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Journal of Virology, October 2008, p. 10162-10174, Vol. 82, No. 20
0022-538X/08/$08.00+0     doi:10.1128/JVI.01027-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

A Viral Noncoding RNA Generated by cis-Element-Mediated Protection against 5'->3' RNA Decay Represses both Cap-Independent and Cap-Dependent Translation{triangledown}

Hiro-oki Iwakawa, Hiroyuki Mizumoto,{dagger} Hideaki Nagano, Yuka Imoto, Kazuma Takigawa, Siriruk Sarawaneeyaruk, Masanori Kaido, Kazuyuki Mise, and Tetsuro Okuno*

Laboratory of Plant Pathology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan

Received 15 May 2008/ Accepted 5 August 2008

Positive-strand RNA viruses use diverse mechanisms to regulate viral and host gene expression for ensuring their efficient proliferation or persistence in the host. We found that a small viral noncoding RNA (0.4 kb), named SR1f, accumulated in Red clover necrotic mosaic virus (RCNMV)-infected plants and protoplasts and was packaged into virions. The genome of RCNMV consists of two positive-strand RNAs, RNA1 and RNA2. SR1f was generated from the 3' untranslated region (UTR) of RNA1, which contains RNA elements essential for both cap-independent translation and negative-strand RNA synthesis. A 58-nucleotide sequence in the 3' UTR of RNA1 (Seq1f58) was necessary and sufficient for the generation of SR1f. SR1f was neither a subgenomic RNA nor a defective RNA replicon but a stable degradation product generated by Seq1f58-mediated protection against 5'->3' decay. SR1f efficiently suppressed both cap-independent and cap-dependent translation both in vitro and in vivo. SR1f trans inhibited negative-strand RNA synthesis of RCNMV genomic RNAs via repression of replicase protein production but not via competition of replicase proteins in vitro. RCNMV seems to use cellular enzymes to generate SR1f that might play a regulatory role in RCNMV infection. Our results also suggest that Seq1f58 is an RNA element that protects the 3'-side RNA sequences against 5'->3' decay in plant cells as reported for the poly(G) tract and stable stem-loop structure in Saccharomyces cerevisiae.

* Corresponding author. Mailing address: Sakyo-Ku, Kitashirakawa, Kyoto 606-8502, Japan. Phone and fax: 81-75-753-6131. E-mail: okuno{at}kais.kyoto-u.ac.jp

{triangledown} Published ahead of print on 13 August 2008.

{dagger} Present address: Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

Journal of Virology, October 2008, p. 10162-10174, Vol. 82, No. 20
0022-538X/08/$08.00+0     doi:10.1128/JVI.01027-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.





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