Altering the context of an RNA bulge switches the binding specificities of two viral Tat proteins.
The bovine immunodeficiency virus (BIV) Tat protein binds with high affinity to its TAR RNA site through a large set of specific RNA-protein contacts whereas human immunodeficiency virus (HIV) Tat makes relatively few contacts to HIV TAR and requires the assistance of a cellular protein to bind with high affinity. The two TAR sites are structurally very similar, but BIV Tat appears unable to make the same set of high-affinity contacts to HIV TAR. To determine the basis of this discrimination, we examined BIV Tat binding to a series of hybrid TARs both in vivo and in vitro. We expected that differences in the architectures of the bulges might account for the binding specificity; however, the results show that flanking base pairs provide the key determinants. Based on these data, we designed a novel TAR that is recognized by both BIV Tat and HIV Tat. This RNA may be viewed as a primordial TAR from which two distinct recognition strategies can be evolved.
Smith
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CA
Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448, USA.
Crotty
S
S
Harada
Y
Y
Frankel
A D
AD
D000818:Animals; D001120:Arginine / Q000235:genetics; D001482:Base Composition; D001483:Base Sequence; D002417:Cattle; D015696:Gene Products, tat / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D016087:Immunodeficiency Virus, Bovine / Q000235:genetics*; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009690:Nucleic Acid Conformation; D011485:Protein Binding / Q000235:genetics; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D054322:tat Gene Products, Human Immunodeficiency Virus
D015696:Gene Products, tat; D012367:RNA, Viral; D054322:tat Gene Products, Human Immunodeficiency Virus; D001120:Arginine