RNA secondary structure and squence conservation in C1 region of human immunodeficiency virus type 1 env gene.
We have analyzed amino acid, nucleotide sequence, and RNA secondary structure variability in the env gene of human immunodeficiency virus type (HIV-1). In applying algorithms for computing optimal RNA-folding patterns to a nonredundant data set of 178 env nucleotide sequences, we found a conserved RNA stem-loop structure in the first conserved (C1) region of the env gene. This detailed examination also revealed the known secondary structure conservation of the Rev-responsive element (RRE). This finding is also supported by a higher third position conservation of the translatable reading frame along these subregions. The typical folding of the C1 region consists of two isolated stem-loop structures. These highly conserved structures are likely to have a biological function. This assumption is supported by the conservation of the third position along the coding region of these structures. The third position retains a conservation level above what would be statistically expected.
Peleg
Ofer
O
Genome Diversity Center, Institute of Evolution, Haifa University, Mt. Carmel, Haifa 31905, Israel.
Brunak
Søren
S
Trifonov
Edward N
EN
Nevo
Eviatar
E
Bolshoy
Alexander
A
D000465:Algorithms; D001483:Base Sequence; D015752:Genes, env; D015497:HIV-1 / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012326:RNA Splicing; D012367:RNA, Viral / Q000737:chemistry*; D013816:Thermodynamics
D012367:RNA, Viral