Codon usage of HIV regulatory genes is not determined by nucleotide composition

Collection Location Koleksi E-book & E-Journal Perpustakaan Pusat Unila
Edition Vol. 163, Issue 2
Call Number
ISBN/ISSN 14328798
Author(s) Phakaratsakul, Supinya...[et al.]
Subject(s) Biomedicine
Classification NONE
Series Title
GMD E-Journal
Language English
Publisher Springer
Publishing Year 2018
Publishing Place Switzerland
Abstract/Notes Abstract Codon usage bias can be a result of either mutational
bias or selection for translational efficiency and/or
accuracy. Previous data has suggested that nucleotide composition
constraint was the main determinant of HIV codon
usage, and that nucleotide composition and codon usage
were different between the regulatory genes, tat and rev,
and other viral genes. It is not clear whether translational
selection contributed to the codon usage difference and how
nucleotide composition and translational selection interact to
determine HIV codon usage. In this study, a model of codon
bias due to GC composition with modification for the A-rich
third codon position was used to calculate predicted HIV
codon frequencies based on its nucleotide composition. The
predicted codon usage of each gene was compared with the
actual codon frequency. The predicted codon usage based
on GC composition matched well with the actual codon frequencies
for the structural genes (gag, pol and env). However,
the codon usage of the regulatory genes (tat and rev)
could not be predicted. Codon usage of the regulatory genes
was also relatively unbiased showing the highest effective
number of codons (ENC). Moreover, the codon adaptation index (CAI) of the regulatory genes showed better adaptation
to human codons when compared to other HIV genes.
Therefore, the early expressed genes responsible for regulation
of the replication cycle, tat and rev, were more similar
to humans in terms of codon usage and GC content than
other HIV genes. This may help these genes to be expressed
efficiently during the early stages of infection.
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