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Complex Codon Usage Pattern and Compositional Features of Retroviruses

DOI: 10.1155/2013/848123

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Abstract:

Retroviruses infect a wide range of organisms including humans. Among them, HIV-1, which causes AIDS, has now become a major threat for world health. Some of these viruses are also potential gene transfer vectors. In this study, the patterns of synonymous codon usage in retroviruses have been studied through multivariate statistical methods on ORFs sequences from the available 56 retroviruses. The principal determinant for evolution of the codon usage pattern in retroviruses seemed to be the compositional constraints, while selection for translation of the viral genes plays a secondary role. This was further supported by multivariate analysis on relative synonymous codon usage. Thus, it seems that mutational bias might have dominated role over translational selection in shaping the codon usage of retroviruses. Codon adaptation index was used to identify translationally optimal codons among genes from retroviruses. The comparative analysis of the preferred and optimal codons among different retroviral groups revealed that four codons GAA, AAA, AGA, and GGA were significantly more frequent in most of the retroviral genes inspite of some differences. Cluster analysis also revealed that phylogenetically related groups of retroviruses have probably evolved their codon usage in a concerted manner under the influence of their nucleotide composition. 1. Introduction The retroviruses are a diverse family of enveloped single stranded retro transcribing RNA viruses unique for their use of reverse transcription of the viral RNA into linear double stranded DNA during replication and the subsequent integration of the DNA into the host genome. Members of this family cause diseases in a wide range of organisms, including humans [1]. Human immunodeficiency virus 1 (HIV-1) is responsible for acquired immunodeficiency syndrome (AIDS) and is largely dependent on transmission of contaminated body fluids during sexual intercourse, pregnancy, and so forth [2]. More than 30 million people worldwide are living with HIV. Besides, retroviruses are increasingly becoming valuable tools in molecular biology and have been used successfully in gene therapy [3]. Based on morphology, pathogenicity, and molecular phylogenetics, retroviruses have been classified into two subfamilies: Orthoretrovirinae, Spumaretrovirinae and rest of the viruses are unclassified. The Orthoretrovirinae is further classified into six genera: Alpharetrovirus, Betaretrovirus, Deltaretrovirus, Epsilonretrovirus, Gammaretrovirus, and Lentivirus. The analysis of codon usage of whole organisms and/or organisms from

