HIV-1 Rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA.
We have used an iterative in vitro genetic selection to identify the important structural features of the viral RNA element bound by the Rev protein of human immunodeficiency virus type 1 (HIV-1). Functional Rev-binding RNAs were selected from a pool of 10(13) variants of the wild-type Rev-binding domain. Bases conserved among the binding species define a 20 nucleotide core binding element. Covariation of some of these conserved bases indicates that the Rev-binding element is a stem-bulge-stem with a G:G base pair in the bulge. Mutational studies show that this non-Watson-Crick base pair is required for Rev binding in vitro and Rev responsiveness in vivo. We propose that the G:G base pair distorts the sugar-phosphate backbone of viral RNA and that this distortion is a critical determinant of recognition by Rev.
Bartel
D P
DP
Department of Molecular Biology, Massachusetts General Hospital, Boston 02114.
Zapp
M L
ML
Green
M R
MR
Szostak
J W
JW
D001483:Base Sequence; D001665:Binding Sites; D004252:DNA Mutational Analysis; D015694:Gene Products, rev / Q000378:metabolism*; D015497:HIV-1 / Q000235:genetics* / Q000648:ultrastructure; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D011485:Protein Binding; D012367:RNA, Viral / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D012045:Regulatory Sequences, Nucleic Acid; D013329:Structure-Activity Relationship; D054321:rev Gene Products, Human Immunodeficiency Virus
D015694:Gene Products, rev; D009841:Oligonucleotides; D012367:RNA, Viral; D016601:RNA-Binding Proteins; D054321:rev Gene Products, Human Immunodeficiency Virus