Literature DB >> 26260261

Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning.

Pavel V Baranov1, John F Atkins2, Martina M Yordanova1.   

Abstract

The non-universality of the genetic code is now widely appreciated. Codes differ between organisms, and certain genes are known to alter the decoding rules in a site-specific manner. Recently discovered examples of decoding plasticity are particularly spectacular. These examples include organisms and organelles with disruptions of triplet continuity during the translation of many genes, viruses that alter the entire genetic code of their hosts and organisms that adjust their genetic code in response to changing environments. In this Review, we outline various modes of alternative genetic decoding and expand existing terminology to accommodate recently discovered manifestations of this seemingly sophisticated phenomenon.

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Year:  2015        PMID: 26260261     DOI: 10.1038/nrg3963

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  182 in total

Review 1.  Translational recoding in archaea.

Authors:  Beatrice Cobucci-Ponzano; Mosè Rossi; Marco Moracci
Journal:  Extremophiles       Date:  2012-09-27       Impact factor: 2.395

2.  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

3.  A persistent untranslated sequence within bacteriophage T4 DNA topoisomerase gene 60.

Authors:  W M Huang; S Z Ao; S Casjens; R Orlandi; R Zeikus; R Weiss; D Winge; M Fang
Journal:  Science       Date:  1988-02-26       Impact factor: 47.728

4.  A functional -1 ribosomal frameshift signal in the human paraneoplastic Ma3 gene.

Authors:  Norma M Wills; Barry Moore; Andrew Hammer; Raymond F Gesteland; John F Atkins
Journal:  J Biol Chem       Date:  2006-01-05       Impact factor: 5.157

5.  Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA.

Authors:  Gayathri Srinivasan; Carey M James; Joseph A Krzycki
Journal:  Science       Date:  2002-05-24       Impact factor: 47.728

6.  An atypical RNA pseudoknot stimulator and an upstream attenuation signal for -1 ribosomal frameshifting of SARS coronavirus.

Authors:  Mei-Chi Su; Chung-Te Chang; Chiu-Hui Chu; Ching-Hsiu Tsai; Kung-Yao Chang
Journal:  Nucleic Acids Res       Date:  2005-07-29       Impact factor: 16.971

7.  Identification of stop codon readthrough genes in Saccharomyces cerevisiae.

Authors:  Olivier Namy; Guillemette Duchateau-Nguyen; Isabelle Hatin; Sylvie Hermann-Le Denmat; Michel Termier; Jean-Pierre Rousset
Journal:  Nucleic Acids Res       Date:  2003-05-01       Impact factor: 16.971

8.  The tmRNA website.

Authors:  Corey M Hudson; Kelly P Williams
Journal:  Nucleic Acids Res       Date:  2014-11-05       Impact factor: 16.971

Review 9.  Repeat-associated non-ATG (RAN) translation in neurological disease.

Authors:  John D Cleary; Laura P W Ranum
Journal:  Hum Mol Genet       Date:  2013-08-04       Impact factor: 6.150

Review 10.  RAN translation and frameshifting as translational challenges at simple repeats of human neurodegenerative disorders.

Authors:  Marzena Wojciechowska; Marta Olejniczak; Paulina Galka-Marciniak; Magdalena Jazurek; Wlodzimierz J Krzyzosiak
Journal:  Nucleic Acids Res       Date:  2014-09-12       Impact factor: 16.971

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  32 in total

1.  Widespread and dynamic translational control of red blood cell development.

Authors:  Juan R Alvarez-Dominguez; Xu Zhang; Wenqian Hu
Journal:  Blood       Date:  2016-11-29       Impact factor: 22.113

2.  Interrogation of Eukaryotic Stop Codon Readthrough Signals by in Vitro RNA Selection.

Authors:  Andrew V Anzalone; Sakellarios Zairis; Annie J Lin; Raul Rabadan; Virginia W Cornish
Journal:  Biochemistry       Date:  2019-02-13       Impact factor: 3.162

Review 3.  Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use.

Authors:  John F Atkins; Gary Loughran; Pramod R Bhatt; Andrew E Firth; Pavel V Baranov
Journal:  Nucleic Acids Res       Date:  2016-07-19       Impact factor: 16.971

Review 4.  Beyond the Triplet Code: Context Cues Transform Translation.

Authors:  Gloria A Brar
Journal:  Cell       Date:  2016-12-15       Impact factor: 41.582

Review 5.  Exploiting non-canonical translation to identify new targets for T cell-based cancer immunotherapy.

Authors:  Céline M Laumont; Claude Perreault
Journal:  Cell Mol Life Sci       Date:  2017-08-19       Impact factor: 9.261

6.  Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome.

Authors:  Sezen Meydan; James Marks; Dorota Klepacki; Virag Sharma; Pavel V Baranov; Andrew E Firth; Tōnu Margus; Amira Kefi; Nora Vázquez-Laslop; Alexander S Mankin
Journal:  Mol Cell       Date:  2019-03-20       Impact factor: 17.970

7.  Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons in Condylostoma magnum.

Authors:  Stephen M Heaphy; Marco Mariotti; Vadim N Gladyshev; John F Atkins; Pavel V Baranov
Journal:  Mol Biol Evol       Date:  2016-08-08       Impact factor: 16.240

Review 8.  Roadblocks and resolutions in eukaryotic translation.

Authors:  Anthony P Schuller; Rachel Green
Journal:  Nat Rev Mol Cell Biol       Date:  2018-08       Impact factor: 94.444

9.  Quantitative assessment of ribosome drop-off in E. coli.

Authors:  Celine Sin; Davide Chiarugi; Angelo Valleriani
Journal:  Nucleic Acids Res       Date:  2016-03-01       Impact factor: 16.971

Review 10.  RNA G-Quadruplexes in Biology: Principles and Molecular Mechanisms.

Authors:  Marta M Fay; Shawn M Lyons; Pavel Ivanov
Journal:  J Mol Biol       Date:  2017-05-26       Impact factor: 5.469

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