title: Genetic characterization of natural variants of Vpu from HIV-1 infected individuals from Northern India and their impact on virus release and cell death.
abstract: BACKGROUND
  Genetic studies reveal that vpu is one of the most variable regions in HIV-1 genome. Functional studies have been carried out mostly with Vpu derived from laboratory adapted subtype B pNL 4-3 virus. The rationale of this study was to characterize genetic variations that are present in the vpu gene from HIV-1 infected individuals from North-India (Punjab/Haryana) and determine their functional relevance.
  
  
  METHODS
  Functionally intact vpu gene variants were PCR amplified from genomic DNA of HIV-1 infected individuals. These variants were then subjected to genetic analysis and unique representative variants were cloned under CMV promoter containing expression vector as well as into pNL 4-3 HIV-1 virus for intracellular expression studies. These variants were characterized with respect to their ability to promote virus release as well as cell death.
  
  
  RESULTS
  Based on phylogenetic analysis and extensive polymorphisms with respect to consensus Vpu B and C, we were able to arbitrarily assign variants into two major groups (B and C). The group B variants always showed significantly higher virus release activity and exhibited moderate levels of cell death. On the other hand, group C variants displayed lower virus release activity but greater cell death potential. Interestingly, Vpu variants with a natural S61A mutation showed greater intracellular stability. These variants also exhibited significant reduction in their intracellular ubiquitination and caused greater virus release. Another group C variant that possessed a non-functional β-TrcP binding motif due to two critical serine residues (S52 and S56) being substituted with isoleucine residues, showed reduced virus release activity but modest cytotoxic activity.
  
  
  CONCLUSIONS
  The natural variations exhibited by our Vpu variants involve extensive polymorphism characterized by substitution and deletions that contribute toward positive selection. We identified two major groups and an extremely rare β-TrcP binding motif mutant that show widely varying biological activities with potential implications for conferring subtype-specific pathogenesis.
authors.affiliation: Laboratory of Virology, National Institute of Immunology, New Delhi, India.
authors.forename: Sachin
authors.initials: S
authors.lastname: Verma
authors.forename: Larance
authors.initials: L
authors.lastname: Ronsard
authors.forename: Richa
authors.initials: R
authors.lastname: Kapoor
authors.forename: Akhil C
authors.initials: AC
authors.lastname: Banerjea
mesh_terms: D000328:Adult; D000595:Amino Acid Sequence; D016923:Cell Death / Q000235:genetics; D003001:Cloning, Molecular; D003587:Cytomegalovirus / Q000235:genetics; D057809:HEK293 Cells; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D054298:Human Immunodeficiency Virus Proteins / Q000145:classification / Q000235:genetics*; D006801:Humans; D007194:India; D008297:Male; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011401:Promoter Regions, Genetic; D054730:Protein Interaction Domains and Motifs; D020033:Protein Isoforms / Q000145:classification / Q000235:genetics; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D054334:Viral Regulatory and Accessory Proteins / Q000145:classification / Q000235:genetics*; D000086082:Viroporin Proteins
chemical_list: D054298:Human Immunodeficiency Virus Proteins; D020033:Protein Isoforms; D054334:Viral Regulatory and Accessory Proteins; C514859:vpu protein, Human immunodeficiency virus 1; D000086082:Viroporin Proteins
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