizing our ability to probe the mechanisms of biological reactions. Here, we compare the mechanistic information available from single-molecule experiments with the information typically obtained from ensemble studies and show how these two experimental approaches interface with each other. We next present a basic overview of the toolkit for observing and manipulating biology one molecule at a time. We close by presenting a case study demonstrating the impact that single-molecule approaches have had on our understanding of one of life's most fundamental biochemical reactions: the translation of a messenger RNA into its encoded protein by the ribosome.
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Affiliation(s)
- Ignacio Tinoco
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA
| | - Ruben L. Gonzalez
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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60
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Zheng A, Yamamoto R, Sokabe M, Tanaka I, Yao M. Crystallization and preliminary X-ray crystallographic analysis of eIF5BΔN and the eIF5BΔN-eIF1AΔN complex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:730-3. [PMID: 21636924 PMCID: PMC3107155 DOI: 10.1107/s1744309111015910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 04/27/2011] [Indexed: 11/10/2022]
Abstract
The binding between two universally conserved translation initiation factors, eIF5B and eIF1A, is important in the initiation step of eukaryotic protein synthesis on the ribosome. Through this interaction, eIF1A assists in recruiting eIF5B to the initiating 40S subunit; eIF5B then encourages the joining of the 60S subunit to form an initiating 80S ribosome. Here, the expression, purification, crystallization and preliminary X-ray analyses of eIF5BΔN and the eIF5BΔN-eIF1AΔN complex from Saccharomyces cerevisiae are reported. The crystal of eIF5BΔN diffracted to 2.45 Å resolution and belonged to space group P4(1)2(1)2, with unit-cell parameters a = b = 130.0, c = 71.7 Å. The asymmetric unit was estimated to contain one molecule. The initial phase was obtained by Se-SAD. The crystal of the eIF5BΔN-eIF1AΔN complex diffracted to 3.3 Å resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 101.9, b = 120.9, c = 132.8 Å. The asymmetric unit was estimated to contain two complex molecules.
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Affiliation(s)
- Aiping Zheng
- Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Reo Yamamoto
- Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Masaaki Sokabe
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Isao Tanaka
- Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Min Yao
- Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
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61
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Chen C, Stevens B, Kaur J, Cabral D, Liu H, Wang Y, Zhang H, Rosenblum G, Smilansky Z, Goldman YE, Cooperman BS. Single-molecule fluorescence measurements of ribosomal translocation dynamics. Mol Cell 2011; 42:367-77. [PMID: 21549313 PMCID: PMC3090999 DOI: 10.1016/j.molcel.2011.03.024] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 12/01/2010] [Accepted: 03/08/2011] [Indexed: 11/22/2022]
Abstract
We employ single-molecule fluorescence resonance energy transfer (smFRET) to study structural dynamics over the first two elongation cycles of protein synthesis, using ribosomes containing either Cy3-labeled ribosomal protein L11 and A- or P-site Cy5-labeled tRNA or Cy3- and Cy5-labeled tRNAs. Pretranslocation (PRE) complexes demonstrate fluctuations between classical and hybrid forms, with concerted motions of tRNAs away from L11 and from each other when classical complex converts to hybrid complex. EF-G⋅GTP binding to both hybrid and classical PRE complexes halts these fluctuations prior to catalyzing translocation to form the posttranslocation (POST) complex. EF-G dependent translocation from the classical PRE complex proceeds via transient formation of a short-lived hybrid intermediate. A-site binding of either EF-G to the PRE complex or of aminoacyl-tRNA⋅EF-Tu ternary complex to the POST complex markedly suppresses ribosome conformational lability.
