title: Genetic and functional analysis of HIV-1 Rev Responsive Element (RRE) sequences from North-India.
abstract: 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.
authors.affiliation: Division of Virology, National Institute of Immunology, JNU Campus, Aruna Asaf Ali Marg, New Delhi-110067, India. akhil@nii.res.in.
authors.forename: Yogeshwar
authors.initials: Y
authors.lastname: Sharma
authors.forename: Ujjwal
authors.initials: U
authors.lastname: Neogi
authors.forename: Vikas
authors.initials: V
authors.lastname: Sood
authors.forename: Snigdha
authors.initials: S
authors.lastname: Banerjee
authors.forename: Subodh
authors.initials: S
authors.lastname: Samrat
authors.forename: Ajay
authors.initials: A
authors.lastname: Wanchu
authors.forename: Surjit
authors.initials: S
authors.lastname: Singh
authors.forename: Akhil C
authors.initials: AC
authors.lastname: Banerjea