51
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Jamiolkowski RM, Chen C, Cooperman BS, Goldman YE. tRNA Fluctuations Observed on Stalled Ribosomes Are Suppressed during Ongoing Protein Synthesis. Biophys J 2018; 113:2326-2335. [PMID: 29211986 DOI: 10.1016/j.bpj.2017.08.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/25/2017] [Accepted: 08/30/2017] [Indexed: 01/13/2023] Open
Abstract
The pretranslocation complex of the ribosome can undergo spontaneous fluctuations of messenger RNA and transfer RNAs (tRNAs) between classical and hybrid states, and occupation of the hybrid tRNA positions has been proposed to precede translocation. The classical and hybrid state tRNA positions have been extensively characterized when the ribosome is stalled along the messenger RNA by either the absence or delayed addition of elongation factor G (EF-G), or by the presence of antibiotics or GTP analogs that block translocation. However, during multiple ongoing elongation cycles when both EF-G and ternary complexes are present, EF-G can bind to the pretranslocation complex much faster than the timescale of the classic-hybrid transitions. Using single-molecule fluorescence resonance energy transfer between adjacent tRNAs and between A-site tRNA and ribosomal protein L11, we found that the tRNAs do not fluctuate between the hybrid and classical states, but instead adopt a position with fluorescence resonance energy transfer efficiencies between those of the stalled classical and hybrid states.
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Affiliation(s)
- Ryan M Jamiolkowski
- Pennsylvania Muscle Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Chunlai Chen
- Pennsylvania Muscle Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania; School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Yale E Goldman
- Pennsylvania Muscle Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
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52
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Noller HF, Lancaster L, Zhou J, Mohan S. The ribosome moves: RNA mechanics and translocation. Nat Struct Mol Biol 2017; 24:1021-1027. [PMID: 29215639 DOI: 10.1038/nsmb.3505] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/13/2017] [Indexed: 11/09/2022]
Abstract
During protein synthesis, mRNA and tRNAs must be moved rapidly through the ribosome while maintaining the translational reading frame. This process is coupled to large- and small-scale conformational rearrangements in the ribosome, mainly in its rRNA. The free energy from peptide-bond formation and GTP hydrolysis is probably used to impose directionality on those movements. We propose that the free energy is coupled to two pawls, namely tRNA and EF-G, which enable two ratchet mechanisms to act separately and sequentially on the two ribosomal subunits.
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Affiliation(s)
- Harry F Noller
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, California, USA
| | - Laura Lancaster
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, California, USA
| | - Jie Zhou
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, California, USA
| | - Srividya Mohan
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, California, USA
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53
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Noller HF. The parable of the caveman and the Ferrari: protein synthesis and the RNA world. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0187. [PMID: 28138073 DOI: 10.1098/rstb.2016.0187] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 11/12/2022] Open
Abstract
The basic steps of protein synthesis are carried out by the ribosome, a very large and complex ribonucleoprotein particle. In keeping with its proposed emergence from an RNA world, all three of its core mechanisms-aminoacyl-tRNA selection, catalysis of peptide bond formation and coupled translocation of mRNA and tRNA-are embodied in the properties of ribosomal RNA, while its proteins play a supportive role.This article is part of the themed issue 'Perspectives on the ribosome'.
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Affiliation(s)
- Harry F Noller
- Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, CA 95064, USA .,Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
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54
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Frank J. The translation elongation cycle-capturing multiple states by cryo-electron microscopy. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0180. [PMID: 28138066 DOI: 10.1098/rstb.2016.0180] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 12/17/2022] Open
Abstract
During the work cycle of elongation, the ribosome, a molecular machine of vast complexity, exists in a large number of states distinguished by constellation of its subunits, its subunit domains and binding partners. Single-particle cryogenic electron microscopy (cryo-EM), developed over the past 40 years, is uniquely suited to determine the structure of molecular machines in their native states. With the emergence, 10 years ago, of unsupervised clustering techniques in the analysis of single-particle data, it has been possible to determine multiple structures from a sample containing ribosomes equilibrating in different thermally accessible states. In addition, recent advances in detector technology have made it possible to reach near-atomic resolution for some of these states. With these capabilities, single-particle cryo-EM has been at the forefront of exploring ribosome dynamics during its functional cycle, along with single-molecule fluorescence resonance energy transfer and molecular dynamics computations, offering insights into molecular architecture uniquely honed by evolution to capitalize on thermal energy in the ambient environment.This article is part of the themed issue 'Perspectives on the ribosome'.
