SrasV1, Main, Exploration, bibRecord, 001F32

Analysis of base and codon usage by rubella virus

Identifieur interne : 001F32 ( Main/Exploration ); précédent : 001F31; suivant : 001F33

Analysis of base and codon usage by rubella virus

Auteurs : Yumei Zhou [États-Unis] ; Xianfeng Chen [États-Unis] ; Hiroshi Ushijima [Japon] ; Teryl K. Frey [États-Unis]

Source :

Archives of Virology [ 0304-8608 ] ; 2012-05-01.

RBID : ISTEX:D150070D944A91BFB9BDE10F95D710BCCE71940A

Abstract

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.

Url:

https://api.istex.fr/ark:/67375/VQC-0N20WC97-G/fulltext.pdf

DOI: 10.1007/s00705-012-1243-9

Affiliations:

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Le document en format XML

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<front><div type="abstract" xml:lang="en">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.</div>
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Analysis of base and codon usage by rubella virus

Analysis of base and codon usage by rubella virus

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Abstract

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