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Nucleic Acids Research, 2003, Vol. 31, No. 9 2434-2442
© 2003 Oxford University Press

Structural elements in the internal ribosome entry site of Plautia stali intestine virus responsible for binding with ribosomes

Takashi Nishiyama, Hiroshi Yamamoto1, Norihiro Shibuya, Yoshinori Hatakeyama, Akira Hachimori1, Toshio Uchiumi1 and Nobuhiko Nakashima

National Institute of Agrobiological Sciences, Owashi, Tsukuba, Ibaraki 305-8634, Japan and 1 Institute of High Polymer Research, Faculty of Textile Science and Technology, Shinshu University, Ueda 386-8567, Japan

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

Plautia stali intestine virus (PSIV) has an internal ribosome entry site (IRES) at the intergenic region of the genome. The PSIV IRES initiates translation with glutamine rather than the universal methionine. To analyze the mechanism of IRES-mediated initiation, binding of IRES RNA to salt-washed ribosomes in the absence of translation factors was studied. Among the three pseudoknots (PKs I, II and III) within the IRES, PK III was the most important for ribosome binding. Chemical footprint analyses showed that the loop parts of the two stem–loop structures in Domain 2, which are highly conserved in related viruses, are protected by 40S but not by 60S ribosomes. Because PK III is close to the two loops, these structural elements were considered to be important for binding of the 40S subunit. Competitive binding analyses showed that the IRES RNA does not bind poly(U)-programmed ribosomes preincubated with tRNAPhe or its anticodon stem– loop (ASL) fragment. However, Domain 3-deleted IRES bound to programmed ribosomes preincubated with the ASL, suggesting that Domains 1 and 2 have roles in IRES binding to 40S subunits and that Domain 3 is located at the ribosome decoding site.


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