References

[1]  J. M. Coffin, “Retroviridae: the viruses and their replication,” in Fields Virologyed, B. N. Fields, D. M. Knipe, and P. M. Howley, Eds., pp. 1767–1847, Lippincott-Raven, Philadelphia, Pa, USA, 3rd edition, 1996.
[2]  R. A. Weiss, “How does HIV cause AIDS?” Science, vol. 260, no. 5112, pp. 1273–1279, 1993.
[3]  R. Kurth and N. Bannert, Retroviruses: Molecular Biology. Genomics and Pathogenesis, Caister Academic Press, Berlin, Germany, 2010.
[4]  M. Bulmer, “The selection-mutation-drift theory of synonymous codon usage,” Genetics, vol. 129, no. 3, pp. 897–907, 1991.
[5]  S. RoyChoudhury and D. Mukherjee, “A detailed comparative analysis on the overall codon usage pattern in herpesviruses,” Virus Research, vol. 148, no. 1-2, pp. 31–43, 2010.
[6]  L. Duret, “Evolution of synonymous codon usage in metazoans,” Current Opinion in Genetics and Development, vol. 12, no. 6, pp. 640–649, 2002.
[7]  G. M. Jenkins and E. C. Holmes, “The extent of codon usage bias in human RNA viruses and its evolutionary origin,” Virus Research, vol. 92, no. 1, pp. 1–7, 2003.
[8]  J. Peden, Analysis of Codon Usage, University of Nottingham, Department of Genetics, Nottingham, UK, 1997, http://codonw.sourceforge.net.
[9]  J. O. McInerney, “GCUA: general codon usage analysis,” Bioinformatics, vol. 14, no. 4, pp. 372–373, 1998.
[10]  F. Wright, “The “effective number of codons” used in a gene,” Gene, vol. 87, no. 1, pp. 23–29, 1990.
[11]  A. Carbone, “Codon bias is a major factor explaining phage evolution in translationally biased hosts,” Journal of Molecular Evolution, vol. 66, no. 3, pp. 210–223, 2008.
[12]  I. S. Belalov and A. N. Lukashev, “Causes and implications of codon usage bias in RNA viruses,” PLoS ONE, vol. 8, no. 2, Article ID e56642, 2013.
[13]  Y. Zhang, Y. Liu, W. Liu et al., “Analysis of synonymous codon usage in hepatitis A virus,” Virology Journal, vol. 8, article 174, 2011.
[14]  S. Roychoudhury, A. Pan, and D. Mukherjee, “Genus specific evolution of codon usage and nucleotide compositional traits of poxviruses,” Virus Genes, vol. 42, no. 2, pp. 189–199, 2011.
[15]  Q. Zhong, W. Xu, Y. Wu, and H. Xu, “Patterns of synonymous codon usage on human metapneumovirus and its influencing factors,” Journal of Biomedicine and Biotechnology, vol. 2012, Article ID 460837, 7 pages, 2012.
[16]  N. Goni, A. Iriarte, V. Comas, et al., “Pandemic influenza A virus codon usage revisited: biases, adaptation and implications for vaccine strain development,” Virology Journal, vol. 9, article 263, 2012.
[17]  E. P. C. Rocha and A. Danchin, “Base composition bias might result from competition for metabolic resources,” Trends in Genetics, vol. 18, no. 6, pp. 291–294, 2002.
[18]  L. A. Shackelton, C. R. Parrish, and E. C. Holmes, “Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses,” Journal of Molecular Evolution, vol. 62, no. 5, pp. 551–563, 2006.
[19]  E. Cowe and P. M. Sharp, “Molecular evolution of bacteriophages: discrete patterns of codon usage in T4 genes are related to the time of gene expression,” Journal of Molecular Evolution, vol. 33, no. 1, pp. 13–22, 1991.
[20]  S. Michely, E. Toulza, L. Subirana, et al., “Evolution of codon usage in the smallest photosynthetic eukaryotes and their giant viruses,” Genome Biology and Evolution, vol. 5, no. 5, pp. 848–859, 2013.
[21]  J. Vartanian, A. Meyerhans, M. Sala, and S. Wain-Hobson, “G → A hypermutation of the human immunodeficiency virus type 1 genome: evidence for dCTP pool imbalance during reverse transcription,” Proceedings of the National Academy of Sciences of the United States of America, vol. 91, no. 8, pp. 3092–3096, 1994.
[22]  A. Takaori-Kondo, “APOBEC family proteins: novel antiviral innate immunity,” International Journal of Hematology, vol. 83, no. 3, pp. 213–216, 2006.
[23]  K. Sato, T. Izumi, N. Misawa et al., “Remarkable lethal G-to-A mutations in vif-proficient HIV-1 provirus by individual APOBEC3 proteins in humanized mice,” Journal of Virology, vol. 84, no. 18, pp. 9546–9556, 2010.
[24]  B. Brekhout, A. T. Das, and N. Beerens, “HIV-1 RNA editing, hypermutation and error-prone reverse transcription,” Science, vol. 292, no. 5514, article 7, 2001.
[25]  L. M. Mansky, “Retrovirus mutation rates and their role in genetic variation,” Journal of General Virology, vol. 79, no. 6, pp. 1337–1345, 1998.
[26]  R. Shankarappa, J. B. Margolick, S. J. Gange et al., “Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection,” Journal of Virology, vol. 73, no. 12, pp. 10489–10502, 1999.
[27]  C. Williamson, L. Morris, M. F. Maughan, et al., “Characterization and selection of HIV-1 subtype C isolates for use in vaccine development,” AIDS Research and Human Retroviruses, vol. 19, no. 2, pp. 133–144, 2003.
[28]  H. A. Ross and A. G. Rodrigo, “Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration,” Journal of Virology, vol. 76, no. 22, pp. 11715–11720, 2002.
[29]  H. Tang, K. L. Kuhen, and F. Wong-Staal, “Lentivirus replication and regulation,” Annual Review of Genetics, vol. 33, pp. 133–170, 1999.
[30]  K. Nguyen, M. Llano, H. Akari et al., “Codon optimization of the HIV-1 vpu and vif genes stabilizes their mRNA and allows for highly efficient Rev-independent expression,” Virology, vol. 319, no. 2, pp. 163–175, 2004.

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