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Affiliation(s)
- Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, Black Building, 650 W. 168th Street, New York, NY 10032, USA .,Howard Hughes Medical Institute, Columbia University, Black Building, 650 W. 168th Street, New York, NY 10032, USA.,Department of Biological Sciences, Columbia University, Black Building, 650 W. 168th Street, New York, NY 10032, USA
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55
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Heuer A, Thomson E, Schmidt C, Berninghausen O, Becker T, Hurt E, Beckmann R. Cryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae. eLife 2017; 6. [PMID: 29155690 PMCID: PMC5695908 DOI: 10.7554/elife.30189] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/03/2017] [Indexed: 01/10/2023] Open
Abstract
Mechanistic understanding of eukaryotic ribosome formation requires a detailed structural knowledge of the numerous assembly intermediates, generated along a complex pathway. Here, we present the structure of a late pre-40S particle at 3.6 Å resolution, revealing in molecular detail how assembly factors regulate the timely folding of pre-18S rRNA. The structure shows that, rather than sterically blocking 40S translational active sites, the associated assembly factors Tsr1, Enp1, Rio2 and Pno1 collectively preclude their final maturation, thereby preventing untimely tRNA and mRNA binding and error prone translation. Moreover, the structure explains how Pno1 coordinates the 3’end cleavage of the 18S rRNA by Nob1 and how the late factor’s removal in the cytoplasm ensures the structural integrity of the maturing 40S subunit.
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Affiliation(s)
- André Heuer
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Emma Thomson
- Heidelberg University Biochemistry Center, Heidelberg University, Heidelberg, Germany
| | - Christian Schmidt
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Otto Berninghausen
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Thomas Becker
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Ed Hurt
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany.,Heidelberg University Biochemistry Center, Heidelberg University, Heidelberg, Germany
| | - Roland Beckmann
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany
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56
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López-Alonso JP, Kaminishi T, Kikuchi T, Hirata Y, Iturrioz I, Dhimole N, Schedlbauer A, Hase Y, Goto S, Kurita D, Muto A, Zhou S, Naoe C, Mills DJ, Gil-Carton D, Takemoto C, Himeno H, Fucini P, Connell SR. RsgA couples the maturation state of the 30S ribosomal decoding center to activation of its GTPase pocket. Nucleic Acids Res 2017; 45:6945-6959. [PMID: 28482099 PMCID: PMC5499641 DOI: 10.1093/nar/gkx324] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 04/19/2017] [Indexed: 01/18/2023] Open
Abstract
During 30S ribosomal subunit biogenesis, assembly factors are believed to prevent accumulation of misfolded intermediate states of low free energy that slowly convert into mature 30S subunits, namely, kinetically trapped particles. Among the assembly factors, the circularly permuted GTPase, RsgA, plays a crucial role in the maturation of the 30S decoding center. Here, directed hydroxyl radical probing and single particle cryo-EM are employed to elucidate RsgA΄s mechanism of action. Our results show that RsgA destabilizes the 30S structure, including late binding r-proteins, providing a structural basis for avoiding kinetically trapped assembly intermediates. Moreover, RsgA exploits its distinct GTPase pocket and specific interactions with the 30S to coordinate GTPase activation with the maturation state of the 30S subunit. This coordination validates the architecture of the decoding center and facilitates the timely release of RsgA to control the progression of 30S biogenesis.
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Affiliation(s)
- Jorge Pedro López-Alonso
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Tatsuya Kaminishi
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Takeshi Kikuchi
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Yuya Hirata
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Idoia Iturrioz
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Neha Dhimole
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Andreas Schedlbauer
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Yoichi Hase
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Simon Goto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Akira Muto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Shu Zhou
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Chieko Naoe
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Deryck J Mills
- Max Planck Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - David Gil-Carton
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Chie Takemoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Hyouta Himeno
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Paola Fucini
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Sean R Connell
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
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57
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Ribosome structural dynamics in translocation: yet another functional role for ribosomal RNA. Q Rev Biophys 2017; 50:e12. [DOI: 10.1017/s0033583517000117] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractRibosomes are remarkable ribonucleoprotein complexes that are responsible for protein synthesis in all forms of life. They polymerize polypeptide chains programmed by nucleotide sequences in messenger RNA in a mechanism mediated by transfer RNA. One of the most challenging problems in the ribosome field is to understand the mechanism of coupled translocation of mRNA and tRNA during the elongation phase of protein synthesis. In recent years, the results of structural, biophysical and biochemical studies have provided extensive evidence that translocation is based on the structural dynamics of the ribosome itself. Detailed structural analysis has shown that ribosome dynamics, like aminoacyl-tRNA selection and catalysis of peptide bond formation, is made possible by the properties of ribosomal RNA.
