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Genetic and functional analysis of HIV-1 Rev Responsive Element (RRE) sequences from North-India

By Yogeshwar Sharma, Ujjwal Neogi, Vikas Sood, Snigdha Banerjee, Subodh Samrat, Ajay Wanchu, Surjit Singh and Akhil C Banerjea


HIV-1 Rev protein regulates the expression of HIV-1 transcripts by binding to a highly structured stem loop structure called the Rev Responsive Element (RRE) present in the genomic and partially spliced RNAs. Genetic variation in this structure is likely to affect binding of Rev protein and ultimately overall gene expression and replication. We characterized RRE sequences from 13 HIV-1 infected individuals from North India which also included two mother-child pairs following vertical transmission. We observed high degree of conservation of sequences, including the 9-nt (CACUAUGGG) long sequence in stem-loop B, required for efficient binding of Rev protein. All of our 13 RRE sequences possessed G to A (position 66) mutation located in the critical branched-stem-loop B which is not present in consensus C or B sequence. We derived a consensus RRE structure which showed interesting changes in the stem-loop structures including the stem-loop B. Mother-Child RRE sequences showed conservation of unique polymorphisms as well as some new mutations in child RRE sequences. Despite these changes, the ability to form multiple essential stem-loop structures required for Rev binding was conserved. RRE RNA derived from one of the samples, VT5, retained the ability to bind Rev protein under in vitro conditions although it showed alternate secondary structure. This is the first study from India describing the structural and possible functional implications due to very unique RRE sequence heterogeneity and its possible role in vertical transmission and gene expression

Topics: Research
Publisher: BioMed Central
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Provided by: PubMed Central

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  1. (1997). Bohnlein E: High transdominant RevM10 protein levels are required to inhibit HIV-1 replication in cell lines and primary T cells: implication for gene therapy of AIDS. Gene Ther
  2. (1991). BR: HIV-1 structural gene expression requires the binding of multiple Rev monomers to the viral RRE: Implications for HIV1 latency. Cell
  3. Hammarskjold M-L: Selection and characterization of human immunodeficiency virus type 1 mutants that are resistant to
  4. (1990). Human immunodeficiency virus rev protein recognizes a target sequence in rev-responsive element RNA within the context of RNA secondary structure.
  5. (1996). JR: Alpha helix RNA major groove recognition
  6. (1998). Malim MH: The HIV-1 Rev protein. Annu Rev Microbiol
  7. (2003). Si-RNAs, ribozymes, and RNA decoys in modeling stem cell based gene therapy for HIV/ AIDS. Anticancer Res