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Affiliation(s)
- Chunlai Chen
- Pennsylvania Muscle Institute, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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62
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Dynamics of the translational machinery. Curr Opin Struct Biol 2011; 21:137-45. [PMID: 21256733 DOI: 10.1016/j.sbi.2010.11.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Accepted: 11/25/2010] [Indexed: 11/20/2022]
Abstract
The recent growth in single molecule studies of translation has provided an insight into the molecular mechanism of ribosomal function. Single molecule fluorescence approaches allowed direct observation of the structural rearrangements occurring during translation and revealed dynamic motions of the ribosome and its ligands. These studies demonstrated how ligand binding affects dynamics of the ribosome, and the role of the conformational sampling in large-scale rearrangements intrinsic to translation elongation. The application of time-resolved cryo-electron microscopy revealed new conformational intermediates during back-translocation providing an insight into ribosomal dynamics from an alternative perspective. Recent developments permitted examination of conformational and compositional dynamics of the ribosome in real-time through multiple cycles of elongation at the single molecule level. The zero-mode waveguide approach allowed direct observation of the compositional dynamics of tRNA occupancy on the elongating ribosome. The emergence of single molecule in vivo techniques provided insights into the mechanism and regulation of translation at the organismal level.
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63
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Abstract
Our current understanding of the mechanism of translation is based on nearly fifty years of biochemical and biophysical studies. This mechanism, which requires the ribosome to manipulate tRNA and step repetitively along the mRNA, implies movement. High-resolution structures of the ribosome and its ligands have recently described translation in atomic detail, capturing the endpoints of large-scale rearrangements of the ribosome. Direct observation of the dynamic events that underlie the mechanism of translation is challenged by ensemble averaging in bulk solutions. Single-molecule methods, which eliminate these averaging effects, have emerged as powerful tools to probe the mechanism of translation. Single-molecule fluorescence experiments have described the dynamic motion of the ribosome and tRNA. Single-molecule force measurements have directly probed the forces stabilizing ribosomal complexes. Recent developments have allowed real-time observation of ribosome movement and dynamics during translation. This review covers the contributions of single-molecule studies to our understanding of the dynamic nature of translation.
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64
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Aitken CE, Puglisi JD. Following the intersubunit conformation of the ribosome during translation in real time. Nat Struct Mol Biol 2010; 17:793-800. [PMID: 20562856 PMCID: PMC4459212 DOI: 10.1038/nsmb.1828] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 04/08/2010] [Indexed: 11/09/2022]
Abstract
We report the direct observation of conformational rearrangements of the ribosome during multiple rounds of elongation. Using single-molecule fluorescence resonance energy transfer, we monitored the intersubunit conformation of the ribosome in real time as it proceeds from codon to codon. During each elongation cycle, the ribosome unlocks upon peptide bond formation, then reverts to the locked state upon translocation onto the next codon. Our data reveal both the specific and cumulative effects of antibiotics on individual steps of translation and uncover the processivity of the ribosome as it elongates. Our approach interrogates the precise molecular events occurring at each codon of the mRNA within the full context of ongoing translation.
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65
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Real-time tRNA transit on single translating ribosomes at codon resolution. Nature 2010; 464:1012-7. [PMID: 20393556 PMCID: PMC4466108 DOI: 10.1038/nature08925] [Citation(s) in RCA: 273] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 02/18/2010] [Indexed: 11/23/2022]
Abstract
Translation by the ribosome occurs by a complex mechanism involving the coordinated interaction of multiple nucleic acid and protein ligands. Here we have used zero-mode waveguides (ZMWs) and sophisticated detection instrumentation to allow real-time observation of translation at physiologically-relevant (μM) ligand concentrations. Translation at each codon is monitored by stable binding of tRNAs – labeled with distinct fluorophores – to translating ribosomes, allowing direct detection of the identity of tRNA molecules bound to the ribosome, and therefore, the underlying mRNA sequence. We observe the transit of tRNAs on single translating ribosomes and have determined the number of tRNA molecules simultaneously bound to the ribosome, at each codon of an mRNA. Our results show that ribosomes are only briefly occupied by two tRNAs and that release of deacylated tRNA from the E site is uncoupled from binding of A-site tRNA and occurs rapidly after translocation. The methods outlined here have broad application to the study of mRNA sequences, and the mechanism and regulation of translation.
