Secondary Structure is the Major Determinant for Interaction of HIV rev Protein with RNA

Abstract

A region in the human immunodeficiency virus (HIV) env message, with the potential to form a complex secondary structure (designated RRE), interacts with the rev protein (Rev). This interaction is believed to mediate export of HIV structural messenger RNAs from the nucleus to the cytoplasm. In this report the regions essential for Rev interaction with the RRE are further characterized and the functional significance of Rev-RRE interaction in vivo is examined. A single hairpin loop structure within the RRE was found to be a primary determinant for Rev binding in vitro and Rev response in vivo. Maintenance of secondary structure, rather than primary nucleotide sequence alone, appeared to be necessary for Rev-RNA interaction, which distinguishes it from the mechanism for cis-acting elements in DNA. Limited changes within the 200 nucleotides, which preserved the proper RRE conformational structure, were well tolerated for Rev binding and function. Thus, variation among the RRE elements present in the diverse HIV isolates would have little, if any, effect on Rev responsiveness.

Resistance to RevM10 inhibition reflects a conformational switch in the HIV-1 Rev response element

“…Although the use of subgenomic heterologous reporter constructs suggest stem-loop II is the only region required for Rev function (24,25), other studies, using less artificial constructs, highlight the importance of sequences throughout the RRE (26)(27)(28)(29)(30)(31). For example, mutations that disrupt the stem of stem-loop V create a nonfunctional RRE in both HIV-1 (26) and HIV-2 (31).…”

Activation of the double‐stranded RNA‐dependent eIF‐2α kinase by cellular RNA from 3T3‐F442A cells

“…Translation of several mRNAs has been shown to involve the interaction of structural elements with specific initiation factors and ribosomes [1 -31, factors which destablize mRNAs 14 -61, factors which mobilize the mRNA from the nucleus to the cytoplasm [7], and factors which regulate the translation of mRNAs in response to cellular needs as has been demonstrated for the iron-responsive elements in the 5' untranslated region of ferritin mRNA [8, 91. Secondary structures within single-stranded viral RNAs have also been shown to regulate the activity of the dsRNA-dependent eIF-2a kinase, a potent inhibitor of protein synthesis [lo-121.…”

The Nucleic Acid-binding Domain and Translational Repression Activity of a Xenopus Terminal Uridylyl Transferase

“…ARMs are flexible RNA-binding domains that typically confer specificity for particular RNAs by recognizing RNA sequences and/or structures (61,62). For example, the ARM in Rev specifically recognizes and binds its RNA target (63)(64)(65)(66). Critical arginines in the ARM make base-specific contacts with the RNA and are necessary for binding.…”