The distribution of synonymous codon choice in the translation initiation region of dengue virus

• Published in: PloS one Vol. 8; no. 10; p. e77239
• Main Authors: Zhou, Jian-hua, Zhang, Jie, Sun, Dong-jie, Ma, Qi, Chen, Hao-tai, Ma, Li-na, Ding, Yao-zhong, Liu, Yong-sheng
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 25.10.2013; Public Library of Science (PLoS)
• Subjects: Adaptation; Aedes; Aedes - virology; Aedes aegypti; Aedes albopictus; Animals; Aquatic insects; Bias; Biological evolution; Biology; Codon; Codons; Culicidae; Dengue; Dengue - virology; Dengue fever; Dengue Virus - genetics; Dengue Virus - metabolism; E coli; Efficiency; Epidemics; Escherichia coli; Gene expression; Genomes; Genotype & phenotype; Genotypes; Geographical distribution; Host Specificity; Host-Pathogen Interactions - genetics; Humans; Laboratories; Molecular Typing; Mosquitoes; Mutation; Open Reading Frames; Pan troglodytes - virology; Peptide Chain Initiation, Translational; Phylogenetics; Primates; Principal components analysis; Proteins; Ribonucleic acid; RNA; RNA viruses; RNA, Transfer - genetics; RNA, Transfer - metabolism; Translation; Translation initiation; tRNA; Vector-borne diseases; Viral diseases; Viruses
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0077239

Dengue is the most common arthropod-borne viral (Arboviral) illness in humans. The genetic features concerning the codon usage of dengue virus (DENV) were analyzed by the relative synonymous codon usage, the effective number of codons and the codon adaptation index. The evolutionary distance between DENV and the natural hosts (Homo sapiens, Pan troglodytes, Aedes albopictus and Aedes aegypti) was estimated by a novel formula. Finally, the synonymous codon usage preference for the translation initiation region of this virus was also analyzed. The result indicates that the general trend of the 59 synonymous codon usage of the four genotypes of DENV are similar to each other, and this pattern has no link with the geographic distribution of the virus. The effect of codon usage pattern of Aedes albopictus and Aedes aegypti on the formation of codon usage of DENV is stronger than that of the two primates. Turning to the codon usage preference of the translation initiation region of this virus, some codons pairing to low tRNA copy numbers in the two primates have a stronger tendency to exist in the translation initiation region than those in the open reading frame of DENV. Although DENV, like other RNA viruses, has a high mutation to adapt its hosts, the regulatory features about the synonymous codon usage have been 'branded' on the translation initiation region of this virus in order to hijack the translational mechanisms of the hosts.