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Journal article
Evidence of Divergent Amino Acid Usage in Comparative Analyses of R5- and X4-Associated HIV-1 Vpr Sequences
International journal of genomics, v 2017, pp 4081585-11
23 May 2017
PMID: 28620613
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Vpr is an HIV-1 accessory protein that plays numerous roles during viral replication, and some of which are cell type dependent. To test the hypothesis that HIV-1 tropism extends beyond the envelope into the vpr gene, studies were performed to identify the associations between coreceptor usage and Vpr variation in HIV-1-infected patients. Colinear HIV-1 Env-V3 and Vpr amino acid sequences were obtained from the LANL HIV-1 sequence database and from well-suppressed patients in the Drexel/Temple Medicine CNS AIDS Research and Eradication Study (CARES) Cohort. Genotypic classification of Env-V3 sequences as X4 (CXCR4-utilizing) or R5 (CCR5-utilizing) was used to group colinear Vpr sequences. To reveal the sequences associated with a specific coreceptor usage genotype, Vpr amino acid sequences were assessed for amino acid diversity and Jensen-Shannon divergence between the two groups. Five amino acid alphabets were used to comprehensively examine the impact of amino acid substitutions involving side chains with similar physiochemical properties. Positions 36, 37, 41, 89, and 96 of Vpr were characterized by statistically significant divergence across multiple alphabets when X4 and R5 sequence groups were compared. In addition, consensus amino acid switches were found at positions 37 and 41 in comparisons of the R5 and X4 sequence populations. These results suggest an evolutionary link between Vpr and gp120 in HIV-1-infected patients.
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Details
- Title
- Evidence of Divergent Amino Acid Usage in Comparative Analyses of R5- and X4-Associated HIV-1 Vpr Sequences
- Creators
- Gregory C. Antell - Drexel UniversityWill Dampier - Drexel UniversityBenjamas Aiamkitsumrit - Drexel UniversityMichael R. Nonnemacher - Drexel UniversityVanessa Pirrone - Drexel UniversityWen Zhong - Drexel UniversityKatherine Kercher - Drexel UniversityShendra Passic - Drexel UniversityJean Williams - Drexel UniversityYucheng Liu - Drexel UniversityTony James - Drexel UniversityJeffrey M. Jacobson - Drexel UniversityZsofia Szep - Drexel UniversityBrian Wigdahl - Drexel UniversityFred C. Krebs - Drexel University
- Contributors
- Margarita Hadzopoulou-Cladaras (Editor)
- Publication Details
- International journal of genomics, v 2017, pp 4081585-11
- Publisher
- Hindawi
- Grant note
- College of Medicine, Drexel University National Institutes of Health T32 MH079785 / Ruth L. Kirschstein National Research Service MH092177 / National Institute of Mental Health Comprehensive NeuroAIDS Core Center DA19807 / National Institute of Drug Abuse NS46263; NS32092; NS089435 / National Institute of Neurological Disorders and Stroke
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Microbiology and Immunology; Infectious Diseases (and HIV Medicine)
- Web of Science ID
- WOS:000401799100001
- Scopus ID
- 2-s2.0-85021702048
- Other Identifier
- 991019168059304721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Biochemistry & Molecular Biology
- Biotechnology & Applied Microbiology
- Genetics & Heredity