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66
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Petrov A, Puglisi JD. Site-specific labeling of Saccharomyces cerevisiae ribosomes for single-molecule manipulations. Nucleic Acids Res 2010; 38:e143. [PMID: 20501598 PMCID: PMC2910073 DOI: 10.1093/nar/gkq390] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Site-specific labeling of Escherichia coli ribosomes has allowed application of single-molecule fluorescence spectroscopy and force methods to probe the mechanism of translation. To apply these approaches to eukaryotic translation, eukaryotic ribosomes must be specifically labeled with fluorescent labels and molecular handles. Here, we describe preparation and labeling of the small and large yeast ribosomal subunits. Phylogenetically variable hairpin loops in ribosomal RNA are mutated to allow hybridization of oligonucleotides to mutant ribosomes. We demonstrate specific labeling of the ribosomal subunits, and their use in single-molecule fluorescence and force experiments.
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Affiliation(s)
- Alexey Petrov
- Department of Structural Biology and Stanford Magnetic Resonance Laboratory, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
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67
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The ribosomal stalk plays a key role in IF2-mediated association of the ribosomal subunits. J Mol Biol 2010; 399:145-53. [PMID: 20385143 DOI: 10.1016/j.jmb.2010.04.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 04/05/2010] [Accepted: 04/06/2010] [Indexed: 11/22/2022]
Abstract
Ribosomal "stalk" protein L12 is known to activate translational GTPases EF-G and EF-Tu, but not much is known about its role in relation to other two translational G factors, IF2 and RF3. Here, we have clarified the role of L12 in IF2-mediated initiation of bacterial protein synthesis. With fast kinetics measurements, we have compared L12-depleted 50S subunits with the native ones in subunit association, GTP hydrolysis, P(i) (inorganic phosphate) release and IF2 release assays. L12 depletion from 50S subunit slows the subunit association step significantly ( approximately 40 fold) only when IF2.GTP is present on the 30S preinitiation complex. This demonstrates that rapid subunit association depends on a specific interaction between the L12 stalk on the 50S subunit and IF2.GTP on the 30S subunit. L12 depletion, however, did not affect the individual rates of the subsequent steps including GTP hydrolysis on IF2 and P(i) release. Thus, L12 is not a GTPase activating protein (GAP) for IF2 unlike as suggested for EF-G and EF-Tu.
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68
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Munro JB, Altman RB, Tung CS, Sanbonmatsu KY, Blanchard SC. A fast dynamic mode of the EF-G-bound ribosome. EMBO J 2010; 29:770-81. [PMID: 20033061 PMCID: PMC2829159 DOI: 10.1038/emboj.2009.384] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 11/23/2009] [Indexed: 11/09/2022] Open
Abstract
A key intermediate in translocation is an 'unlocked state' of the pre-translocation ribosome in which the P-site tRNA adopts the P/E hybrid state, the L1 stalk domain closes and ribosomal subunits adopt a ratcheted configuration. Here, through two- and three-colour smFRET imaging from multiple structural perspectives, EF-G is shown to accelerate structural and kinetic pathways in the ribosome, leading to this transition. The EF-G-bound ribosome remains highly dynamic in nature, wherein, the unlocked state is transiently and reversibly formed. The P/E hybrid state is energetically favoured, but exchange with the classical P/P configuration persists; the L1 stalk adopts a fast dynamic mode characterized by rapid cycles of closure and opening. These data support a model in which P/E hybrid state formation, L1 stalk closure and subunit ratcheting are loosely coupled, independent processes that must converge to achieve the unlocked state. The highly dynamic nature of these motions, and their sensitivity to conformational and compositional changes in the ribosome, suggests that regulating the formation of this intermediate may present an effective avenue for translational control.
