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Domains on the hepatitis C virus internal ribosome entry site for 40s subunit binding

Published online by Cambridge University Press:  23 August 2002

J. ROBIN LYTLE ,
LILY WU  and
HUGH D. ROBERTSON
J. ROBIN LYTLE
Affiliation:
Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, USA Present address: Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06536, USA.
LILY WU
Affiliation:
Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, USA
HUGH D. ROBERTSON
Affiliation:
Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, USA
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Abstract

The internal ribosome entry site (IRES) of the hepatitis C virus (HCV) RNA is known to interact with the 40S ribosomal subunit alone, in the absence of any additional initiation factors or Met-tRNAi. Previous work from this laboratory on the 80S and 48S ribosomal initiation complexes involving the HCV IRES showed that stem-loop III, the pseudoknot domain, and some coding sequence were protected from pancreatic RNase digestion. Stem-loop II is never protected by these complexes. Furthermore, there is no prior evidence reported showing extensive direct binding of stem-loop II to ribosomes or subunits. Using direct analysis of RNase-protected HCV IRES domains bound to 40S ribosomal subunits, we have determined that stem-loops II and III and the pseudoknot of the HCV IRES are involved in this initial binding step. The start AUG codon is only minimally protected. The HCV-40S subunit binary complex thus involves recognition and binding of stem-loop II, revealing its role in the first step of a multistep initiation process that may also involve rearrangement of the bound IRES RNA as it progresses.

Keywords

40S subunithepatitis C virusinternal ribosome entry site (IRES)RNase protectiontranslation initiation
Type
Research Article
Information
RNA , Volume 8 , Issue 8 , August 2002 , pp. 1045 - 1055
Copyright
© 2002 RNA Society

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