Literature DB >> 23722586

Frameshifting dynamics.

Ignacio Tinoco1, Hee-Kyung Kim, Shannon Yan.   

Abstract

Translation of messenger RNA by a ribosome occurs three nucleotides at a time from start signal to stop. However, a frameshift means that some nucleotides are read twice or some are skipped, and the following sequence of amino acids is completely different from the sequence in the original frame. In some messenger RNAs, including viral RNAs, frameshifting is programmed with RNA signals to produce specific ratios of proteins vital to the replication of the organism. The mechanisms that cause frameshifting have been studied for many years, but there are no definitive conclusions. We review ribosome structure and dynamics in relation to frameshifting dynamics provided by classical ensemble studies, and by new single-molecule methods using optical tweezers and FRET.
Copyright © 2013 Wiley Periodicals, Inc.

Entities:  

Keywords:  FRET; fluorescence; optical tweezers; programmed frameshifting; ribosome structure; single molecule; translation

Mesh:

Substances:

Year:  2013        PMID: 23722586      PMCID: PMC4011568          DOI: 10.1002/bip.22293

Source DB:  PubMed          Journal:  Biopolymers        ISSN: 0006-3525            Impact factor:   2.505


  104 in total

1.  Allosteric vs. spontaneous exit-site (E-site) tRNA dissociation early in protein synthesis.

Authors:  Chunlai Chen; Benjamin Stevens; Jaskiran Kaur; Zeev Smilansky; Barry S Cooperman; Yale E Goldman
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-03       Impact factor: 11.205

Review 2.  The ribosome as a molecular machine: the mechanism of tRNA-mRNA movement in translocation.

Authors:  Marina V Rodnina; Wolfgang Wintermeyer
Journal:  Biochem Soc Trans       Date:  2011-04       Impact factor: 5.407

Review 3.  Dynamics of the translational machinery.

Authors:  Alexey Petrov; Guy Kornberg; Seán O'Leary; Albert Tsai; Sotaro Uemura; Joseph D Puglisi
Journal:  Curr Opin Struct Biol       Date:  2011-01-20       Impact factor: 6.809

4.  Single-molecule fluorescence measurements of ribosomal translocation dynamics.

Authors:  Chunlai Chen; Benjamin Stevens; Jaskarin Kaur; Diana Cabral; Hanqing Liu; Yuhong Wang; Haibo Zhang; Gabriel Rosenblum; Zeev Smilansky; Yale E Goldman; Barry S Cooperman
Journal:  Mol Cell       Date:  2011-05-06       Impact factor: 17.970

5.  Ultrahigh-resolution optical trap with single-fluorophore sensitivity.

Authors:  Matthew J Comstock; Taekjip Ha; Yann R Chemla
Journal:  Nat Methods       Date:  2011-02-20       Impact factor: 28.547

6.  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

7.  Correlated conformational events in EF-G and the ribosome regulate translocation.

Authors:  James B Munro; Michael R Wasserman; Roger B Altman; Leyi Wang; Scott C Blanchard
Journal:  Nat Struct Mol Biol       Date:  2010-11-07       Impact factor: 15.369

8.  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

9.  A ribosomal misincorporation of Lys for Arg in human triosephosphate isomerase expressed in Escherichia coli gives rise to two protein populations.

Authors:  Beatriz Aguirre; Miguel Costas; Nallely Cabrera; Guillermo Mendoza-Hernández; Donald L Helseth; Paulette Fernández; Marietta Tuena de Gómez-Puyou; Ruy Pérez-Montfort; Alfredo Torres-Larios; Armando Gómez Puyou
Journal:  PLoS One       Date:  2011-06-28       Impact factor: 3.240

10.  The ribosome uses two active mechanisms to unwind messenger RNA during translation.

Authors:  Xiaohui Qu; Jin-Der Wen; Laura Lancaster; Harry F Noller; Carlos Bustamante; Ignacio Tinoco
Journal:  Nature       Date:  2011-07-06       Impact factor: 49.962

View more
  12 in total

1.  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

Review 2.  Mechanisms of mRNA frame maintenance and its subversion during translation of the genetic code.

Authors:  Jack A Dunkle; Christine M Dunham
Journal:  Biochimie       Date:  2015-02-21       Impact factor: 4.079

3.  Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions.

Authors:  Jin Chen; Arthur Coakley; Michelle O'Connor; Alexey Petrov; Seán E O'Leary; John F Atkins; Joseph D Puglisi
Journal:  Cell       Date:  2015-11-19       Impact factor: 41.582

Review 4.  Translation Elongation and Recoding in Eukaryotes.

Authors:  Thomas E Dever; Jonathan D Dinman; Rachel Green
Journal:  Cold Spring Harb Perspect Biol       Date:  2018-08-01       Impact factor: 10.005

5.  Ribosome excursions during mRNA translocation mediate broad branching of frameshift pathways.

Authors:  Shannon Yan; Jin-Der Wen; Carlos Bustamante; Ignacio Tinoco
Journal:  Cell       Date:  2015-02-19       Impact factor: 41.582

Review 6.  Ribosome dynamics during decoding.

Authors:  Marina V Rodnina; Niels Fischer; Cristina Maracci; Holger Stark
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2017-03-19       Impact factor: 6.237

7.  EF-G catalyzed translocation dynamics in the presence of ribosomal frameshifting stimulatory signals.

Authors:  Hee-Kyung Kim; Ignacio Tinoco
Journal:  Nucleic Acids Res       Date:  2017-03-17       Impact factor: 16.971

8.  Dynamic pathways of -1 translational frameshifting.

Authors:  Jin Chen; Alexey Petrov; Magnus Johansson; Albert Tsai; Seán E O'Leary; Joseph D Puglisi
Journal:  Nature       Date:  2014-06-11       Impact factor: 49.962

9.  A general strategy to inhibiting viral -1 frameshifting based on upstream attenuation duplex formation.

Authors:  Hao-Teng Hu; Che-Pei Cho; Ya-Hui Lin; Kung-Yao Chang
Journal:  Nucleic Acids Res       Date:  2015-11-26       Impact factor: 16.971

10.  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

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.