Categorizing Host-Dependent RNA Viruses by Their Codon Usage Preference

• Main Authors: Ming-Wei Su, 蘇明威
• Other Authors: Woei-Chyn Chu
• Format: Others
• Language: en_US
• Published: 2010
• Online Access: http://ndltd.ncl.edu.tw/handle/36264768223558698976

博士 === 國立陽明大學 === 醫學工程研究所 === 98 === To understand the extent and causes of codon usage bias and nucleotide composition is very important in studying viral evolution and relationship between viruses and host cells. Viruses have to exploit host transcription and translation mechanisms to replicate in a hostile host cellular environment, and therefore, it is likely that the infected host may impose pressure on viral evolution. The purpose of this study is to find the relationship between virus codon usage preference and host specific characteristics. In many prokaryotes and some lower eukaryotes it is known that synonymous codon are not randomly used by natural selection, however in viruses, the codon usage preference has not been extensively discussed. Earlier studies in Escherichia coli, yeast, and Drosophila showed that highly expressed genes, such as ribosomal genes, had a strong extent of codon usage preference, and found that codon usage patterns is related to the isoaccepting tRNA content of individual organisms so called translation selection. Through the translation selection effect this study had presumed that the viral codon usage preference may be influenced by virus-host co-evolution. For this reason, viruses that infected the same host may possess a similar preference pattern in their codon usage. In this study, codon usage preference pattern was used to investigate the host specific character of viruses. Host radiation process allows viruses to expend to one or more novel hosts occurred recently in influenza A H1N1 virus. We also try to find the differences of codon usage patterns between human infected and swine infected H1N1 viruses. Newly developed codon preference space mapping method further helps us to evaluate the correlation between virus and host codon usage preference.