Literature DB >> 22388519

Structural insights into initial and intermediate steps of the ribosome-recycling process.

Takeshi Yokoyama1, Tanvir R Shaikh, Nobuhiro Iwakura, Hideko Kaji, Akira Kaji, Rajendra K Agrawal.   

Abstract

The ribosome-recycling factor (RRF) and elongation factor-G (EF-G) disassemble the 70S post-termination complex (PoTC) into mRNA, tRNA, and two ribosomal subunits. We have determined cryo-electron microscopic structures of the PoTC·RRF complex, with and without EF-G. We find that domain II of RRF initially interacts with universally conserved residues of the 23S rRNA helices 43 and 95, and protein L11 within the 50S ribosomal subunit. Upon EF-G binding, both RRF and tRNA are driven towards the tRNA-exit (E) site, with a large rotational movement of domain II of RRF towards the 30S ribosomal subunit. During this intermediate step of the recycling process, domain II of RRF and domain IV of EF-G adopt hitherto unknown conformations. Furthermore, binding of EF-G to the PoTC·RRF complex reverts the ribosome from ratcheted to unratcheted state. These results suggest that (i) the ribosomal intersubunit reorganizations upon RRF binding and subsequent EF-G binding could be instrumental in destabilizing the PoTC and (ii) the modes of action of EF-G during tRNA translocation and ribosome-recycling steps are markedly different.

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Year:  2012        PMID: 22388519      PMCID: PMC3321202          DOI: 10.1038/emboj.2012.22

Source DB:  PubMed          Journal:  EMBO J        ISSN: 0261-4189            Impact factor:   11.598


  64 in total

1.  Crystal structure of the ribosome at 5.5 A resolution.

Authors:  M M Yusupov; G Z Yusupova; A Baucom; K Lieberman; T N Earnest; J H Cate; H F Noller
Journal:  Science       Date:  2001-03-29       Impact factor: 47.728

2.  Crystal structure of Thermotoga maritima ribosome recycling factor: a tRNA mimic.

Authors:  M Selmer; S Al-Karadaghi; G Hirokawa; A Kaji; A Liljas
Journal:  Science       Date:  1999-12-17       Impact factor: 47.728

3.  Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction.

Authors:  Zhexin Xiang; Cinque S Soto; Barry Honig
Journal:  Proc Natl Acad Sci U S A       Date:  2002-05-28       Impact factor: 11.205

4.  Fitting atomic models into electron-microscopy maps.

Authors:  M G Rossmann
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-10

5.  Orientation of ribosome recycling factor in the ribosome from directed hydroxyl radical probing.

Authors:  Laura Lancaster; Michael C Kiel; Akira Kaji; Harry F Noller
Journal:  Cell       Date:  2002-10-04       Impact factor: 41.582

6.  Structure and binding mode of a ribosome recycling factor (RRF) from mesophilic bacterium.

Authors:  Hiroaki Nakano; Takuya Yoshida; Susumu Uchiyama; Masako Kawachi; Hitomi Matsuo; Takayuki Kato; Atsushi Ohshima; Yoshiharu Yamaichi; Takeshi Honda; Hiroaki Kato; Yuriko Yamagata; Tadayasu Ohkubo; Yuji Kobayashi
Journal:  J Biol Chem       Date:  2002-10-30       Impact factor: 5.157

7.  Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process.

Authors:  Mikel Valle; Jayati Sengupta; Neil K Swami; Robert A Grassucci; Nils Burkhardt; Knud H Nierhaus; Rajendra K Agrawal; Joachim Frank
Journal:  EMBO J       Date:  2002-07-01       Impact factor: 11.598

8.  Solution structure of the ribosome recycling factor from Aquifex aeolicus.

Authors:  T Yoshida; S Uchiyama; H Nakano; H Kashimori; H Kijima; T Ohshima; Y Saihara; T Ishino; H Shimahara; T Yoshida; K Yokose; T Ohkubo; A Kaji; Y Kobayashi
Journal:  Biochemistry       Date:  2001-02-27       Impact factor: 3.162