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58
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Gulay SP, Bista S, Varshney A, Kirmizialtin S, Sanbonmatsu KY, Dinman JD. Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle. Nucleic Acids Res 2017; 45:4958-4971. [PMID: 28334755 PMCID: PMC5416885 DOI: 10.1093/nar/gkx112] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 02/06/2017] [Indexed: 11/15/2022] Open
Abstract
Chemical modification was used to quantitatively determine the flexibility of nearly the entire rRNA component of the yeast ribosome through 8 discrete stages of translational elongation, revealing novel observations at the gross and fine-scales. These include (i) the bulk transfer of energy through the intersubunit bridges from the large to the small subunit after peptidyltransfer, (ii) differences in the interaction of the sarcin ricin loop with the two elongation factors and (iii) networked information exchange pathways that may functionally facilitate intra- and intersubunit coordination, including the 5.8S rRNA. These analyses reveal hot spots of fluctuations that set the stage for large-scale conformational changes essential for translocation and enable the first molecular dynamics simulation of an 80S complex. Comprehensive datasets of rRNA base flexibilities provide a unique resource to the structural biology community that can be computationally mined to complement ongoing research toward the goal of understanding the dynamic ribosome.
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Affiliation(s)
- Suna P Gulay
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sujal Bista
- Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - Amitabh Varshney
- Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - Serdal Kirmizialtin
- Chemistry Program, New York University Abu Dhabi, Abu Dhabi, UAE.,The New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Karissa Y Sanbonmatsu
- The New Mexico Consortium, Los Alamos, NM 87544, USA.,Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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59
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Effect of Fusidic Acid on the Kinetics of Molecular Motions During EF-G-Induced Translocation on the Ribosome. Sci Rep 2017; 7:10536. [PMID: 28874811 PMCID: PMC5585275 DOI: 10.1038/s41598-017-10916-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/16/2017] [Indexed: 11/08/2022] Open
Abstract
The translocation step of protein synthesis entails binding and dissociation of elongation factor G (EF-G), movements of the two tRNA molecules, and motions of the ribosomal subunits. The translocation step is targeted by many antibiotics. Fusidic acid (FA), an antibiotic that blocks EF-G on the ribosome, may also interfere with some of the ribosome rearrangements, but the exact timing of inhibition remains unclear. To follow in real-time the dynamics of the ribosome–tRNA–EF-G complex, we have developed a fluorescence toolbox which allows us to monitor the key molecular motions during translocation. Here we employed six different fluorescence observables to investigate how FA affects translocation kinetics. We found that FA binds to an early translocation intermediate, but its kinetic effect on tRNA movement is small. FA does not affect the synchronous forward (counterclockwise) movements of the head and body domains of the small ribosomal subunit, but exerts a strong effect on the rates of late translocation events, i.e. backward (clockwise) swiveling of the head domain and the transit of deacylated tRNA through the E′ site, in addition to blocking EF-G dissociation. The use of ensemble kinetics and numerical integration unraveled how the antibiotic targets molecular motions within the ribosome-EF-G complex.
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60
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Maji S, Shahoei R, Schulten K, Frank J. Quantitative Characterization of Domain Motions in Molecular Machines. J Phys Chem B 2017; 121:3747-3756. [PMID: 28199113 PMCID: PMC5479934 DOI: 10.1021/acs.jpcb.6b10732] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The work of molecular machines such as the ribosome is accompanied by conformational changes, often characterized by relative motions of their domains. The method we have developed seeks to quantify these motions in a general way, facilitating comparisons of results obtained by different researchers. Typically there are multiple snapshots of a structure in the form of pdb coordinates resulting from flexible fitting of low-resolution density maps, from X-ray crystallography, or from molecular dynamics simulation trajectories. Our objective is to characterize the motion of each domain as a coordinate transformation using moments of inertia tensor, a method we developed earlier. What has been missing until now are ancillary tools that make this task practical, general, and biologically informative. We have provided a comprehensive solution to this task with a set of tools implemented on the VMD platform. These tools address the need for reproducible segmentation of domains, and provide a generalized description of their motions using principal axes of inertia. Although this methodology has been specifically developed for studying ribosome motion, it is applicable to any molecular machine.
