Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding

Two crystal structures indicate how conformational changes in the ribosome assist protein synthesis. During protein synthesis, the ribosome controls the movement of tRNA and mRNA by means of large-scale structural rearrangements. We describe structures of the intact bacterial ribosome from Escherichia coli that reveal how the ribosome binds tRNA in two functionally distinct states, determined to a resolution of ~3.2 angstroms by means of x-ray crystallography. One state positions tRNA in the peptidyl-tRNA binding site. The second, a fully rotated state, is stabilized by ribosome recycling factor and binds tRNA in a highly bent conformation in a hybrid peptidyl/exit site. The structures help to explain how the ratchet-like motion of the two ribosomal subunits contributes to the mechanisms of translocation, termination, and ribosome recycling.

[1]  T. Creighton Methods in Enzymology , 1968, The Yale Journal of Biology and Medicine.

[2]  A. Spirin,et al.  Factor-free ("non-enzymic") and factor-dependent systems of translation of polyuridylic acid by Escherichia coli ribosomes. , 1976, Journal of molecular biology.

[3]  J. Cate,et al.  Structures of the Ribosome in Intermediate States of Ratcheting , 2009, Science.

[4]  Paul C. Whitford,et al.  1 Supplemental Information , 2008 .

[5]  J. Frank,et al.  Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: Functional implications , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[6]  A. Kelley,et al.  The Mechanism for Activation of GTP Hydrolysis on the Ribosome , 2010, Science.

[7]  V. Ramakrishnan,et al.  What recent ribosome structures have revealed about the mechanism of translation , 2009, Nature.

[8]  A. Kaji,et al.  Mutations influencing the frr gene coding for ribosome recycling factor (RRF). , 2000, Journal of molecular biology.

[9]  Christian M T Spahn,et al.  Navigating the ribosome's metastable energy landscape. , 2009, Trends in biochemical sciences.

[10]  Nan Yu,et al.  The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs , 2002, BMC Bioinformatics.

[11]  T. Steitz,et al.  Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit. , 2003, RNA.

[12]  Scott M Stagg,et al.  Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy , 2003, Nature Structural Biology.

[13]  Joachim Frank,et al.  A ratchet-like inter-subunit reorganization of the ribosome during translocation , 2000, Nature.

[14]  Michael B. Feldman,et al.  Aminoglycoside activity observed on single pre-translocation ribosome complexes. , 2010, Nature chemical biology.

[15]  Zigurts K. Majumdar,et al.  The antibiotic viomycin traps the ribosome in an intermediate state of translocation , 2007, Nature Structural &Molecular Biology.

[16]  Stephen Neidle,et al.  Principles of nucleic acid structure , 2007 .

[17]  M. Rodnina,et al.  Distinct functions of elongation factor G in ribosome recycling and translocation. , 2009, RNA.

[18]  W. Wintermeyer,et al.  Binding of the 3′ terminus of tRNA to 23S rRNA in the ribosomal exit site actively promotes translocation. , 1989, The EMBO journal.

[19]  M. Selmer,et al.  Crystal structure of the ribosome recycling factor bound to the ribosome , 2007, Nature Structural &Molecular Biology.

[20]  Julio O. Ortiz,et al.  The Native 3D Organization of Bacterial Polysomes , 2009, Cell.

[21]  Robert J. Stern,et al.  The Origin of the Great Bend of the Nile from SIR-C/X-SAR Imagery , 1996, Science.

[22]  S. Joseph,et al.  The A-site Finger in 23 S rRNA Acts as a Functional Attenuator for Translocation* , 2006, Journal of Biological Chemistry.

[23]  S. Steinberg,et al.  A hierarchical model for evolution of 23S ribosomal RNA , 2009, Nature.

[24]  S. Joseph,et al.  Identification of molecular interactions between P-site tRNA and the ribosome essential for translocation , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[25]  J. Ballesta,et al.  Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation , 2004, The EMBO journal.

