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Journal of Biochemistry Advance Access published online on November 26, 2007
Journal of Biochemistry, doi:10.1093/jb/mvm225
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© 2007 The Japanese Biochemical Society

Recognition of a bulged RNA by peptides derived from the influenza NS1 protein

Tatsuhiko Someya1,2, Kazumi Hosono1, Kaori Morimura, Hiroshi Takaku and Gota Kawai*

Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, JAPAN

*Corresponding author. Prof. Kawai, Gota, Fax: +81-47-478-0425, E-mail: gkawai{at}sea.it-chiba.ac.jp

Received August 27, 2007; Accepted November 12, 2007


  Abstract

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 analyzed 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 analyzed. 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.

Key Words: influenza virus, NS1 protein, RNA-binding protein, U6 snRNA, NMR, gel shift

1These authors contribute to this work equally.

2Present address: Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tenodai, Tsukuba-shi, Ibaraki 305-8572, JAPAN


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