The central part of the 5.8 S rRNA is differently arranged in programmed and free human ribosomes

• Published in: Biochemical journal 2005-04, Vol.387 (Pt 1), p.139-145
• Main Authors: Graifer, Dmitri, Molotkov, Maxim, Eremina, Anna, Ven'yaminova, Aliya, Repkova, Marina, Karpova, Galina
• Format: Article
• Language: English
• Subjects: Base Sequence - genetics; Cross-Linking Reagents - metabolism; Gene Rearrangement - physiology; Humans; Molecular Sequence Data; Nucleic Acid Conformation; Ribonucleotides - metabolism; Ribosomal Proteins - genetics; Ribosomal Proteins - metabolism; Ribosomes - chemistry; Ribosomes - metabolism; RNA, Ribosomal, 5.8S - chemistry; RNA, Ribosomal, 5.8S - metabolism
• ISSN: 0264-6021; 1470-8728
• DOI: 10.1042/BJ20041450

A sequence-specific modification of the human 5.8 S rRNA in isolated 60 S subunits, non-programmed 80 S ribosomes and ribosomes complexed with mRNA and tRNAs was studied with the use of a derivative of the nonaribonucleotide UCUGUGUUU bearing a perfluorophenylazide group on the C-5 atom of the 5'-terminal uridine. Part of the oligonucleotide moiety of the derivative was complementary to the 5.8 S rRNA sequence ACACA in positions 82-86 flanked by two guanines at the 5'-terminus. The target for the cross-linking was identified as nucleotide G89 on the 5.8 S RNA. In addition, several ribosomal proteins were modified by the oligonucleotide derivative bound to the 5.8 S rRNA and proteins L6 and L8 were among them. Application of these results to known cryo-electron microscopy images of eukaryotic 60 S subunits made it possible to suggest that the central part of the 5.8 S rRNA containing the sequence 82-86 and proteins L6 and L8 are located at the base of the L1 stalk of the 60 S subunit. The efficacy of cross-linking in non-programmed 80 S ribosomes was much lower than in isolated 60 S subunits and in programmed 80 S ribosomes. We suggest that the difference in the accessibilities of the central part of the 5.8 S rRNA in the programmed and non-programmed 80 S ribosomes is caused by a conformational switch that seems to be required to dissociate the 80 S ribosomes into the subunits after termination of translation to allow initiation of translation of a new template.