9.  Post-termination complex disassembly by ribosome recycling factor, a functional tRNA mimic.

Authors:  Go Hirokawa; Michael C Kiel; Aiko Muto; Maria Selmer; V Samuel Raj; Anders Liljas; Kazuei Igarashi; Hideko Kaji; Akira Kaji
Journal:  EMBO J       Date:  2002-05-01       Impact factor: 11.598

10.  Structures of the bacterial ribosome in classical and hybrid states of tRNA binding.

Authors:  Jack A Dunkle; Leyi Wang; Michael B Feldman; Arto Pulk; Vincent B Chen; Gary J Kapral; Jonas Noeske; Jane S Richardson; Scott C Blanchard; Jamie H Doudna Cate
Journal:  Science       Date:  2011-05-20       Impact factor: 47.728

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  24 in total

1.  Elongation factor G is a critical target during oxidative damage to the translation system of Escherichia coli.

Authors:  Takanori Nagano; Kouji Kojima; Toru Hisabori; Hidenori Hayashi; Eugene Hayato Morita; Takashi Kanamori; Tomoko Miyagi; Takuya Ueda; Yoshitaka Nishiyama
Journal:  J Biol Chem       Date:  2012-07-06       Impact factor: 5.157

2.  Ribosomal 60S-subunit production: the final scene.

Authors:  Célia Plisson-Chastang; Natacha Larburu; Pierre-Emmanuel Gleizes
Journal:  Nat Struct Mol Biol       Date:  2015-11       Impact factor: 15.369

Review 3.  EF-G and EF4: translocation and back-translocation on the bacterial ribosome.

Authors:  Hiroshi Yamamoto; Yan Qin; John Achenbach; Chengmin Li; Jaroslaw Kijek; Christian M T Spahn; Knud H Nierhaus
Journal:  Nat Rev Microbiol       Date:  2013-12-23       Impact factor: 60.633

Review 4.  Structural basis for protein synthesis: snapshots of the ribosome in motion.

Authors:  Jonas Noeske; Jamie H D Cate
Journal:  Curr Opin Struct Biol       Date:  2012-08-04       Impact factor: 6.809

Review 5.  Intersubunit Bridges of the Bacterial Ribosome.

Authors:  Qi Liu; Kurt Fredrick
Journal:  J Mol Biol       Date:  2016-02-13       Impact factor: 5.469

6.  70S-scanning initiation is a novel and frequent initiation mode of ribosomal translation in bacteria.

Authors:  Hiroshi Yamamoto; Daniela Wittek; Romi Gupta; Bo Qin; Takuya Ueda; Roland Krause; Kaori Yamamoto; Renate Albrecht; Markus Pech; Knud H Nierhaus
Journal:  Proc Natl Acad Sci U S A       Date:  2016-02-17       Impact factor: 11.205

7.  The kinetic mechanism of bacterial ribosome recycling.

Authors:  Yuanwei Chen; Akira Kaji; Hideko Kaji; Barry S Cooperman
Journal:  Nucleic Acids Res       Date:  2017-09-29       Impact factor: 16.971

8.  Mechanism of fusidic acid inhibition of RRF- and EF-G-dependent splitting of the bacterial post-termination ribosome.

Authors:  Anneli Borg; Michael Pavlov; Måns Ehrenberg
Journal:  Nucleic Acids Res       Date:  2016-03-21       Impact factor: 16.971

9.  Key Intermediates in Ribosome Recycling Visualized by Time-Resolved Cryoelectron Microscopy.

Authors:  Ziao Fu; Sandip Kaledhonkar; Anneli Borg; Ming Sun; Bo Chen; Robert A Grassucci; Måns Ehrenberg; Joachim Frank
Journal:  Structure       Date:  2016-11-03       Impact factor: 5.006

10.  Mechanism of eIF6 release from the nascent 60S ribosomal subunit.

Authors:  Félix Weis; Emmanuel Giudice; Mark Churcher; Li Jin; Christine Hilcenko; Chi C Wong; David Traynor; Robert R Kay; Alan J Warren
Journal:  Nat Struct Mol Biol       Date:  2015-10-19       Impact factor: 15.369

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