Comprehensive analysis of the overall codon usage patterns in equine infectious anemia virus

Virology Journal

Xiaojun Wang¹  Ping Wei²  Weigang Cai¹  Yuezhi Lin¹  Xin Yin² 

[1] Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China;College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China

关键词: Evolution;    Codon usage bias;    Equine infectious anemia virus (EIAV);   

Others  :  819994
DOI  :  10.1186/1743-422X-10-356

 received in 2013-10-18, accepted in 2013-12-11,  发布年份 2013

【 摘 要 】

Background

Equine infectious anemia virus (EIAV) is an important animal model for understanding the relationship between viral persistence and the host immune response during lentiviral infections. Comparison and analysis of the codon usage model between EIAV and its hosts is important for the comprehension of viral evolution. In our study, the codon usage pattern of EIAV was analyzed from the available 29 full-length EIAV genomes through multivariate statistical methods.

Finding

Effective number of codons (ENC) suggests that the codon usage among EIAV strains is slightly biased. The ENC-plot analysis demonstrates that mutation pressure plays a substantial role in the codon usage pattern of EIAV, whereas other factors such as geographic distribution and host translation selection also take part in the process of EIAV evolution. Comparative analysis of codon adaptation index (CAI) values among EIAV and its hosts suggests that EIAV utilize the translational resources of horse more efficiently than that of donkey.

Conclusion

The codon usage bias in EIAV is slight and mutation pressure is the main factor that affects codon usage variation in EIAV. These results suggest that EIAV genomic biases are the result of the co-evolution of genome composition and the ability to evade the host’s immune response.

【 授权许可】

   
2013 Yin et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

【 参考文献 】

• [1]Leroux C, Cadore JL, Montelaro RC: Equine Infectious Anemia Virus (EIAV): what has HIV's country cousin got to tell us? Vet Res 2004, 35:485-512.
• [2]Craigo JK, Montelaro RC: EIAV envelope diversity: shaping viral persistence and encumbering vaccine efficacy. Curr HIV Res 2010, 8:81-86.
• [3]Cook SJ, Cook RF, Montelaro RC, Issel CJ: Differential responses of Equus caballus and Equus asinus to infection with two pathogenic strains of equine infectious anemia virus. Vet Microbiol 2001, 79:93-109.
• [4]Hershberg R, Petrov DA: Selection on codon bias. Annu Rev Genet 2008, 42:287-299.
• [5]Karlin S, Mrazek J: What drives codon choices in human genes? J Mol Biol 1996, 262:459-472.
• [6]Shackelton LA, Holmes EC: The evolution of large DNA viruses: combining genomic information of viruses and their hosts. Trends Microbiol 2004, 12:458-465.
• [7]Ma XX, Feng YP, Chen L, Zhao YQ, Liu JL, Guo JZ, Guo PH, Yang JT, Lu JX, Chen SE, Ma ZR: Mapping codon usage in sequence regions flanking cleavage positions in the hepatitis A virus polyprotein. Genet Mol Res 2013, 12:2306-2319.
• [8]Zhang Y, Liu Y, Liu W, Zhou J, Chen H, Wang Y, Ma L, Ding Y, Zhang J: Analysis of synonymous codon usage in hepatitis A virus. Virol J 2011, 8:174. BioMed Central Full Text
• [9]Moratorio G, Iriarte A, Moreno P, Musto H, Cristina J: A detailed comparative analysis on the overall codon usage patterns in West Nile virus. Infect Genet Evol 2013, 14:396-400.
• [10]Zhou JH, You YN, Chen HT, Zhang J, Ma LN, Ding YZ, Pejsak Z, Liu YS: The effects of the synonymous codon usage and tRNA abundance on protein folding of the 3C protease of foot-and-mouth disease virus. Infect Genet Evol 2013, 16:270-274.
• [11]Goni N, Iriarte A, Comas V, Sonora M, Moreno P, Moratorio G, Musto H, Cristina J: Pandemic influenza A virus codon usage revisited: biases, adaptation and implications for vaccine strain development. Virol J 2012, 9:263. BioMed Central Full Text
• [12]van der Kuyl AC, Berkhout B: The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus. Retrovirology 2012, 9:92. BioMed Central Full Text
• [13]Pandit A, Sinha S: Differential trends in the codon usage patterns in HIV-1 genes. PLoS One 2011, 6:e28889.
• [14]Kypr J, Mrazek J: Unusual codon usage of HIV. Nature 1987, 327:20.
• [15]van Hemert FJ, Berkhout B: The tendency of lentiviral open reading frames to become A-rich: constraints imposed by viral genome organization and cellular tRNA availability. J Mol Evol 1995, 41:132-140.
• [16]Sharp PM, Li WH: An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol 1986, 24:28-38.
• [17]Comeron JM, Aguade M: An evaluation of measures of synonymous codon usage bias. J Mol Evol 1998, 47:268-274.
• [18]Puigbo P, Bravo IG, Garcia-Vallve S: E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI). BMC Bioinformatics 2008, 9:65. BioMed Central Full Text
• [19]Tao P, Dai L, Luo M, Tang F, Tien P, Pan Z: Analysis of synonymous codon usage in classical swine fever virus. Virus Genes 2009, 38:104-112.
• [20]Zielonka J, Bravo IG, Marino D, Conrad E, Perkovic M, Battenberg M, Cichutek K, Munk C: Restriction of equine infectious anemia virus by equine APOBEC3 cytidine deaminases. J Virol 2009, 83:7547-7559.
• [21]Bogerd HP, Tallmadge RL, Oaks JL, Carpenter S, Cullen BR: Equine infectious anemia virus resists the antiretroviral activity of equine APOBEC3 proteins through a packaging-independent mechanism. J Virol 2008, 82:11889-11901.
• [22]Capomaccio S, Cappelli K, Cook RF, Nardi F, Gifford R, Marenzoni ML, Passamonti F: Geographic structuring of global EIAV isolates: a single origin for New World strains? Virus Res 2012, 163:656-659.
• [23]Zheng YH, Sentsui H, Kono Y, Ikuta K: Mutations occurring during serial passage of Japanese equine infectious anemia virus in primary horse macrophages. Virus Res 2000, 68:93-98.
• [24]Dong JB, Zhu W, Cook FR, Goto Y, Horii Y, Haga T: Identification of a novel equine infectious anemia virus field strain isolated from feral horses in southern Japan. J Gen Virol 2013, 94:360-365.
• [25]Puigbo P, Bravo IG, Garcia-Vallve S: CAIcal: a combined set of tools to assess codon usage adaptation. Biol Direct 2008, 3:38. BioMed Central Full Text