title: Derivation of primary sequences and secondary structures of rev responsive element from HIV-1 infected mothers and infants following vertical transmission.
abstract: We have characterized the primary RRE sequences of HIV-1, including in vivo genetic variation and functional motifs required for Rev-RRE interactions as well as evaluated the RNA secondary structures of RRE derived from five mother-infant pairs following vertical transmission. Multiple (157) RRE sequences derived from mother-infant pairs showed that primary nucleotide sequences of RRE were highly conserved with a low degree of viral heterogeneity following vertical transmission. We found that the RRE sequences from mothers and infants folded and retained all the essential stem-loop formation required for Rev-RRE interactions. More importantly, a primary 9-nucleotide (5'-CACTATGGG-3') RRE sequence in the stem-loop B that is required for optimal Rev recognition and must be presented as a stem-bulge-stem structure was highly conserved in most of the sequences. The domains required for RRE-host protein interactions were also conserved in most of the RRE sequences. Taken together, the primary RRE sequences in the context of secondary structures were maintained and the Rev-RRE interaction domains were conserved following vertical transmission, which is consistent with a crucial role of RRE in HIV-1 pathogenesis.
authors.affiliation: Department of Immunobiology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, AZ 85724, USA.
authors.forename: Rajesh
authors.initials: R
authors.lastname: Ramakrishnan
authors.forename: Nafees
authors.initials: N
authors.lastname: Ahmad
mesh_terms: D000328:Adult; D001483:Base Sequence; D001665:Binding Sites; D002675:Child, Preschool; D017124:Conserved Sequence; D019143:Evolution, Molecular; D005260:Female; D015752:Genes, env; D015658:HIV Infections / Q000635:transmission / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D007223:Infant; D018445:Infectious Disease Transmission, Vertical; D008297:Male; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011110:Polymorphism, Genetic; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D012367:RNA, Viral