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Affiliation(s)
- Suvrajit Maji
- Department of Biochemistry and Molecular Biophysics, Columbia University
| | - Rezvan Shahoei
- Department of Physics, University of Illinois at Urbana-Champaign
- Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign
- Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University
- Howard Hughes Medical Institute, Columbia University
- Department of Biological Sciences, Columbia University
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61
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Recurring RNA structural motifs underlie the mechanics of L1 stalk movement. Nat Commun 2017; 8:14285. [PMID: 28176782 PMCID: PMC5309774 DOI: 10.1038/ncomms14285] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/15/2016] [Indexed: 01/19/2023] Open
Abstract
The L1 stalk of the large ribosomal subunit undergoes large-scale movements coupled to the translocation of deacylated tRNA during protein synthesis. We use quantitative comparative structural analysis to localize the origins of L1 stalk movement and to understand its dynamic interactions with tRNA and other structural elements of the ribosome. Besides its stacking interactions with the tRNA elbow, stalk movement is directly linked to intersubunit rotation, rotation of the 30S head domain and contact of the acceptor arm of deacylated tRNA with helix 68 of 23S rRNA. Movement originates from pivoting at stacked non-canonical base pairs in a Family A three-way junction and bending in an internal G-U-rich zone. Use of these same motifs as hinge points to enable such dynamic events as rotation of the 30S subunit head domain and in flexing of the anticodon arm of tRNA suggests that they represent general strategies for movement of functional RNAs. Translocation of the tRNA on the ribosome is associated with large-scale molecular movements of the ribosomal L1 stalk. Here the authors identify the key determinants that allow these dramatic movements, and suggest they represent general strategies used to enable large-scale motions in functional RNAs.
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62
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Xie P. On the pathway of ribosomal translocation. Int J Biol Macromol 2016; 92:401-415. [PMID: 27431796 DOI: 10.1016/j.ijbiomac.2016.07.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/12/2016] [Accepted: 07/14/2016] [Indexed: 11/29/2022]
Abstract
The translocation of tRNAs coupled with mRNA in the ribosome is a critical process in the elongation cycle of protein synthesis. The translocation entails large-scale conformational changes of the ribosome and involves several intermediate states with tRNAs in different positions with respect to 30S and 50S ribosomal subunits. However, the detailed role of the intermediate states is unknown and the detailed mechanism and pathway of translocation is unclear. Here based on previous structural, biochemical and single-molecule data we present a translocation pathway by incorporating several intermediate states. With the pathway, we study theoretically (i) the kinetics of 30S head rotation associated with translocation catalyzed by wild-type EF-G, (ii) the dynamics of fluctuations between different tRNA states during translocation interfered with EF-G mutants and translocation-specific antibiotics, (iii) the kinetics of tRNA movement in 50S subunit and mRNA movement in 30S subunit in the presence of wild-type EF-G, EF-G mutants and translocation-specific antibiotics, (iv) the dynamics of EF-G sampling to the ribosome during translocation, etc., providing consistent and quantitative explanations of various available biochemical and single-molecule experimental data published in the literature. Moreover, we study the kinetics of 30S head rotation in the presence of EF-G mutants, providing predicted results. These have significant implications for the molecular mechanism and pathway of ribosomal translocation.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
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63
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Rahrig RR, Zirbel CL. DETECTING CONFORMATIONAL DIFFERENCES BETWEEN RNA 3D STRUCTURES. JP JOURNAL OF BIOSTATISTICS 2016; 12:99-115. [PMID: 27330250 DOI: 10.17654/jpjbdec2015_099_115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
A method is described for detecting local conformational differences between two 3D structures of the same RNA molecule. These could be distinct 3D structures of the same molecule from the same organism, or homologous molecules from different organisms. In this approach, we detect the variability that exists among the relative translation and rotation operations that are needed to superimpose local neighborhoods after an initial rigid-body global superposition. Each translation and rotation is represented by a three dimensional vector. Thus, we investigate the variability within sets of multivariate data. We demonstrate that the method is able to identify both small- and large-scale conformational changes. Matlab/Octave programs to read RNA 3D structure files and compare structures have been developed and are freely accessible at: https://github.com/BGSU-RNA/ConformationalChange.
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Affiliation(s)
- Ryan R Rahrig
- Department of Mathematics and Statistics, Ohio Northern University, Ada, OH 45810, U. S. A
| | - Craig L Zirbel
- Department of Mathematics and Statistics, Ohio Northern University, Ada, OH 45810, U. S. A
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64
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Qin B, Yamamoto H, Ueda T, Varshney U, Nierhaus KH. The Termination Phase in Protein Synthesis is not Obligatorily Followed by the RRF/EF-G-Dependent Recycling Phase. J Mol Biol 2016; 428:3577-87. [PMID: 27261258 DOI: 10.1016/j.jmb.2016.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 05/18/2016] [Accepted: 05/22/2016] [Indexed: 11/30/2022]
Abstract
It is general wisdom that termination of bacterial protein synthesis is obligatorily followed by recycling governed by the factors ribosomal recycling factor (RRF), EF-G, and IF3, where the ribosome dissociates into its subunits. In contrast, a recently described 70S-scanning mode of initiation holds that after termination, scanning of 70S can be triggered by fMet-tRNA to the initiation site of a downstream cistron. Here, we analyze the apparent conflict. We constructed a bicistronic mRNA coding for luciferases and showed with a highly resolved in vitro system that the expression of the second cistron did not at all depend on the presence of active RRF. An in vivo analysis cannot be performed in a straightforward way, since RRF is essential for viability and therefore, the RRF gene cannot be knocked out. However, we found an experimental window, where the RRF amount could be reduced to below 2.5%, and in this situation, the expression of the second cistron of a bicistronic luciferase mRNA was only moderately reduced. Both in vitro and in vivo results suggested that RRF-dependent recycling is not an obligatory step after termination, in agreement with the previous findings concerning 70S-scanning initiation. In this view, recycling after termination is a special case of the general RRF function, which happens whenever fMet-tRNA is not available for triggering 70S scanning.
