DOI: 10.1261/rna.2594011. HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove

HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove

10.1261/rna.2594011

Crossref journal-article

Cold Spring Harbor Laboratory

RNA (246)

Abstract

Hepatitis C virus (HCV) uses a structured internal ribosome entry site (IRES) RNA to recruit the translation machinery to the viral RNA and begin protein synthesis without the ribosomal scanning process required for canonical translation initiation. Different IRES structural domains are used in this process, which begins with direct binding of the 40S ribosomal subunit to the IRES RNA and involves specific manipulation of the translational machinery. We have found that upon initial 40S subunit binding, the stem–loop domain of the IRES that contains the start codon unwinds and adopts a stable configuration within the subunit's decoding groove. This configuration depends on the sequence and structure of a different stem–loop domain (domain IIb) located far from the start codon in sequence, but spatially proximal in the IRES•40S complex. Mutation of domain IIb results in misconfiguration of the HCV RNA in the decoding groove that includes changes in the placement of the AUG start codon, and a substantial decrease in the ability of the IRES to initiate translation. Our results show that two distal regions of the IRES are structurally communicating at the initial step of 40S subunit binding and suggest that this is an important step in driving protein synthesis.

Bibliography

Filbin, M. E., & Kieft, J. S. (2011). HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunitâs decoding groove. RNA, 17(7), 1258â1273.

Authors 2

Megan E. Filbin (first)
Jeffrey S. Kieft (additional)

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Dates

Type	When
Created	14 years, 2 months ago (May 24, 2011, midnight)
Deposited	3 years, 9 months ago (Nov. 21, 2021, 9:05 a.m.)
Indexed	2 months ago (June 17, 2025, 6:29 a.m.)
Issued	14 years, 2 months ago (May 23, 2011)
Published	14 years, 2 months ago (May 23, 2011)
Published Online	14 years, 2 months ago (May 23, 2011)
Published Print	14 years, 1 month ago (July 1, 2011)

Funders 0

None

BibTeX

@article{Filbin_2011, title={HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit’s decoding groove}, volume={17}, ISSN={1469-9001}, url={http://dx.doi.org/10.1261/rna.2594011}, DOI={10.1261/rna.2594011}, number={7}, journal={RNA}, publisher={Cold Spring Harbor Laboratory}, author={Filbin, Megan E. and Kieft, Jeffrey S.}, year={2011}, month=may, pages={1258–1273} }

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