Codon Pair Bias Is a Direct Consequence of Dinucleotide Bias

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review

106 Scopus Citations
View graph of relations

Author(s)

Detail(s)

Original languageEnglish
Pages (from-to)55-67
Journal / PublicationCell Reports
Volume14
Issue number1
Online published24 Dec 2015
Publication statusPublished - 5 Jan 2016
Externally publishedYes

Link(s)

Abstract

Codon pair bias is a remarkably stable characteristic of a species. Although functionally uncharacterized, robust virus attenuation was achieved by recoding of viral proteins using underrepresented codon pairs. Because viruses replicate exclusively inside living cells, we posited that their codon pair preferences reflect those of their host(s). Analysis of many human viruses showed, however, that the encoding of viruses is influenced only marginally by host codon pair preferences. Furthermore, examination of codon pair preferences of vertebrate, insect, and arthropod-borne viruses revealed that the latter do not utilize codon pairs overrepresented in arthropods more frequently than other viruses. We found, however, that codon pair bias is a direct consequence of dinucleotide bias. We conclude that codon pair bias does not play a major role in the encoding of viral proteins and that virus attenuation by codon pair deoptimization has the same molecular underpinnings as attenuation based on an increase in CpG/TpA dinucleotides. Kunec and Osterrieder demonstrate that the encoding of viral proteins is not influenced by codon pair preferences of their host but that it can be influenced by host dinucleotide bias. Codon pair bias is primarily a consequence of dinucleotide bias. Attenuation by codon pair deoptimization works through an increase in CpG dinucleotides in recoded genes.

Research Area(s)

Citation Format(s)

Codon Pair Bias Is a Direct Consequence of Dinucleotide Bias. / Kunec, Dusan; Osterrieder, Nikolaus.
In: Cell Reports, Vol. 14, No. 1, 05.01.2016, p. 55-67.

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review

Download Statistics

No data available