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Open Access Highly Accessed Research article

Codon pairs of the HIV-1 vif gene correlate with CD4+ T cell count

Maria Clara Bizinoto1, Shiori Yabe2, Élcio Leal3*, Hirohisa Kishino2, Leonardo de Oliveira Martins4, Mariana Leão de Lima1, Edsel Renata Morais1, Ricardo Sobhie Diaz1 and Luiz Mário Janini1

Author Affiliations

1 Department of Medicine, Federal University of São Paulo, São Paulo, Brazil

2 Graduate School of Agriculture and Life Sciences, University of Tokyo, Tokyo, Japan

3 Institute of Biotechnology, Federal University of Pará, Pará, Brazil

4 Bioinformatics and Molecular Evolution Laboratory, Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain

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BMC Infectious Diseases 2013, 13:173  doi:10.1186/1471-2334-13-173

Published: 11 April 2013

Abstract

Background

The human APOBEC3G (A3G) protein activity is associated with innate immunity against HIV-1 by inducing high rates of guanosines to adenosines (G-to-A) mutations (viz., hypermutation) in the viral DNA. If hypermutation is not enough to disrupt the reading frames of viral genes, it may likely increase the HIV-1 diversity. To counteract host innate immunity HIV-1 encodes the Vif protein that binds A3G protein and form complexes to be degraded by cellular proteolysis.

Methods

Here we studied the pattern of substitutions in the vif gene and its association with clinical status of HIV-1 infected individuals. To perform the study, unique vif gene sequences were generated from 400 antiretroviral-naïve individuals.

Results

The codon pairs: 78–154, 85–154, 101–157, 105–157, and 105–176 of vif gene were associated with CD4+ T cell count lower than 500 cells per mm3. Some of these codons were located in the 81LGQGVSIEW89 region and within the BC-Box. We also identified codons under positive selection clustered in the N-terminal region of Vif protein, between 21WKSLVK26 and 40YRHHY44 regions (i.e., 31, 33, 37, 39), within the BC-Box (i.e., 155, 159) and the Cullin5-Box (i.e., 168) of vif gene. All these regions are involved in the Vif-induced degradation of A3G/F complexes and the N-terminal of Vif protein binds to viral and cellular RNA.

Conclusions

Adaptive evolution of vif gene was mostly to optimize viral RNA binding and A3G/F recognition. Additionally, since there is not a fully resolved structure of the Vif protein, codon pairs associated with CD4+ T cell count may elucidate key regions that interact with host cell factors. Here we identified and discriminated codons under positive selection and codons under functional constraint in the vif gene of HIV-1.

Keywords:
HIV-1; Epistasis; APOBEC; Vif; Hypermutation; Positive selection; Co-evolution