Differential bicodon usage in lowly and highly abundant proteins

PeerJ
Luis Diambra

Abstract

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

References

Mar 16, 2017·BMC Genomics·Christina McCarthyLuis Diambra
Sep 26, 2020·Frontiers in Cell and Developmental Biology·Andres Mariano Alonso, Luis Diambra
May 11, 2017·BMC Genomics·Yuriko Harigaya, Roy Parker
Jun 17, 2020·Brain : a Journal of Neurology·Artem KimMarie de Tayrac

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Related Concepts

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

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