A small stretch of poor codon usage at the beginning of dengue virus open reading frame may act as a translational checkpoint

Abstract

Objective Rare codons were previously shown to be enriched at the beginning of the dengue virus (DENV) open reading frame. However, the role of rare codons in regulating translation efficiency and replication of DENV remains unclear. The present study aims to clarify the significance of rare codon usage at the beginning of DENV transcripts using the codon adaptation index (CAI). Methodology CAIs of the whole starting regions of DENV transcripts as well as 18-codon sliding windows of the regions were analyzed. Results One of the intriguing findings is that those rare codons do not typically result in uniformly low CAI in the starting region with rare codons. However, it shows a notable local drop in CAI around the 50th codon in all dengue serotypes. This suggests that there may be a translational checkpoint at this site and that the rare codon usage upstream to this checkpoint may not be related to translational control.

Characterization of Genotype V Japanese Encephalitis Virus Isolates from Republic of Korea

“…Despite 43279 showed no substitutions in the amino acid sequence, it differed by one nucleotide in both the Env and Ns3 gene sequences compared to K15P38. Although these differences seem minor, variations in its genome sequence could have influenced the RNA secondary structure or codon usage, potentially affecting the replication cycle [ 31–33 ]. Sangju has been fully sequenced only for the Env gene, and when compared to 43413, the differences are more significant than those between 43279 and K15P38.…”