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Analysis of base and codon usage by rubella virus

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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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Acknowledgments

This research was supported by a grant from NIH (AI21389).

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  1. Xianfeng Chen

    Present address: Gastroenteritis and Respiratory Virus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, GA, 30333, USA

  2. Hiroshi Ushijima

    Present address: Division of Microbiology, Department of Pathology and Microbiology, School of Medicine, Nihon University, 30-1 Oyaguchi Kamicho, Itabashi-ku, Tokyo, 173-8610, Japan

Authors and Affiliations

  1. Department of Biology, Georgia State University, Atlanta, GA, 30303, USA

    Yumei Zhou, Xianfeng Chen & Teryl K. Frey

  2. Department of Developmental Medical Sciences, Institute of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan

    Hiroshi Ushijima

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Zhou, Y., Chen, X., Ushijima, H. et al. Analysis of base and codon usage by rubella virus. Arch Virol 157, 889–899 (2012). https://doi.org/10.1007/s00705-012-1243-9

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