Periodic Conformational Changes in rRNA: Monitoring the Dynamics of Translating Ribosomes

• Published in: Molecular cell 2000-07, Vol.6 (1), p.159-171
• Main Authors: Polacek, Norbert, Patzke, Sebastian, Nierhaus, Knud H., Barta, Andrea
• Format: Article
• Language: English
• Subjects: Base Sequence; Binding Sites; Escherichia coli - genetics; Escherichia coli - metabolism; Molecular Sequence Data; Nucleic Acid Conformation; Protein Biosynthesis; Ribosomes - metabolism; RNA, Bacterial - chemistry; RNA, Bacterial - genetics; RNA, Bacterial - metabolism; RNA, Ribosomal - chemistry; RNA, Ribosomal - genetics; RNA, Ribosomal - metabolism; RNA, Ribosomal, 23S - chemistry; RNA, Ribosomal, 23S - genetics; RNA, Ribosomal, 23S - metabolism; RNA, Transfer, Phe - chemistry; RNA, Transfer, Phe - genetics; RNA, Transfer, Phe - metabolism; tRNA Phe
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/S1097-2765(05)00009-2

In protein synthesis, a tRNA transits the ribosome via consecutive binding to the A (acceptor), P (peptidyl), and E (exit) site; these tRNA movements are catalyzed by elongation factor G (EF-G) and GTP. Site-specific Pb 2+ cleavage was applied to trace tertiary alterations in tRNA and all rRNAs on pre- and posttranslocational ribosomes. The cleavage pattern of deacylated tRNA and AcPhe-tRNA changed individually upon binding to the ribosome; however, these different conformations were unaffected by translocation. On the other hand, translocation affects 23S rRNA structure. Significantly, the Pb 2+ cleavage pattern near the peptidyl transferase center was different before and after translocation. This structural rearrangement emerged periodically during elongation, thus providing evidence for a dynamic and mobile role of 23S rRNA in translocation.