Activities of adenovirus virus-associated RNAs: Purification and characterization of RNA binding proteins

Most human adenoviruses encode two virus-associated (VA) RNAs, VA RNA(I) and VA RNA(II), that accumulate to high levels in the cytoplasm of infected cells. The function of VA RNA(I) in blocking the activation of the cellular kinase PKR is well known, but the role of VA RNA(II) is obscure. Herein we characterize and purify several human proteins that interact preferentially with VA RNA(II) in Northwestern blot assays. Two of these proteins were identified as RNA helicase A and NF90, a component of the heterodimeric nuclear factor of activated T cells (NFAT), They copurified with the smaller NFAT subunit, NF45, which did not bind VA RNA(II), and with an unidentified protein, p97, which did bind VA RNA(II). Both RNA helicase A and NF90 contain two copies of a double-stranded (ds) RNA binding motif and bind strongly to dsRNA. NF90 interacts with RNAs in the following order of affinity: dsRNA > VA RNA(II) > VA RNA(I) > single-stranded RNA. Furthermore, VA RNA(II) is more effective than VA RNA(I) as an inhibitor of RNA helicase activity, These data identify RNA helicase A and NF90 as cellular proteins with an affinity for dsRNA and other structured RNA molecules and suggest that their functions are subject to regulation by RNA ligands including VA RNA(II).