Wobbling Forth and Drifting Back: The Evolutionary History and Impact of Bacterial tRNA Modifications.

Molecular Biology and Evolution
Gaurav D Diwan, Deepa Agashe

Abstract

Along with tRNAs, enzymes that modify anticodon bases are a key aspect of translation across the tree of life. tRNA modifications extend wobble pairing, allowing specific ("target") tRNAs to recognize multiple codons and cover for other ("nontarget") tRNAs, often improving translation efficiency and accuracy. However, the detailed evolutionary history and impact of tRNA modifying enzymes has not been analyzed. Using ancestral reconstruction of five tRNA modifications across 1093 bacteria, we show that most modifications were ancestral to eubacteria, but were repeatedly lost in many lineages. Most modification losses coincided with evolutionary shifts in nontarget tRNAs, often driven by increased bias in genomic GC and associated codon use, or by genome reduction. In turn, the loss of tRNA modifications stabilized otherwise highly dynamic tRNA gene repertoires. Our work thus traces the complex history of bacterial tRNA modifications, providing the first clear evidence for their role in the evolution of bacterial translation.

References

Aug 1, 1985·Proceedings of the National Academy of Sciences of the United States of America·S YokoyamaT Miyazawa
Aug 1, 1966·Journal of Molecular Biology·F H Crick
Jan 27, 1999·Bioinformatics·S R Eddy
Apr 27, 1999·Journal of Biomolecular Structure & Dynamics·R C MorrisM S Elliott
Aug 31, 2000·Journal of Molecular Biology·C NotredameJ Heringa
Jul 12, 2002·The EMBO Journal·Jeannette WolfWalter Keller
Mar 3, 2004·Proceedings of the National Academy of Sciences of the United States of America·Swaine L ChenHarley H McAdams
Sep 18, 2004·Bioinformatics·D CharifG Perrière
Apr 19, 2005·Biochimica Et Biophysica Acta·Yuko YamadaKatsutoshi Murao
Oct 11, 2005·Nucleic Acids Research·Ross OverbeekVeronika Vonstein
Mar 1, 2006·BMC Bioinformatics·Jonathan P Bollback
Dec 26, 2006·Journal of Molecular Biology·Paul F AgrisWilliam D Graham
Nov 6, 2008·Nucleic Acids Research·Patricia P Chan, Todd M Lowe
Jul 14, 2009·PLoS Genetics·Ruth Hershberg, Dmitri A Petrov
Apr 3, 2012·Cell·Eva Maria NovoaLluís Ribas de Pouplana
Jan 9, 2013·Nucleic Acids Research·Takaaki TaniguchiTsutomu Suzuki
Aug 15, 2013·Nature Communications·Nicola SegataCurtis Huttenhower
May 1, 2014·EcoSal Plus·Glenn R Björk, Tord G Hagervall
Dec 26, 2015·Nucleic Acids Research·Nandini ManickamPhilip J Farabaugh
May 6, 2016·Frontiers in Cellular and Infection Microbiology·Ting GaoRui Zhou
Nov 12, 2016·Nature Communications·Yok Hian ChionhPeter C Dedon
Jan 28, 2017·ACS Chemical Biology·Rémi ZallotValérie de Crécy-Lagard
Feb 18, 2017·Biomolecules·Rémi ZallotValérie de Crécy-Lagard
Nov 7, 2017·Nucleic Acids Research·Pietro BoccalettoJanusz M Bujnicki

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Citations

Dec 28, 2018·Molecular Biology and Evolution·Àlbert Rafels-YbernLluís Ribas de Pouplana
Jul 10, 2019·IUBMB Life·Emil M Nilsson, Rebecca W Alexander
Jul 29, 2020·Trends in Microbiology·Valérie de Crécy-Lagard, Marshall Jaroch
Apr 3, 2021·Frontiers in Molecular Biosciences·Ricardo EhrlichMónica Marín
May 1, 2021·Genes·Sundaramoorthy SrinivasanLluís Ribas de Pouplana
Jun 15, 2021·Nucleic Acids Research·Adrian Gabriel TorresLluís Ribas de Pouplana
Dec 5, 2018·Biochemistry·Leticia Pollo-Oliveira, Valérie de Crécy-Lagard

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