[26]  J. Holton,et al.  Structures of the Bacterial Ribosome at 3.5 Å Resolution , 2005, Science.

[27]  Shigeyuki Yokoyama,et al.  Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. , 2007, Molecular cell.

[28]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[29]  E. Kandel,et al.  Control of Memory Formation Through Regulated Expression of a CaMKII Transgene , 1996, Science.

[30]  M. Yusupov,et al.  Crystal Structure of the Eukaryotic Ribosome , 2010, Science.

[31]  C. Kundrot,et al.  RNA Tertiary Structure Mediation by Adenosine Platforms , 1996, Science.

[32]  A. Spirin The Ribosome as a Conveying Thermal Ratchet Machine , 2009, The Journal of Biological Chemistry.

[33]  J. Holton,et al.  Structural basis for aminoglycoside inhibition of bacterial ribosome recycling , 2007, Nature Structural &Molecular Biology.

[34]  Gregor Blaha,et al.  The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome , 2010, Nature Structural &Molecular Biology.

[35]  M. Selmer,et al.  Structure of the 70S Ribosome Complexed with mRNA and tRNA , 2006, Science.

[36]  R. Green,et al.  Multiple effects of S13 in modulating the strength of intersubunit interactions in the ribosome during translation. , 2005, Journal of molecular biology.

[37]  Yong-Gui Gao,et al.  The Crystal Structure of the Ribosome Bound to EF-Tu and Aminoacyl-tRNA , 2009, Science.

[38]  C. Kundrot,et al.  Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing , 1996, Science.

[39]  BMC Bioinformatics , 2005 .

[40]  J. Cate,et al.  Accessibility of 18S rRNA in human 40S subunits and 80S ribosomes at physiological magnesium ion concentrations--implications for the study of ribosome dynamics. , 2005, RNA.

[41]  J. Cate,et al.  Ribosome structure and dynamics during translocation and termination. , 2010, Annual review of biophysics.

[42]  Tal Pupko,et al.  ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids , 2010, Nucleic Acids Res..

[43]  Joachim Frank,et al.  Cryo‐EM reveals an active role for aminoacyl‐tRNA in the accommodation process , 2002, The EMBO journal.

[44]  Måns Ehrenberg,et al.  Peptidyl-tRNA Regulates the GTPase Activity of Translation Factors , 2003, Cell.

[45]  J. Frank,et al.  Transfer RNA in the hybrid P/E state: Correlating molecular dynamics simulations with cryo-EM data , 2007, Proceedings of the National Academy of Sciences.

[46]  Taekjip Ha,et al.  Spontaneous intersubunit rotation in single ribosomes. , 2008, Molecular cell.

[47]  宁北芳,et al.  疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A , 2005 .

[48]  M. Rodnina,et al.  Energetic contribution of tRNA hybrid state formation to translocation catalysis on the ribosome , 2000, Nature Structural Biology.

[49]  Harry F. Noller,et al.  Intermediate states in the movement of transfer RNA in the ribosome , 1989, Nature.

[50]  Marina V. Rodnina,et al.  Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy , 2010, Nature.

[51]  R. L. Gonzalez,et al.  Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling , 2009, Nature Structural &Molecular Biology.

[52]  Joachim Frank,et al.  The process of mRNA–tRNA translocation , 2007, Proceedings of the National Academy of Sciences.

[53]  Joachim Frank,et al.  Locking and Unlocking of Ribosomal Motions , 2003, Cell.

[54]  H. Noller,et al.  EF‐G‐catalyzed translocation of anticodon stem–loop analogs of transfer RNA in the ribosome , 1998, The EMBO journal.

[55]  Joachim Frank,et al.  Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies. , 2005, Molecular cell.

[56]  H. Noller,et al.  Orientation of Ribosome Recycling Factor in the Ribosome from Directed Hydroxyl Radical Probing , 2002, Cell.