Molecular Environment of the Subdomain IIIe Loop of the RNA IRES Element of Hepatitis C Virus on the Human 40S Ribosomal Subunit

E. S. Laletina a , D. M. Graifer a , A. A. Malygin a , I. N. Shatsky b , and G. G. Karpova a #

# Phone: +7 (383) 335-6229, e-mail:
a Institute of Chemical Biology and Fundamental Medicine, Siberian Division, Russian Academy of Sciences, pr. akademika Lavrent'eva 3, Novosibirsk, 630090 Russia
b Belozerskii Institute of Physicochemical Biology, Moscow State University , Vorob'evy gory, Moscow , 119899 Russia

Received June 9, 2005; in final form, June 28, 2005

Abstract: The molecular environment of the internal ribosome entry site (IRES element) of hepatitis C viral (HCV) RNA in the binary complex with the human 40S ribosomal subunit was studied. To this end, RNA derivatives bearing mild UV--reactive perfluorophenylazide groups at nucleotide G87 in IRES domain II and at nucleotide A296 in the subdomain IIIe loop were used, which were prepared by the RNA complementarily-addressed modification with alkylating oligonucleotide derivatives. None of the RNA derivatives were shown to be crosslinked to the 18S rRNA of the 40S subunit. It was found that the photoreactive group of IRES nucleotide A296 crosslinked to the 40S subunit S2/S3a, S5, and p40 (SOA) proteins. No protein crosslinking was observed for the RNA derivative containing the same photoreactive group at nucleotide G87. It was concluded that the subdomain IIIe loop of the HCV RNA IRES element in the complex with the 40S subunit is located on the solvent side of the subunit between the head and the body aside the "beak" near the exit from the mRNA-binding channel.

Key words: 80S ribosome, 40S subunit, hepatitis C virus, IRES element, photocrosslinking , ribosomal proteins

Russian Journal of Bioorganic Chemistry 2006, 32 (3):280-287