title: Cell proteins bind specifically to West Nile virus minus-strand 3' stem-loop RNA.
abstract: The first 96 nucleotides of the 5'noncoding region (NCR) of West Nile virus (WNV) genomic RNA were previously reported to form thermodynamically predicted stem-loop (SL) structures that are conserved among flaviviruses. The complementary minus-strand 3' NCR RNA, which is thought to function as a promoter for the synthesis of plus-strand RNA, forms a corresponding predicted SL structure. RNase probing of the WNV 3' minus-strand stem-loop RNA [WNV (-)3' SL RNA] confirmed the existence of a terminal secondary structure. RNA-protein binding studies were performed with BHK S100 cytoplasmic extracts and in vitro-synthesized WNV (-)3' SL RNA as the probe. Three RNA-protein complexes (complexes 1,2, and 3) were detected by a gel mobility shift assay, and the specificity of the RNA-protein interactions was confirmed by gel mobility shift and UV-induced cross-linking competition assays. Four BHK cell proteins with molecular masses of 108, 60, 50, and 42 kDa were detected by UV-induced cross-linking to the WNV (-)3' SL RNA. A preliminary mapping study indicated that all four proteins bound to the first 75 nucleotides of the WNV 3' minus-strand RNA, the region that contains the terminal SL. A flavivirus resistance phenotype was previously shown to be inherited in mice as a single, autosomal dominant allele. The efficiencies of infection of resistant cells and susceptible cells are similar, but resistant cells (C3H/RV) produce less genomic RNA than congenic, susceptible cells (C3H/He). Three RNA-protein complexes and four UV-induced cross-linked cell proteins with mobilities identical to those detected in BHK cell extracts with the WNV (-)3' SL RNA were found in both C3H/RV and C3H/He cell extracts. However, the half-life of the C3H/RV complex 1 was three times longer than that of the C3H/He complex 1. It is possible that the increased binding activity of one of the resistant cell proteins for the flavivirus minus-strand RNA could result in a reduced synthesis of plus-strand RNA as observed with the flavivirus resistance phenotype.
authors.affiliation: Department of Biology, Georgia State University, Atlanta 30303, USA.
authors.forename: P Y
authors.initials: PY
authors.lastname: Shi
authors.forename: W
authors.initials: W
authors.lastname: Li
authors.forename: M A
authors.initials: MA
authors.lastname: Brinton
mesh_terms: D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D017124:Conserved Sequence; D006224:Cricetinae; D017931:DNA Primers; D005416:Flavivirus / Q000235:genetics; D016679:Genome, Viral; D007668:Kidney; D007700:Kinetics; D051379:Mice; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016133:Polymerase Chain Reaction; D012367:RNA, Viral / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000302:isolation & purification / Q000378:metabolism*; D012260:Ribonucleases; D013816:Thermodynamics; D014158:Transcription, Genetic; D014771:Virion; D014902:West Nile virus / Q000235:genetics*
chemical_list: D017931:DNA Primers; D012367:RNA, Viral; D016601:RNA-Binding Proteins; D012260:Ribonucleases