Analysis of base and codon usage by rubella virus.
ABSTRACT Rubella virus (RUBV), a small, plus-strand RNA virus that is an important human pathogen, has the unique feature that the GC content of its genome (70%) is the highest (by 20%) among RNA viruses. To determine the effect of this GC content on genomic evolution, base and codon usage were analyzed across viruses from eight diverse genotypes of RUBV. Despite differences in frequency of codon use, the favored codons in the RUBV genome matched those in the human genome for 18 of the 20 amino acids, indicating adaptation to the host. Although usage patterns were conserved in corresponding genes in the diverse genotypes, within-genome comparison revealed that both base and codon usages varied regionally, particularly in the hypervariable region (HVR) of the P150 replicase gene. While directional mutation pressure was predominant in determining base and codon usage within most of the genome (with the strongest tendency being towards C's at third codon positions), natural selection was predominant in the HVR region. The GC content of this region was the highest in the genome (>80%), and it was not clear if selection at the nucleotide level accompanied selection at the amino acid level. Dinucleotide frequency analysis of the RUBV genome revealed that TpA usage was lower than expected, similar to mammalian genes; however, CpG usage was not suppressed, and TpG usage was not enhanced, as is the case in mammalian genes.
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ABSTRACT: In this study, we calculated the codon usage bias in severe acute respiratory syndrome Coronavirus (SARSCoV) and performed a comparative analysis of synonymous codon usage patterns in SARSCoV and 10 other evolutionary related viruses in the Nidovirales. Although there is a significant variation in codon usage bias among different SARSCoV genes, codon usage bias in SARSCoV is a little slight, which is mainly determined by the base compositions on the third codon position. By comparing synonymous codon usage patterns in different viruses, we observed that synonymous codon usage pattern in these virus genes was virus specific and phylogenetically conserved, but it was not host specific. Phylogenetic analysis based on codon usage pattern suggested that SARSCoV was diverged far from all three known groups of Coronavirus. Compositional constraints could explain most of the variation of synonymous codon usage among these virus genes, while gene function is also correlated to synonymous codon usages to a certain extent. However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes.Virus Research 06/2004; 101(2):155-61. · 2.75 Impact Factor
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ABSTRACT: The expression of both the env and gag gene products of human immunodeficiency virus type 1 (HIV-1) is known to be limited by cis elements in the viral RNA that impede egress from the nucleus and reduce the efficiency of translation. Identifying these elements has proven difficult, as they appear to be disseminated throughout the viral genome. Here, we report that selective codon usage appears to account for a substantial fraction of the inefficiency of viral protein synthesis, independent of any effect on improved nuclear export. The codon usage effect is not specific to transcripts of HIV-1 origin. Re-engineering the coding sequence of a model protein (Thy-1) with the most prevalent HIV-1 codons significantly impairs Thy-1 expression, whereas altering the coding sequence of the jellyfish green fluorescent protein gene to conform to the favored codons of highly expressed human proteins results in a substantial increase in expression efficiency. Codon-usage effects are a major impediment to the efficient expression of HIV-1 genes. Although mammalian genes do not show as profound a bias as do Escherichia coli genes, other proteins that are poorly expressed in mammalian cells can benefit from codon re-engineering.Current Biology 04/1996; 6(3):315-24. · 9.49 Impact Factor
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ABSTRACT: DAMBE (data analysis in molecular biology and evolution) is an integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data with a user-friendly Windows 95/98/2000/NT interface. DAMBE is free and can be downloaded from http://web.hku.hk/~xxia/software/software.htm. The current version is 4.0.36.Journal of Heredity 01/2001; 92(4):371-3. · 2.00 Impact Factor