Recognition of a bulged RNA by peptides derived from the influenza NS1 protein.
A competition assay for RNA binding by the influenza virus NS1 protein using model RNAs, U6-45, corresponding to U6 snRNA revealed that deletion of each of the three bulged-out parts reduced the NS1 protein binding and, in contrast, by deleting all three of the bulged-out parts, simultaneously, and thus producing a double-stranded RNA, the binding was recovered. A common feature of target RNAs of the NS1 protein, U6 snRNA, poly(A) and viral RNA, is the stretch of 'bulged-out' A residues. Thus, the NS1 protein was found to recognize either the stretch of 'bulged-out' A residues or dsRNA which is also a target of the NS1 protein. Furthermore, a basic peptide, NS1-2, derived from the helix-2 of the RNA binding site of NS1 protein was designed and its binding to the U6 snRNA was analysed by using a model RNA for U6 snRNA, U6-34. The NMR signals due to H8/H6 and H1' of U6-34 were assigned and their changes upon binding of NS1-2 were analysed. It was indicated that NS1-2 interacts with the residues in the bulge-out region of U6-34. These results suggest that NS1-2 recognizes the U6 snRNA in a similar manner to NS1 protein.
Someya
Tatsuhiko
T
Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba, Japan.
Hosono
Kazumi
K
Morimura
Kaori
K
Takaku
Hiroshi
H
Kawai
Gota
G
D000595:Amino Acid Sequence; D001483:Base Sequence; D024202:Electrophoretic Mobility Shift Assay; D006801:Humans; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D012342:RNA, Small Nuclear / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012260:Ribonucleases / Q000378:metabolism; D017361:Viral Nonstructural Proteins / Q000737:chemistry / Q000378:metabolism*
C085820:INS1 protein, influenza virus; D010455:Peptides; D012342:RNA, Small Nuclear; C405486:U6 small nuclear RNA; D017361:Viral Nonstructural Proteins; D012260:Ribonucleases