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Affiliation(s)
- James B Munro
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Roger B Altman
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Chang-Shung Tung
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Kevin Y Sanbonmatsu
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
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András CD, Csajági C, Orbán CK, Albert C, Ábrahám B, Miklóssy I. A possible explanation of the germicide effect of carbon dioxide in supercritical state based on molecular-biological evidence. Med Hypotheses 2010; 74:325-9. [DOI: 10.1016/j.mehy.2009.08.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 08/24/2009] [Indexed: 12/01/2022]
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Fei J, Wang J, Sternberg SH, MacDougall DD, Elvekrog MM, Pulukkunat DK, Englander MT, Gonzalez RL. A highly purified, fluorescently labeled in vitro translation system for single-molecule studies of protein synthesis. Methods Enzymol 2010; 472:221-59. [PMID: 20580967 PMCID: PMC4748369 DOI: 10.1016/s0076-6879(10)72008-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) has emerged as a powerful tool for mechanistic investigations of increasingly complex biochemical systems. Recently, we and others have successfully used smFRET to directly investigate the role of structural dynamics in the function and regulation of the cellular protein synthesis machinery. A significant challenge to these experiments, and to analogous experiments in similarly complex cellular machineries, is the need for specific and efficient fluorescent labeling of the biochemical system at locations that are both mechanistically informative and minimally perturbative to the biological activity. Here, we describe the development of a highly purified, fluorescently labeled in vitro translation system that we have successfully designed for smFRET studies of protein synthesis. The general approaches we outline should be amenable to single-molecule fluorescence studies of other complex biochemical systems.
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Affiliation(s)
- Jingyi Fei
- Department of Chemistry, Columbia University, New York, NY 10027 Tel.: (212) 854-0162 FAX: (212) 932-1289 J.F. J.W. D.D.M M.M.E. D.K.P. M.T.E.
| | - Jiangning Wang
- Department of Chemistry, Columbia University, New York, NY 10027 Tel.: (212) 854-0162 FAX: (212) 932-1289 J.F. J.W. D.D.M M.M.E. D.K.P. M.T.E.
| | - Samuel H. Sternberg
- Department of Chemistry, Columbia University, New York, NY 10027 Tel.: (212) 854-0162 FAX: (212) 932-1289 J.F. J.W. D.D.M M.M.E. D.K.P. M.T.E.
| | - Daniel D. MacDougall
- Department of Chemistry, Columbia University, New York, NY 10027 Tel.: (212) 854-0162 FAX: (212) 932-1289 J.F. J.W. D.D.M M.M.E. D.K.P. M.T.E.
| | - Margaret M. Elvekrog
- Department of Chemistry, Columbia University, New York, NY 10027 Tel.: (212) 854-0162 FAX: (212) 932-1289 J.F. J.W. D.D.M M.M.E. D.K.P. M.T.E.
| | - Dileep K. Pulukkunat
- Department of Chemistry, Columbia University, New York, NY 10027 Tel.: (212) 854-0162 FAX: (212) 932-1289 J.F. J.W. D.D.M M.M.E. D.K.P. M.T.E.
| | - Michael T. Englander
- Department of Chemistry, Columbia University, New York, NY 10027 Tel.: (212) 854-0162 FAX: (212) 932-1289 J.F. J.W. D.D.M M.M.E. D.K.P. M.T.E.
- Integrated Program in Cellular, Molecular, and Biomedical Sciences
| | - Ruben L. Gonzalez
- Department of Chemistry, Columbia University, New York, NY 10027 Tel.: (212) 854-1096 FAX: (212) 932-1289
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Abstract
There is mounting evidence indicating that protein synthesis is driven and regulated by mechanisms that direct stochastic, large-scale conformational fluctuations of the translational apparatus. This mechanistic paradigm implies that a free-energy landscape governs the conformational states that are accessible to and sampled by the translating ribosome. This scenario presents interdependent opportunities and challenges for structural and dynamic studies of protein synthesis. Indeed, the synergism between cryogenic electron microscopic and X-ray crystallographic structural studies, on the one hand, and single-molecule fluorescence resonance energy transfer (smFRET) dynamic studies, on the other, is emerging as a powerful means for investigating the complex free-energy landscape of the translating ribosome and uncovering the mechanisms that direct the stochastic conformational fluctuations of the translational machinery. In this review, we highlight the principal insights obtained from cryogenic electron microscopic, X-ray crystallographic, and smFRET studies of the elongation stage of protein synthesis and outline the emerging themes, questions, and challenges that lie ahead in mechanistic studies of translation.
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Affiliation(s)
- Joachim Frank
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, New York 10032
- Department of Biological Sciences, Columbia University, New York City, New York 10027
| | - Ruben L. Gonzalez
- Department of Chemistry, Columbia University, New York City, New York 10027
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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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