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Affiliation(s)
- Bo Qin
- Max-Planck-Institut für molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany; Institut für Medizinische Physik und Biophysik, Charité, Charitéplatz 1, 10117 Berlin, Germany
| | - Hiroshi Yamamoto
- Max-Planck-Institut für molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany; Institut für Medizinische Physik und Biophysik, Charité, Charitéplatz 1, 10117 Berlin, Germany.
| | - Takuya Ueda
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba Prefecture 277-8562, Japan
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Knud H Nierhaus
- Max-Planck-Institut für molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany; Institut für Medizinische Physik und Biophysik, Charité, Charitéplatz 1, 10117 Berlin, Germany
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65
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Ling C, Ermolenko DN. Structural insights into ribosome translocation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:620-36. [PMID: 27117863 PMCID: PMC4990484 DOI: 10.1002/wrna.1354] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 03/15/2016] [Accepted: 03/18/2016] [Indexed: 11/23/2022]
Abstract
During protein synthesis, tRNA and mRNA are translocated from the A to P to E sites of the ribosome thus enabling the ribosome to translate one codon of mRNA after the other. Ribosome translocation along mRNA is induced by the universally conserved ribosome GTPase, elongation factor G (EF‐G) in bacteria and elongation factor 2 (EF‐2) in eukaryotes. Recent structural and single‐molecule studies revealed that tRNA and mRNA translocation within the ribosome is accompanied by cyclic forward and reverse rotations between the large and small ribosomal subunits parallel to the plane of the intersubunit interface. In addition, during ribosome translocation, the ‘head’ domain of small ribosomal subunit undergoes forward‐ and back‐swiveling motions relative to the rest of the small ribosomal subunit around the axis that is orthogonal to the axis of intersubunit rotation. tRNA/mRNA translocation is also coupled to the docking of domain IV of EF‐G into the A site of the small ribosomal subunit that converts the thermally driven motions of the ribosome and tRNA into the forward translocation of tRNA/mRNA inside the ribosome. Despite recent and enormous progress made in the understanding of the molecular mechanism of ribosome translocation, the sequence of structural rearrangements of the ribosome, EF‐G and tRNA during translocation is still not fully established and awaits further investigation. WIREs RNA 2016, 7:620–636. doi: 10.1002/wrna.1354 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Clarence Ling
- Department of Biochemistry and Biophysics & Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - Dmitri N Ermolenko
- Department of Biochemistry and Biophysics & Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
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66
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Choreography of molecular movements during ribosome progression along mRNA. Nat Struct Mol Biol 2016; 23:342-8. [PMID: 26999556 DOI: 10.1038/nsmb.3193] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/22/2016] [Indexed: 12/26/2022]
Abstract
During translation elongation, ribosome translocation along an mRNA entails rotations of the ribosomal subunits, swiveling motions of the small subunit (SSU) head and stepwise movements of the tRNAs together with the mRNA. Here, we reconstructed the choreography of the collective motions of the Escherichia coli ribosome during translocation promoted by elongation factor EF-G, by recording the fluorescence signatures of nine different reporters placed on both ribosomal subunits, tRNA and mRNA. We captured an early forward swiveling of the SSU head taking place while the SSU body rotates in the opposite, clockwise direction. Backward swiveling of the SSU head starts upon tRNA translocation and continues until the post-translocation state is reached. This work places structures of translocation intermediates along a time axis and unravels principles of the motions of macromolecular machines.
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67
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68
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Liu Q, Fredrick K. Intersubunit Bridges of the Bacterial Ribosome. J Mol Biol 2016; 428:2146-64. [PMID: 26880335 DOI: 10.1016/j.jmb.2016.02.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/29/2016] [Accepted: 02/05/2016] [Indexed: 02/02/2023]
Abstract
The ribosome is a large two-subunit ribonucleoprotein machine that translates the genetic code in all cells, synthesizing proteins according to the sequence of the mRNA template. During translation, the primary substrates, transfer RNAs, pass through binding sites formed between the two subunits. Multiple interactions between the ribosomal subunits, termed intersubunit bridges, keep the ribosome intact and at the same time govern dynamics that facilitate the various steps of translation such as transfer RNA-mRNA movement. Here, we review the molecular nature of these intersubunit bridges, how they change conformation during translation, and their functional roles in the process.
