Dataset Information

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.

SUBMITTER: Yimyaem M

PROVIDER: S-EPMC10698908 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature

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Publications

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

Yimyaem Maneenop M Jitobaom Kunlakanya K Auewarakul Prasert P

BMC research notes 20231205 1

<h4>Objective</h4>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).<h4>Methodology</h4>CAIs of the whole starting regions of DENV transcripts as well as 18-codon sliding windows ...[more]

PMID: 38053139

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Project description:BackgroundHepatitis E virus (HEV) is a member of the family Hepeviridae and causes acute HEV infections resulting in thousands of deaths worldwide. The zoonotic nature of HEV in addition to its tendency from human to human transmission has led scientists across the globe to work on its different aspects. HEV also accounts for about 30% mortality rates in case of pregnant women. The genome of HEV is organized into three open reading frames (ORFs): ORF1 ORF2 and ORF3. A reading frame encoded protein ORF4 has recently been discovered which is exclusive to GT 1 isolates of HEV. The ORF4 is suggested to play crucial role in pregnancy-associated pathology and enhanced replication. Though studies have documented the ORF4's importance, the genetic features of ORF4 protein genes in terms of compositional patterns have not been elucidated. As codon usage performs critical role in establishment of the host-pathogen relationship, therefore, the present study reports the codon usage analysis (based on nucleotide sequences of HEV ORF4 available in the public database) in three hosts along with the factors influencing the codon usage patterns of the protein genes of ORF4 of HEV.ResultsThe nucleotide composition analysis indicated that ORF4 protein genes showed overrepresentation of C nucleotide and while A nucleotide was the least-represented, with random distribution of G and T(U) nucleotides. The relative synonymous codon usage (RSCU) analysis revealed biasness toward C/G-ended codons (over U/A) in all three natural HEV-hosts (human, rat and ferret). It was observed that all the ORF4 genes were richly endowed with GC content. Further, our results showed the occurrence of both coincidence and antagonistic codon usage patterns among HEV-hosts. The findings further emphasized that both mutational and selection forces influenced the codon usage patterns of ORF4 protein genes.ConclusionsTo the best of our knowledge, this is first bioinformatics study evaluating codon usage patterns in HEV ORF4 protein genes. The findings from this study are expected to increase our understanding toward significant factors involved in evolutionary changes of ORF4.Supplementary informationThe online version contains supplementary material available at 10.1186/s43088-022-00244-w.

Dataset Information

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

Objective

Methodology

Results

Publications

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

Similar Datasets

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