Roles for Synonymous Codon Usage in Protein Biogenesis

Annual Review of Biophysics
Julie L Chaney, Patricia L Clark

Abstract

Owing to the degeneracy of the genetic code, a protein sequence can be encoded by many different synonymous mRNA coding sequences. Synonymous codon usage was once thought to be functionally neutral, but evidence now indicates it is shaped by evolutionary selection and affects other aspects of protein biogenesis beyond specifying the amino acid sequence of the protein. Synonymous rare codons, once thought to have only negative impacts on the speed and accuracy of translation, are now known to play an important role in diverse functions, including regulation of cotranslational folding, covalent modifications, secretion, and expression level. Mutations altering synonymous codon usage are linked to human diseases. However, much remains unknown about the molecular mechanisms connecting synonymous codon usage to efficient protein biogenesis and proper cell physiology. Here we review recent literature on the functional effects of codon usage, including bioinformatics approaches aimed at identifying general roles for synonymous codon usage.

References

Aug 5, 1978·Journal of Molecular Biology·J O ThomasW Szer
Jun 14, 1976·Journal of Molecular Biology·V TalkadD Kennell
Sep 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·C TuJ A Bruenn
May 20, 1989·Journal of Molecular Biology·M A SørensenS Pedersen
Jan 29, 1986·Biochemical and Biophysical Research Communications·M WiedmannT A Rapoport
Jan 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·A Muto, S Osawa
Jul 20, 1973·Science·C B Anfinsen
Jan 1, 1983·Cold Spring Harbor Symposia on Quantitative Biology·T Ikemura, H Ozeki
Nov 25, 1982·Nucleic Acids Research·M Gouy, C Gautier
Jan 11, 1980·Nucleic Acids Research·R GranthamA Pavé
Feb 25, 1995·Nucleic Acids Research·J F Curran
May 1, 1994·Nature Structural Biology·J F SinclairT O Baldwin
Oct 15, 1994·Structure·D Baker, D A Agard
Aug 1, 1996·Protein Science : a Publication of the Protein Society·T A Thanaraj, P Argos
Oct 1, 1996·Protein Science : a Publication of the Protein Society·T A Thanaraj, P Argos
Jul 25, 1997·Journal of Molecular Biology·O G Berg, C G Kurland
Apr 7, 1999·Seminars in Cancer Biology·B S Strauss
Apr 3, 2001·Science·M M YusupovH F Noller
Aug 28, 2001·Journal of Molecular Evolution·N G Smith, A Eyre-Walker
Mar 21, 2002·Nature Reviews. Cancer·Robert W Tindle
Jun 5, 2002·Trends in Genetics : TIG·Eduardo P C Rocha, Antoine Danchin
Jun 11, 2002·Biochemical and Biophysical Research Communications·Patricia CortazzoAtilio Deana
Aug 15, 2002·Trends in Genetics : TIG·Laurence D Hurst
Oct 11, 2003·Protein Expression and Purification·Anders Fuglsang
Oct 17, 2003·Nature·Sina GhaemmaghamiJonathan S Weissman
Feb 14, 2004·Molecular Biology and Evolution·Julien Meunier, Laurent Duret
Mar 3, 2004·Proceedings of the National Academy of Sciences of the United States of America·Swaine L ChenHarley H McAdams
Mar 17, 2004·Nature Structural & Molecular Biology·Xuelian LuoHongtao Yu
Jul 13, 2004·Trends in Biotechnology·Claes GustafssonJeremy Minshull

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Citations

Feb 24, 2016·Life·Tamara Fernández-CaleroMónica Marín
May 7, 2016·Bioinformatics·Pengbo WenJunfeng Xia
Mar 19, 2016·Molecular Cell·Yuichiro Mishima, Yukihide Tomari
Apr 4, 2016·Journal of Molecular Biology·Marina V Rodnina, Wolfgang Wintermeyer
May 8, 2016·Journal of Molecular Evolution·Héctor Musto
Jun 5, 2016·Journal of Molecular Biology·Aditya Radhakrishnan, Rachel Green
Jun 20, 2016·Current Opinion in Structural Biology·Giselle N Jacobson, Patricia L Clark
Jun 29, 2016·RNA Biology·Thomas Philipp HoernesMatthias David Erlacher
Jun 15, 2016·Annual Review of Biophysics·Fabio Trovato, Edward P O'Brien
Jul 29, 2016·Nucleic Acids Research·Guilhem FaureEugene V Koonin
Aug 4, 2016·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Sheng-Lin ShiLi Qin
May 21, 2016·Protein Science : a Publication of the Protein Society·Marina V Rodnina
Sep 21, 2016·Molecular Psychiatry·G PathakM P Kelly
Jun 30, 2016·Human Molecular Genetics·Anton A Komar
Jan 27, 2017·Andrologia·M N ChoudhuryS Chakraborty
Jan 13, 2017·Journal of Proteome Research·Zhijing TanDavid M Lubman
Dec 23, 2016·Journal of Medical Genetics·Vijaya L SimhadriChava Kimchi-Sarfaty
Apr 7, 2018·FEBS Letters·Charlotte MignonBettina Werle
Sep 9, 2017·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Didier Auboeuf
Oct 12, 2017·Nature Reviews. Molecular Cell Biology·Gavin Hanson, Jeff Coller
Jul 11, 2018·Cephalalgia : an International Journal of Headache·Sara BertelliPaola Gavazzo
Feb 6, 2017·Journal of Virology·Francesca Di GiallonardoEdward C Holmes
Mar 14, 2018·Cold Spring Harbor Perspectives in Medicine·Rosa M PintóAlbert Bosch
Mar 27, 2018·Acta Biologica Hungarica·Yi Wen Lu, Tai Sheng Chiu
Dec 7, 2018·The Journal of Biological Chemistry·Kevin C Stein, Judith Frydman
Feb 17, 2018·Scientific Reports·Pramod ShindeSarika Jalan
Feb 6, 2018·Annual Review of Biochemistry·Adi Goldenzweig, Sarel J Fleishman
Apr 30, 2019·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Parvin A BarbhuiyaSupriyo Chakraborty
Oct 27, 2017·Proceedings of the National Academy of Sciences of the United States of America·William M Jacobs, Eugene I Shakhnovich
Jan 17, 2020·Reproduction in Domestic Animals = Zuchthygiene·Siyao WangLinlin Hao
Jan 28, 2020·Genome Génome / Conseil National De Recherches Canada·Aasim MajeedPankaj Bhardwaj
Apr 24, 2019·Journal of Bacteriology·Milton H Saier

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Methods Mentioned

BETA
biosensor
protein folding

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