title: Structural elements in the internal ribosome entry site of Plautia stali intestine virus responsible for binding with ribosomes.
abstract: 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 tRNA(Phe) 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.
authors.affiliation: National Institute of Agrobiological Sciences, Owashi, Tsukuba, Ibaraki 305-8634, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Nishiyama
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Yamamoto
authors.forename: Norihiro
authors.initials: N
authors.lastname: Shibuya
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Hatakeyama
authors.forename: Akira
authors.initials: A
authors.lastname: Hachimori
authors.forename: Toshio
authors.initials: T
authors.lastname: Uchiumi
authors.forename: Nobuhiko
authors.initials: N
authors.lastname: Nakashima
mesh_terms: D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D001667:Binding, Competitive / Q000187:drug effects; D017665:Hydroxyl Radical / Q000494:pharmacology; D007304:Insect Viruses / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis; D012313:RNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D017665:Hydroxyl Radical; D012313:RNA