Differential bicodon usage in lowly and highly abundant proteins

Luis Diambra


Degeneracy in the genetic code implies that different codons can encode the same amino acid. Usage preference of synonymous codons has been observed in all domains of life. There is much evidence suggesting that this bias has a major role on protein elongation rate, contributing to differential expression and to co-translational folding. In addition to codon usage bias, other preference variations have been observed such as codon pairs. In this paper, I report that codon pairs have significant different frequency usage for coding either lowly or highly abundant proteins. These usage preferences cannot be explained by the frequency usage of the single codons. The statistical analysis of coding sequences of nine organisms reveals that in many cases bicodon preferences are shared between related organisms. Furthermore, it is observed that misfolding in the drug-transport protein, encoded by MDR1 gene, is better explained by a big change in the pause propensity due to the synonymous bicodon variant, rather than by a relatively small change in codon usage. These findings suggest that codon pair usage can be a more powerful framework to understand translation elongation rate, protein folding efficiency, and to improve protocols to op...Continue Reading


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Sep 5, 1989·Journal of Molecular Biology·J F Curran, M Yarus
May 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·G A Gutman, G W Hatfield
Nov 25, 1982·Nucleic Acids Research·M Gouy, C Gautier
Nov 1, 1993·Comparative Biochemistry and Physiology. B, Comparative Biochemistry·T H Jukes, S Osawa
Feb 14, 2006·Nucleic Acids Research·J Ross BuchanIan Stansfield
Nov 15, 2006·Molecular Biology and Evolution·Nina Stoletzki, Adam Eyre-Walker
Dec 23, 2006·Science·Chava Kimchi-SarfatyMichael M Gottesman
Dec 28, 2007·PLoS Computational Biology·Tamir TullerEytan Ruppin
Jun 28, 2008·Science·J Robert ColemanSteffen Mueller
Oct 10, 2008·BMC Genomics·Age TatsMaido Remm
Oct 29, 2008·Genome Research·Robin C FriedmanDavid P Bartel
Nov 6, 2008·Annual Review of Genetics·Ruth Hershberg, Dmitri A Petrov
Dec 19, 2008·Nature·Hani S Zaher, Rachel Green
Feb 10, 2009·Nature Structural & Molecular Biology·Gong ZhangZoya Ignatova
Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Tamir TullerEytan Ruppin
Apr 21, 2010·Cell·Gina CannarozziYves Barral
Aug 21, 2010·BMC Evolutionary Biology·Emily H M WongLeo L M Poon
Sep 1, 2011·Nature Reviews. Genetics·Zuben E Sauna, Chava Kimchi-Sarfaty
Oct 25, 2011·Nature Structural & Molecular Biology·Prashant K Khade, Simpson Joseph
Apr 27, 2012·Molecular & Cellular Proteomics : MCP·M WangC von Mering
Jun 19, 2012·Journal of Molecular Biology·Paige S SpencerJosé M Barral
Nov 8, 2012·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Feng-Biao GuoWen Wei
Jan 8, 2014·Journal of the American Chemical Society·Ian M SanderPatricia L Clark
Feb 11, 2014·Nucleic Acids Research·Joao C GuimaraesAdam P Arkin
Jan 1, 2012·Computational and Structural Biotechnology Journal·Paige S Spencer, José M Barral
Apr 12, 2014·Current Opinion in Structural Biology·Felix GlogeBernd Bukau
Jun 6, 2014·PLoS Genetics·Fabienne F V ChevanceKelly T Hughes
Jul 25, 2014·Nucleic Acids Research·Alexandra Dana, Tamir Tuller
Oct 28, 2014·ELife·Justin GardinBruce Futcher
Dec 30, 2014·Molecular Systems Biology·Cristina PopDaphne Koller
Mar 31, 2015·The International Journal of Biochemistry & Cell Biology·Vedrana Bali, Zsuzsanna Bebok
Jul 18, 2015·Molecular Cell·Tessa E F QuaxJohn van der Oost

Related Concepts

Translational Elongation
Gene Expression
Codon Genus
Codon (Nucleotide Sequence)
ABCB1 gene
Genetic Translation Process
Carrier Proteins
Amino Acid [EPC]
Gene Mutant

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