RNA-BINDING PROPERTIES OF CORE PROTEIN OF THE FLAVIVIRUS KUNJIN

Kunjin virus (KUN) C is a typical flavivirus core protein which is tru ncated in vivo to a mature form of 105 residues enriched in lysine and arginine. In order to study the possible association of KUN C with RN A in vitro, we prepared several recombinant C proteins with specific d eletions, each fused at the amino-terminus to glutathione-S-transferas e (GST) and expressed in E. coli. They were reacted with KUN RNA probe s transcribed in vitro from cDNA representing the 5' untranslated regi on (5' UTR, 93 of 96 nucleotides), the 3' UTR (624 nucleotides), and t he 5' UTR plus most of the C coding region (5' core, 440 nucleotides). Fusion protein C107 (incorporating mature C) bound strongly to all KU N RNA probes with apparent specificity, being completely resistant to inhibition by 800 mM NaCl, and to competition by a large excess of tRN A. In reactions with labelled KUN RNA probes putative binding sites we re identified in the isolated amino-terminal (32 residues) and carboxy terminal (26 residues) basic amino acid domains; this binding was stro ngly competed by unlabelled KUN UTR probes but weakly or not at all by tRNA. These small domains probably acted co-operatively in binding of mature C to KUN RNA probes. The KUN RNA-core protein binding reaction s are similar to those reported with other viral coat or capsid protei ns and viral RNAs.