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Nucleic Acids Research 2005 33(13):4265-4275; doi:10.1093/nar/gki731
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Published online 29 July 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

An atypical RNA pseudoknot stimulator and an upstream attenuation signal for –1 ribosomal frameshifting of SARS coronavirus

Mei-Chi Su, Chung-Te Chang, Chiu-Hui Chu1, Ching-Hsiu Tsai1 and Kung-Yao Chang*

Graduate Institute of Biochemistry, National Chung-Hsing University 250 Kuo-Kung Road, Taichung, 402 Taiwan 1Graduate Institute of Biotechnology, National Chung-Hsing University 250 Kuo-Kung Road, Taichung, 402 Taiwan

*To whom correspondence should be addressed. Tel: +886 4 22840468, ext 218; Fax: +886 4 22853487; Email: kychang{at}dragon.nchu.edu.tw

Received March 7, 2005. Revised May 16, 2005. Accepted July 6, 2005.

The –1 ribosomal frameshifting requires the existence of an in cis RNA slippery sequence and is promoted by a downstream stimulator RNA. An atypical RNA pseudoknot with an extra stem formed by complementary sequences within loop 2 of an H-type pseudoknot is characterized in the severe acute respiratory syndrome coronavirus (SARS CoV) genome. This pseudoknot can serve as an efficient stimulator for –1 frameshifting in vitro. Mutational analysis of the extra stem suggests frameshift efficiency can be modulated via manipulation of the secondary structure within the loop 2 of an infectious bronchitis virus-type pseudoknot. More importantly, an upstream RNA sequence separated by a linker 5' to the slippery site is also identified to be capable of modulating the –1 frameshift efficiency. RNA sequence containing this attenuation element can downregulate –1 frameshifting promoted by an atypical pseudoknot of SARS CoV and two other pseudoknot stimulators. Furthermore, frameshift efficiency can be reduced to half in the presence of the attenuation signal in vivo. Therefore, this in cis RNA attenuator represents a novel negative determinant of general importance for the regulation of –1 frameshift efficiency, and is thus a potential antiviral target.


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