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Nucleic Acids Research 2004 32(11):3282-3293; doi:10.1093/nar/gkh657
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Published online 18 June 2004

Nucleic Acids Research, Vol. 32 No. 11 © Oxford University Press 2004; all rights reserved

Variable and conserved elements of human ribosomes surrounding the mRNA at the decoding and upstream sites

Dmitri Graifer, Maxim Molotkov, Valentina Styazhkina, Natalia Demeshkina, Konstantin Bulygin, Anna Eremina, Anton Ivanov, Elena Laletina, Aliya Ven'yaminova and Galina Karpova*

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva, 8, Novosibirsk, 630090, Russia

* To whom correspondence should be addressed. Tel: +3832 35 62 29; Fax: +3832 33 36 77; Email: karpova{at}niboch.nsc.ru

Received March 31, 2004; Revised May 20, 2004; Accepted June 1, 2004

This study is centred upon an important biological problem concerning the structural organization of mammalian ribosomes that cannot be studied by X-ray analysis because 80S ribosome crystals are still unavailable. Here, positioning of the mRNA on 80S ribosomes was studied using mRNA analogues containing the perfluorophenylazide cross-linker on either the guanosine or an uridine residue. The modi-fied nucleotides were directed to positions from –9 to +6 with respect to the first nucleotide of the P site bound codon by a tRNA cognate to the triplet targeted to the P site. Upon mild UV-irradiation, the modified nucleotides at positions +4 to +6 cross-linked to protein S15 and 18S rRNA nucleotides A1823–A1825. In addition, modified guanosines in positions +5 and +6 also cross-linked to G626, and in position +1 to G1702. Cross-linking from the upstream positions was mainly to protein S26 that has no prokaryotic homologues. These findings indicate that the tail of mammalian S15 comes closer to the decoding site than that of its prokaryotic homologue S19, and that the environments of the upstream part of mRNA on 80S and 70S ribosomes differ. On the other hand, the results confirm the widely accepted idea regarding the conserved nature of the decoding site of the small subunit rRNA.


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