title: Variable and conserved elements of human ribosomes surrounding the mRNA at the decoding and upstream sites.
abstract: 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 modified 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.
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva, 8, Novosibirsk, 630090, Russia.
authors.forename: Dmitri
authors.initials: D
authors.lastname: Graifer
authors.forename: Maxim
authors.initials: M
authors.lastname: Molotkov
authors.forename: Valentina
authors.initials: V
authors.lastname: Styazhkina
authors.forename: Natalia
authors.initials: N
authors.lastname: Demeshkina
authors.forename: Konstantin
authors.initials: K
authors.lastname: Bulygin
authors.forename: Anna
authors.initials: A
authors.lastname: Eremina
authors.forename: Anton
authors.initials: A
authors.lastname: Ivanov
authors.forename: Elena
authors.initials: E
authors.lastname: Laletina
authors.forename: Aliya
authors.initials: A
authors.lastname: Ven'yaminova
authors.forename: Galina
authors.initials: G
authors.lastname: Karpova
mesh_terms: D020121:5' Untranslated Regions; D001483:Base Sequence; D001665:Binding Sites; D005815:Genetic Code; D006801:Humans; D046911:Macromolecular Substances; D008954:Models, Biological; D008969:Molecular Sequence Data; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D012337:RNA, Ribosomal, 18S / Q000032:analysis* / Q000737:chemistry; D038621:Regulatory Sequences, Ribonucleic Acid; D012269:Ribosomal Proteins / Q000032:analysis*; D012270:Ribosomes / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D020121:5' Untranslated Regions; D046911:Macromolecular Substances; D012333:RNA, Messenger; D012337:RNA, Ribosomal, 18S; D038621:Regulatory Sequences, Ribonucleic Acid; D012269:Ribosomal Proteins