Molecular environment of the IIId subdomain of the IRES element of hepatitits C virus RNA on the human 40S ribosomal subunit

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Item Type:	Article
Title:	Molecular environment of the IIId subdomain of the IRES element of hepatitits C virus RNA on the human 40S ribosomal subunit
Creators Name:	Babaylova, E.S., Graifer, D.M., Malygin, A.A., Shatsky, I.N., Shtahl, I. and Karpova, G.
Abstract:	The molecular environment of the key subdomain IIId of the internal ribosome entry site (IRES) element of hepatitis C virus (HCV) RNA in the binary complex with the human 40S ribosomal subunit was studied. To this end, HCV IRES derivatives bearing perfluorophenylazido groups activatable by mild UV at nucleotides G263 or A275 in the subdomain IIId stem were used. They were prepared by the complementary addressed modification of the corresponding RNA transcript with alkylating oligodeoxyribonucleotide derivatives. None of the RNA derivatives were shown to be crosslinked to the 18S rRNA. It was found that the photoreactive groups of the IRES G263 and A275 nucleotides are crosslinked to ribosomal proteins S3a, S14, and S16. For the IRES derivative with the photoreactive group in nucleotide G263, the degree of modification of proteins S14 and S16 was greater than that of S3a, whereas the derivative containing the same photoreactive group in nucleotide A275 was mainly crosslinked to proteins S3a and S14. An analysis of the data led to the conclusion that in the binary complex of HCV IRES elements with the small subunit of the 80S ribosome, its subdomain IIId stem is located on the solvent side of the subunit between the head and the body next to the "beak" near the exit of mRNA from the ribosome.
Keywords:	80S Ribosome, Hepatitis C Virus, IRES Element, Photoreactive Crosslinking, Ribosomal Proteins
Source:	Russian Journal of Bioorganic Chemistry
ISSN:	1068-1620
Publisher:	Springer
Volume:	35
Number:	1
Page Range:	94-102
Date:	January 2009
Official Publication:	https://doi.org/10.1134/S1068162009010129
PubMed:	View item in PubMed

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