Literature DB >> 27801619

Translocation as continuous movement through the ribosome.

Riccardo Belardinelli1, Heena Sharma1, Frank Peske1, Wolfgang Wintermeyer1, Marina V Rodnina1.   

Abstract

In each round of translation elongation, tRNAs and mRNA move within the ribosome by one codon at a time. tRNA-mRNA translocation is promoted by elongation factor G (EF-G) at the cost of GTP hydrolysis. The key questions for understanding translocation are how and when the tRNAs move and how EF-G coordinates motions of the ribosomal subunits with tRNA movement. Here we present 2 recent papers which describe the choreography of movements over the whole trajectory of translocation. We present the view that EF-G accelerates translocation by promoting the steps that lead to GTPase-dependent ribosome unlocking. EF-G facilitates the formation of the rotated state of the ribosome and uncouples the backward motions of the ribosomal subunits, forming an open conformation in which the tRNAs can rapidly move. Ribosome dynamics are important not only in translocation, but also in recoding events, such as frameshifting and bypassing, and mediate sensitivity to antibiotics.

Entities:  

Keywords:  EF-G; mRNA; molecular machines; protein synthesis; ribosome; tRNA; translation; translation elongation; translocation

Mesh:

Substances:

Year:  2016        PMID: 27801619      PMCID: PMC5207377          DOI: 10.1080/15476286.2016.1240140

Source DB:  PubMed          Journal:  RNA Biol        ISSN: 1547-6286            Impact factor:   4.652


  61 in total

1.  Energetic contribution of tRNA hybrid state formation to translocation catalysis on the ribosome.

Authors:  Y P Semenkov; M V Rodnina; W Wintermeyer
Journal:  Nat Struct Biol       Date:  2000-11

Review 2.  Translation at the single-molecule level.

Authors:  R Andrew Marshall; Colin Echeverría Aitken; Magdalena Dorywalska; Joseph D Puglisi
Journal:  Annu Rev Biochem       Date:  2008       Impact factor: 23.643

3.  Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation.

Authors:  Jingyi Fei; Pallav Kosuri; Daniel D MacDougall; Ruben L Gonzalez
Journal:  Mol Cell       Date:  2008-05-09       Impact factor: 17.970

4.  Rotation of the head of the 30S ribosomal subunit during mRNA translocation.

Authors:  Zhuojun Guo; Harry F Noller
Journal:  Proc Natl Acad Sci U S A       Date:  2012-11-27       Impact factor: 11.205

5.  A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation.

Authors:  Hee-Kyung Kim; Fei Liu; Jingyi Fei; Carlos Bustamante; Ruben L Gonzalez; Ignacio Tinoco
Journal:  Proc Natl Acad Sci U S A       Date:  2014-03-31       Impact factor: 11.205

6.  Allosteric control of the ribosome by small-molecule antibiotics.

Authors:  Leyi Wang; Arto Pulk; Michael R Wasserman; Michael B Feldman; Roger B Altman; Jamie H Doudna Cate; Scott C Blanchard
Journal:  Nat Struct Mol Biol       Date:  2012-08-19       Impact factor: 15.369

7.  The antibiotic viomycin traps the ribosome in an intermediate state of translocation.

Authors:  Dmitri N Ermolenko; P Clint Spiegel; Zigurts K Majumdar; Robyn P Hickerson; Robert M Clegg; Harry F Noller
Journal:  Nat Struct Mol Biol       Date:  2007-05-21       Impact factor: 15.369

8.  Binding of the 3' terminus of tRNA to 23S rRNA in the ribosomal exit site actively promotes translocation.

Authors:  R Lill; J M Robertson; W Wintermeyer
Journal:  EMBO J       Date:  1989-12-01       Impact factor: 11.598

9.  mRNA translocation occurs during the second step of ribosomal intersubunit rotation.

Authors:  Dmitri N Ermolenko; Harry F Noller
Journal:  Nat Struct Mol Biol       Date:  2011-03-13       Impact factor: 15.369

10.  Mechanisms of ribosome stalling by SecM at multiple elongation steps.

Authors:  Jun Zhang; Xijiang Pan; Kaige Yan; Shan Sun; Ning Gao; Sen-Fang Sui
Journal:  Elife       Date:  2015-12-14       Impact factor: 8.140

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  11 in total

1.  Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state.

Authors:  Jie Zhou; Laura Lancaster; John Paul Donohue; Harry F Noller
Journal:  Proc Natl Acad Sci U S A       Date:  2019-04-01       Impact factor: 11.205

Review 2.  Roles of elusive translational GTPases come to light and inform on the process of ribosome biogenesis in bacteria.

Authors:  Michelle R Gibbs; Kurt Fredrick
Journal:  Mol Microbiol       Date:  2017-12-29       Impact factor: 3.501

3.  Hyper-swivel head domain motions are required for complete mRNA-tRNA translocation and ribosome resetting.

Authors:  Wataru Nishima; Dylan Girodat; Mikael Holm; Emily J Rundlet; Jose L Alejo; Kara Fischer; Scott C Blanchard; Karissa Y Sanbonmatsu
Journal:  Nucleic Acids Res       Date:  2022-08-12       Impact factor: 19.160

4.  Eukaryotic translation elongation factor 2 (eEF2) catalyzes reverse translocation of the eukaryotic ribosome.

Authors:  Denis Susorov; Nikita Zakharov; Ekaterina Shuvalova; Alexander Ivanov; Tatiana Egorova; Alexey Shuvalov; Ivan N Shatsky; Elena Alkalaeva
Journal:  J Biol Chem       Date:  2018-02-16       Impact factor: 5.157

5.  Effect of Fusidic Acid on the Kinetics of Molecular Motions During EF-G-Induced Translocation on the Ribosome.

Authors:  Riccardo Belardinelli; Marina V Rodnina
Journal:  Sci Rep       Date:  2017-09-05       Impact factor: 4.379

6.  Oxidative stress damages rRNA inside the ribosome and differentially affects the catalytic center.

Authors:  Jessica Willi; Pascal Küpfer; Damien Evéquoz; Guillermo Fernandez; Assaf Katz; Christian Leumann; Norbert Polacek
Journal:  Nucleic Acids Res       Date:  2018-02-28       Impact factor: 16.971

7.  High-resolution structures of a thermophilic eukaryotic 80S ribosome reveal atomistic details of translocation.

Authors:  Miglė Kišonaitė; Klemens Wild; Karine Lapouge; Thomas Ruppert; Irmgard Sinning
Journal:  Nat Commun       Date:  2022-01-25       Impact factor: 17.694

8.  Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position.

Authors:  Wei Liu; Dongwon Shin; Martin Ng; Karissa Y Sanbonmatsu; Yitzhak Tor; Barry S Cooperman
Journal:  Molecules       Date:  2017-08-29       Impact factor: 4.411

9.  Translocation kinetics and structural dynamics of ribosomes are modulated by the conformational plasticity of downstream pseudoknots.

Authors:  Bo Wu; Haibo Zhang; Ruirui Sun; Sijia Peng; Barry S Cooperman; Yale E Goldman; Chunlai Chen
Journal:  Nucleic Acids Res       Date:  2018-10-12       Impact factor: 16.971

10.  Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon-anticodon pairing.

Authors:  Eric D Hoffer; Samuel Hong; S Sunita; Tatsuya Maehigashi; Ruben L Gonzalez; Paul C Whitford; Christine M Dunham
Journal:  Elife       Date:  2020-10-05       Impact factor: 8.140

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