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Affiliation(s)
- Qi Liu
- Ohio State Biochemistry Program, Department of Microbiology, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Ohio State Biochemistry Program, Department of Microbiology, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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69
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Abstract
Structural centers of motion (pivot points) in the ribosome have recently been identified by measurement of conformational changes in rRNA resulting from EF-G GTP hydrolysis. This series of measurements is extended here to the ribosome's interactions with the cofactor EF-Tu. Four recent EF-Tu bound ribosome structures were compared to unbound structures. A total of 16 pivots were identified, of which 4 are unique to the EF-Tu interaction. Pivots in the GTPase associated center and the sarcin-ricin loop omitted previously, are found to be mobile in response to both EF-Tu and EF-G binding. Pivots in the intersubunit bridge rRNAs are found to be cofactor specific. Head swiveling motions in the small subunit are observed in the EF-Tu bound structures that were trapped post GTP hydrolysis. As in the case of pivots associated with EF-G, the additional pivots described here are associated with weak points in the rRNA structures such as non-canonical pairs and bulge loops. The combined set of pivots should be regarded as a minimal set. Only several states available to the ribosome have been presented in this work. Future, precise crystal structures in conjunction with experimental data will likely show additional functional pivoting elements in the rRNA.
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Affiliation(s)
- Maxim Paci
- a Department of Biology and Biochemistry , University of Houston , Houston , TX , USA
| | - George E Fox
- a Department of Biology and Biochemistry , University of Houston , Houston , TX , USA
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70
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Sierra RG, Gati C, Laksmono H, Dao EH, Gul S, Fuller F, Kern J, Chatterjee R, Ibrahim M, Brewster AS, Young ID, Michels-Clark T, Aquila A, Liang M, Hunter MS, Koglin JE, Boutet S, Junco EA, Hayes B, Bogan MJ, Hampton CY, Puglisi EV, Sauter NK, Stan CA, Zouni A, Yano J, Yachandra VK, Soltis SM, Puglisi JD, DeMirci H. Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II. Nat Methods 2016; 13:59-62. [PMID: 26619013 PMCID: PMC4890631 DOI: 10.1038/nmeth.3667] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/14/2015] [Indexed: 01/30/2023]
Abstract
We describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond X-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. We used the injector to analyze microcrystals of Geobacillus stearothermophilus thermolysin (2.2-Å structure), Thermosynechococcus elongatus photosystem II (<3-Å diffraction) and Thermus thermophilus small ribosomal subunit bound to the antibiotic paromomycin at ambient temperature (3.4-Å structure).
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Affiliation(s)
- Raymond G. Sierra
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Cornelius Gati
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - Hartawan Laksmono
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - E. Han Dao
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sheraz Gul
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Jan Kern
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Mohamed Ibrahim
- Institute für Biologie, Humboldt University of Berlin, Berlin, Germany
| | | | - Iris D. Young
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Jason E. Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Elia A. Junco
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Michael J. Bogan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Christina Y. Hampton
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Elisabetta V. Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Claudiu A. Stan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Athina Zouni
- Institute für Biologie, Humboldt University of Berlin, Berlin, Germany
| | - Junko Yano
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - S. Michael Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Joseph D. Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hasan DeMirci
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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71
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Zhao C, Rajashankar KR, Marcia M, Pyle AM. Crystal structure of group II intron domain 1 reveals a template for RNA assembly. Nat Chem Biol 2015; 11:967-72. [PMID: 26502156 PMCID: PMC4651773 DOI: 10.1038/nchembio.1949] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 09/18/2015] [Indexed: 12/17/2022]
Abstract
Although the importance of large noncoding RNAs is increasingly appreciated, our understanding of their structures and architectural dynamics remains limited. In particular, we know little about RNA folding intermediates and how they facilitate the productive assembly of RNA tertiary structures. Here, we report the crystal structure of an obligate intermediate that is required during the earliest stages of group II intron folding. Composed of domain 1 from the Oceanobacillus iheyensis group II intron (266 nucleotides), this intermediate retains native-like features but adopts a compact conformation in which the active site cleft is closed. Transition between this closed and the open (native) conformation is achieved through discrete rotations of hinge motifs in two regions of the molecule. The open state is then stabilized by sequential docking of downstream intron domains, suggesting a 'first come, first folded' strategy that may represent a generalizable pathway for assembly of large RNA and ribonucleoprotein structures.
