Literature DB >> 22190491

Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection.

Magnus Johansson1, Jingji Zhang, Måns Ehrenberg.   

Abstract

Rapid and accurate translation of the genetic code into protein is fundamental to life. Yet due to lack of a suitable assay, little is known about the accuracy-determining parameters and their correlation with translational speed. Here, we develop such an assay, based on Mg(2+) concentration changes, to determine maximal accuracy limits for a complete set of single-mismatch codon-anticodon interactions. We found a simple, linear trade-off between efficiency of cognate codon reading and accuracy of tRNA selection. The maximal accuracy was highest for the second codon position and lowest for the third. The results rationalize the existence of proofreading in code reading and have implications for the understanding of tRNA modifications, as well as of translation error-modulating ribosomal mutations and antibiotics. Finally, the results bridge the gap between in vivo and in vitro translation and allow us to calibrate our test tube conditions to represent the environment inside the living cell.

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Year:  2011        PMID: 22190491      PMCID: PMC3252910          DOI: 10.1073/pnas.1116480109

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  25 in total

1.  Recognition of cognate transfer RNA by the 30S ribosomal subunit.

Authors:  J M Ogle; D E Brodersen; W M Clemons ; M J Tarry; A P Carter; V Ramakrishnan
Journal:  Science       Date:  2001-05-04       Impact factor: 47.728

2.  Kinetic determinants of high-fidelity tRNA discrimination on the ribosome.

Authors:  Kirill B Gromadski; Marina V Rodnina
Journal:  Mol Cell       Date:  2004-01-30       Impact factor: 17.970

3.  Kinetic amplification of enzyme discrimination.

Authors:  J Ninio
Journal:  Biochimie       Date:  1975       Impact factor: 4.079

4.  Proofreading of the codon-anticodon interaction on ribosomes.

Authors:  R C Thompson; P J Stone
Journal:  Proc Natl Acad Sci U S A       Date:  1977-01       Impact factor: 11.205

5.  Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity.

Authors:  J J Hopfield
Journal:  Proc Natl Acad Sci U S A       Date:  1974-10       Impact factor: 11.205

6.  The genetic code and error transmission.

Authors:  C Alff-Steinberger
Journal:  Proc Natl Acad Sci U S A       Date:  1969-10       Impact factor: 11.205

7.  Codon--anticodon pairing: the wobble hypothesis.

Authors:  F H Crick
Journal:  J Mol Biol       Date:  1966-08       Impact factor: 5.469

8.  Nonsense-mediated mRNA decay maintains translational fidelity by limiting magnesium uptake.

Authors:  Marcus J O Johansson; Allan Jacobson
Journal:  Genes Dev       Date:  2010-07-15       Impact factor: 11.361

9.  Nucleoside triphosphate regeneration decreases the frequency of translation errors.

Authors:  P C Jelenc; C G Kurland
Journal:  Proc Natl Acad Sci U S A       Date:  1979-07       Impact factor: 11.205

10.  Is there proofreading during polypeptide synthesis?

Authors:  T Ruusala; M Ehrenberg; C G Kurland
Journal:  EMBO J       Date:  1982       Impact factor: 11.598

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  56 in total

1.  Speed, dissipation, and error in kinetic proofreading.

Authors:  Arvind Murugan; David A Huse; Stanislas Leibler
Journal:  Proc Natl Acad Sci U S A       Date:  2012-07-11       Impact factor: 11.205

2.  Human cells have a limited set of tRNA anticodon loop substrates of the tRNA isopentenyltransferase TRIT1 tumor suppressor.

Authors:  Tek N Lamichhane; Sandy Mattijssen; Richard J Maraia
Journal:  Mol Cell Biol       Date:  2013-10-14       Impact factor: 4.272

3.  Another look at mutations in ribosomal protein S4 lends strong support to the domain closure model.

Authors:  Kurt Fredrick
Journal:  J Bacteriol       Date:  2014-12-29       Impact factor: 3.490

4.  Accuracy of initial codon selection by aminoacyl-tRNAs on the mRNA-programmed bacterial ribosome.

Authors:  Jingji Zhang; Ka-Weng Ieong; Magnus Johansson; Måns Ehrenberg
Journal:  Proc Natl Acad Sci U S A       Date:  2015-07-20       Impact factor: 11.205

Review 5.  Relating Structure and Dynamics in RNA Biology.

Authors:  Kevin P Larsen; Junhong Choi; Arjun Prabhakar; Elisabetta Viani Puglisi; Joseph D Puglisi
Journal:  Cold Spring Harb Perspect Biol       Date:  2019-07-01       Impact factor: 10.005

6.  An in vitro tag-and-modify protein sample generation method for single-molecule fluorescence resonance energy transfer.

Authors:  Kambiz M Hamadani; Jesse Howe; Madeleine K Jensen; Peng Wu; Jamie H D Cate; Susan Marqusee
Journal:  J Biol Chem       Date:  2017-07-28       Impact factor: 5.157

Review 7.  Dynamic basis of fidelity and speed in translation: Coordinated multistep mechanisms of elongation and termination.

Authors:  Arjun Prabhakar; Junhong Choi; Jinfan Wang; Alexey Petrov; Joseph D Puglisi
Journal:  Protein Sci       Date:  2017-05-23       Impact factor: 6.725

8.  Elucidating interplay of speed and accuracy in biological error correction.

Authors:  Kinshuk Banerjee; Anatoly B Kolomeisky; Oleg A Igoshin
Journal:  Proc Natl Acad Sci U S A       Date:  2017-05-02       Impact factor: 11.205

9.  N 6-Methyladenosines in mRNAs reduce the accuracy of codon reading by transfer RNAs and peptide release factors.

Authors:  Ka-Weng Ieong; Gabriele Indrisiunaite; Arjun Prabhakar; Joseph D Puglisi; Måns Ehrenberg
Journal:  Nucleic Acids Res       Date:  2021-03-18       Impact factor: 16.971

10.  Lack of tRNA modification isopentenyl-A37 alters mRNA decoding and causes metabolic deficiencies in fission yeast.

Authors:  Tek N Lamichhane; Nathan H Blewett; Amanda K Crawford; Vera A Cherkasova; James R Iben; Thomas J Begley; Philip J Farabaugh; Richard J Maraia
Journal:  Mol Cell Biol       Date:  2013-05-28       Impact factor: 4.272

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