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

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

Research output: Contribution to journalArticle

4 Citations (Scopus)

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.

Original languageEnglish (US)
Article number28
JournalAIDS Research and Therapy
Volume7
DOIs
StatePublished - Aug 3 2010
Externally publishedYes

Fingerprint

env Genes
HIV-1
India
rev Gene Products
Aptitude
Carrier Proteins
Mothers
Inverted Repeat Sequences
RNA
Gene Expression
Mutation
Consensus

ASJC Scopus subject areas

  • Virology
  • Molecular Medicine
  • Pharmacology (medical)

Cite this

Sharma, Y., Neogi, U., Sood, V., Banerjee, S., Samrat, S., Wanchu, A., ... Banerjea, A. C. (2010). Genetic and functional analysis of HIV-1 Rev Responsive Element (RRE) sequences from North-India. AIDS Research and Therapy, 7, [28]. https://doi.org/10.1186/1742-6405-7-28

Genetic and functional analysis of HIV-1 Rev Responsive Element (RRE) sequences from North-India. / Sharma, Yogeshwar; Neogi, Ujjwal; Sood, Vikas; Banerjee, Snigdha; Samrat, Subodh; Wanchu, Ajay; Singh, Surjit; Banerjea, Akhil C.

In: AIDS Research and Therapy, Vol. 7, 28, 03.08.2010.

Research output: Contribution to journalArticle

Sharma, Y, Neogi, U, Sood, V, Banerjee, S, Samrat, S, Wanchu, A, Singh, S & Banerjea, AC 2010, 'Genetic and functional analysis of HIV-1 Rev Responsive Element (RRE) sequences from North-India', AIDS Research and Therapy, vol. 7, 28. https://doi.org/10.1186/1742-6405-7-28
Sharma, Yogeshwar ; Neogi, Ujjwal ; Sood, Vikas ; Banerjee, Snigdha ; Samrat, Subodh ; Wanchu, Ajay ; Singh, Surjit ; Banerjea, Akhil C. / Genetic and functional analysis of HIV-1 Rev Responsive Element (RRE) sequences from North-India. In: AIDS Research and Therapy. 2010 ; Vol. 7.
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