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Affiliation(s)
- Chen Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Kanagalaghatta R. Rajashankar
- NE-CAT and Dept. of Chemistry and Chemical Biology, Cornell University Building 436E, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439
| | - Marco Marcia
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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72
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Abstract
We present a molecular-level model for the origin and evolution of the translation system, using a 3D comparative method. In this model, the ribosome evolved by accretion, recursively adding expansion segments, iteratively growing, subsuming, and freezing the rRNA. Functions of expansion segments in the ancestral ribosome are assigned by correspondence with their functions in the extant ribosome. The model explains the evolution of the large ribosomal subunit, the small ribosomal subunit, tRNA, and mRNA. Prokaryotic ribosomes evolved in six phases, sequentially acquiring capabilities for RNA folding, catalysis, subunit association, correlated evolution, decoding, energy-driven translocation, and surface proteinization. Two additional phases exclusive to eukaryotes led to tentacle-like rRNA expansions. In this model, ribosomal proteinization was a driving force for the broad adoption of proteins in other biological processes. The exit tunnel was clearly a central theme of all phases of ribosomal evolution and was continuously extended and rigidified. In the primitive noncoding ribosome, proto-mRNA and the small ribosomal subunit acted as cofactors, positioning the activated ends of tRNAs within the peptidyl transferase center. This association linked the evolution of the large and small ribosomal subunits, proto-mRNA, and tRNA.
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73
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Caetano-Anollés G, Caetano-Anollés D. Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology. Comput Struct Biotechnol J 2015; 13:427-47. [PMID: 27096056 PMCID: PMC4823900 DOI: 10.1016/j.csbj.2015.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/16/2015] [Accepted: 07/19/2015] [Indexed: 12/11/2022] Open
Abstract
Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in the evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. Computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. Phylogenetic trees of protein structural domains and proteomes and their molecular functions were built from a genomic census of millions of encoded proteins and associated terminal Gene Ontology terms. Trees reveal a ‘metabolic-first’ origin of proteins, the late development of translation, and a patchwork distribution of proteins in biological networks mediated by molecular recruitment. Similarly, the natural history of ancient RNA molecules inferred from trees of molecular substructures built from a census of molecular features shows patchwork-like accretion patterns. Ideographic analyses of ribosomal history uncover the early appearance of structures supporting mRNA decoding and tRNA translocation, the coevolution of ribosomal proteins and RNA, and a first evolutionary transition that brings ribosomal subunits together into a processive protein biosynthetic complex. Nomothetic structural biology studies of tertiary interactions and ancient insertions in rRNA complement these findings, once concentric layering assumptions are removed. Patterns of coaxial helical stacking reveal a frustrated dynamics of outward and inward ribosomal growth possibly mediated by structural grafting. The early rise of the ribosomal ‘turnstile’ suggests an evolutionary transition in natural biological computation. Results make explicit the need to understand processes of molecular growth and information transfer of macromolecules.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101W. Peabody Drive, Urbana, IL 61801, USA; C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Derek Caetano-Anollés
- C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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74
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Achenbach J, Nierhaus KH. The mechanics of ribosomal translocation. Biochimie 2015; 114:80-9. [DOI: 10.1016/j.biochi.2014.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 12/05/2014] [Indexed: 11/16/2022]
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75
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Bock LV, Blau C, Vaiana AC, Grubmüller H. Dynamic contact network between ribosomal subunits enables rapid large-scale rotation during spontaneous translocation. Nucleic Acids Res 2015; 43:6747-60. [PMID: 26109353 PMCID: PMC4538834 DOI: 10.1093/nar/gkv649] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 06/10/2015] [Indexed: 11/13/2022] Open
Abstract
During ribosomal translation, the two ribosomal subunits remain associated through intersubunit bridges, despite rapid large-scale intersubunit rotation. The absence of large barriers hindering rotation is a prerequisite for rapid rotation. Here, we investigate how such a flat free-energy landscape is achieved, in particular considering the large shifts the bridges undergo at the periphery. The dynamics and energetics of the intersubunit contact network are studied using molecular dynamics simulations of the prokaryotic ribosome in intermediate states of spontaneous translocation. Based on observed occupancies of intersubunit contacts, residues were grouped into clusters. In addition to the central contact clusters, peripheral clusters were found to maintain strong steady interactions by changing contacts in the course of rotation. The peripheral B1 bridges are stabilized by a changing contact pattern of charged residues that adapts to the rotational state. In contrast, steady strong interactions of the B4 bridge are ensured by the flexible helix H34 following the movement of protein S15. The tRNAs which span the subunits contribute to the intersubunit binding enthalpy to an almost constant degree, despite their different positions in the ribosome. These mechanisms keep the intersubunit interaction strong and steady during rotation, thereby preventing dissociation and enabling rapid rotation.
