%0 Journal Article
%T Complex Codon Usage Pattern and Compositional Features of Retroviruses
%A Sourav RoyChoudhury
%A Debaprasad Mukherjee
%J Computational and Mathematical Methods in Medicine
%D 2013
%I Hindawi Publishing Corporation
%R 10.1155/2013/848123
%X 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
%U http://www.hindawi.com/journals/cmmm/2013/848123/