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Affiliation(s)
- Lars V Bock
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Blau
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andrea C Vaiana
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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76
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Xie P. Model of ribosomal translocation coupled with intra- and inter-subunit rotations. Biochem Biophys Rep 2015; 2:87-93. [PMID: 29124148 PMCID: PMC5668647 DOI: 10.1016/j.bbrep.2015.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 05/18/2015] [Accepted: 05/18/2015] [Indexed: 11/03/2022] Open
Abstract
The ribosomal translocation involves both intersubunit rotations between the small 30S and large 50S subunits and the intrasubunit rotations of the 30S head relative to the 30S body. However, the detailed molecular mechanism on how the intersubunit and intrasubunit rotations are related to the translocation remains unclear. Here, based on available structural data a model is proposed for the ribosomal translocation, into which both the intersubunit and intrasubunit rotations are incorporated. With the model, we provide quantitative explanations of in vitro experimental data showing the biphasic character in the fluorescence change associated with the mRNA translocation and the character of a rapid increase that is followed by a slow single-exponential decrease in the fluorescence change associated with the 30S head rotation. The calculated translation rate is also consistent with the in vitro single-molecule experimental data.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
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77
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Structural Insights into tRNA Dynamics on the Ribosome. Int J Mol Sci 2015; 16:9866-95. [PMID: 25941930 PMCID: PMC4463622 DOI: 10.3390/ijms16059866] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 11/17/2022] Open
Abstract
High-resolution structures at different stages, as well as biochemical, single molecule and computational approaches have highlighted the elasticity of tRNA molecules when bound to the ribosome. It is well acknowledged that the inherent structural flexibility of the tRNA lies at the heart of the protein synthesis process. Here, we review the recent advances and describe considerations that the conformational changes of the tRNA molecules offer about the mechanisms grounded in translation.
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78
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Paci M, Fox GE. Major centers of motion in the large ribosomal RNAs. Nucleic Acids Res 2015; 43:4640-9. [PMID: 25870411 PMCID: PMC4482067 DOI: 10.1093/nar/gkv289] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 03/24/2015] [Indexed: 01/26/2023] Open
Abstract
Major centers of motion in the rRNAs of Thermus thermophilus are identified by alignment of crystal structures of EF-G bound and EF-G unbound ribosomal subunits. Small rigid helices upstream of these 'pivots' are aligned, thereby decoupling their motion from global rearrangements. Of the 21 pivots found, six are observed in the large subunit rRNA and 15 in the small subunit rRNA. Although the magnitudes of motion differ, with only minor exceptions equivalent pivots are seen in comparisons of Escherichia coli structures and one Saccharomyces cerevisiae structure pair. The pivoting positions are typically associated with structurally weak motifs such as non-canonical, primarily U-G pairs, bulge loops and three-way junctions. Each pivot is typically in direct physical contact with at least one other in the set and often several others. Moving helixes include rRNA segments in contact with the tRNA, intersubunit bridges and helices 28, 32 and 34 of the small subunit. These helices are envisioned to form a network. EF-G rearrangement would then provide directional control of this network propagating motion from the tRNA to the intersubunit bridges to the head swivel or along the same path backward.
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Affiliation(s)
- Maxim Paci
- Department of Biology and Biochemistry, University of Houston, 4800 Cullen Blvd. Houston, TX 77204-5001, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, 4800 Cullen Blvd. Houston, TX 77204-5001, USA
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79
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Amunts A, Brown A, Toots J, Scheres SHW, Ramakrishnan V. Ribosome. The structure of the human mitochondrial ribosome. Science 2015; 348:95-98. [PMID: 25838379 PMCID: PMC4501431 DOI: 10.1126/science.aaa1193] [Citation(s) in RCA: 376] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/05/2015] [Indexed: 01/06/2023]
Abstract
The highly divergent ribosomes of human mitochondria (mitoribosomes) synthesize 13 essential proteins of oxidative phosphorylation complexes. We have determined the structure of the intact mitoribosome to 3.5 angstrom resolution by means of single-particle electron cryogenic microscopy. It reveals 80 extensively interconnected proteins, 36 of which are specific to mitochondria, and three ribosomal RNA molecules. The head domain of the small subunit, particularly the messenger (mRNA) channel, is highly remodeled. Many intersubunit bridges are specific to the mitoribosome, which adopts conformations involving ratcheting or rolling of the small subunit that are distinct from those seen in bacteria or eukaryotes. An intrinsic guanosine triphosphatase mediates a contact between the head and central protuberance. The structure provides a reference for analysis of mutations that cause severe pathologies and for future drug design.
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Affiliation(s)
- Alexey Amunts
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Alan Brown
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Jaan Toots
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Sjors H. W. Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - V. Ramakrishnan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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